PubAnnotation

Id	Subject	Object	Predicate	Lexical cue
T10	0-9	Sentence	denotes	Main Text
T11	11-23	Sentence	denotes	Introduction
T12	24-310	Sentence	denotes	The recent emergence and rapid global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting coronavirus disease 2019 (COVID-19) poses an unprecedented health crisis that was declared a pandemic by the World Health Organization (WHO) on March 11, 2020.
T13	311-522	Sentence	denotes	The origin of SARS-CoV-2 was traced to the city of Wuhan in the province of Hubei, China, where a cluster of viral pneumonia cases was first detected, many in connection with the Huanan Seafood Wholesale Market.
T14	523-842	Sentence	denotes	China reported this outbreak to the WHO on December 31, 2019 and soon after identified the causative pathogen as a betacoronavirus with high sequence homology to bat coronaviruses (CoVs) using angiotensin-converting enzyme 2 (ACE2) receptor as the dominant mechanism of cell entry (Lu et al., 2020a, Wan et al., 2020b).
T15	843-1069	Sentence	denotes	Following a likely zoonotic spillover, human-to-human transmission events were confirmed with clinical presentations ranging from no symptoms to mild fever, cough, and dyspnea to cytokine storm, respiratory failure, and death.
T16	1070-1300	Sentence	denotes	SARS-CoV-2 is also closely related to SARS (retrospectively named SARS-CoV-1) and Middle Eastern respiratory syndrome (MERS) CoVs, causing zoonotic epidemic and local outbreaks in 2003 and 2012, respectively (de Wit et al., 2016).
T17	1301-1539	Sentence	denotes	While SARS-CoV-2 is not as lethal as SARS-CoV-1 or MERS-CoV (Fauci et al., 2020), the considerable spread of the current pandemic has brought tremendous pressure and disastrous consequences for public health and medical systems worldwide.
T18	1540-1764	Sentence	denotes	The scientific response to the crisis has been extraordinary, with a plethora of COVID-19 studies posted in preprint servers in an attempt to rapidly unravel the pathogenesis of COVID-19 and potential therapeutic strategies.
T19	1765-2173	Sentence	denotes	In response, trainees and faculty members of the Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai (PrIISM) have initiated an institutional effort to critically review the preprint literature (Vabret et al., 2020), together with peer-reviewed articles published in traditional journals, and summarize the current state of science on the fast-evolving field of COVID-19 immunology.
T20	2174-2411	Sentence	denotes	We thematically focus on the innate and adaptive immune responses to SARS-CoV-2 and related CoVs, clinical studies and prognostic laboratory correlates, current therapeutic strategies, prospective clinical trials, and vaccine approaches.
T21	2413-2448	Sentence	denotes	Innate Immune Sensing of SARS-CoV-2
T22	2449-2558	Sentence	denotes	Innate immune sensing serves as the first line of antiviral defense and is essential for immunity to viruses.
T23	2559-2660	Sentence	denotes	To date, our understanding of the specific innate immune response to SARS-CoV-2 is extremely limited.
T24	2661-2884	Sentence	denotes	However, the virus-host interactions involving SARS-CoV-2 are likely to recapitulate many of those involving other CoVs, given the shared sequence homology among CoVs and the conserved mechanisms of innate immune signaling.
T25	2885-3194	Sentence	denotes	In the case of RNA viruses such as SARS-CoV-2, these pathways are initiated through the engagement of pattern-recognition receptors (PRRs) by viral single-stranded RNA (ssRNA) and double-stranded RNA (dsRNA) via cytosolic RIG-I like receptors (RLRs) and extracellular and endosomal Toll-like receptors (TLRs).
T26	3195-3281	Sentence	denotes	Upon PRR activation, downstream signaling cascades trigger the secretion of cytokines.
T27	3282-3524	Sentence	denotes	Among these, type I/III interferons (IFNs) are considered the most important for antiviral defense, but other cytokines, such as proinflammatory tumor necrosis factor alpha (TNF-α), and interleukin-1 (IL-1), IL-6, and IL-18 are also released.
T28	3525-3626	Sentence	denotes	Together, they induce antiviral programs in target cells and potentiate the adaptive immune response.
T29	3627-3769	Sentence	denotes	If present early and properly localized, IFN-I can effectively limit CoV infection (Channappanavar et al., 2016, Channappanavar et al., 2019).
T30	3770-4003	Sentence	denotes	Early evidence demonstrated that SARS-CoV-2 is sensitive to IFN-I/III pretreatment in vitro, perhaps to a greater degree than SARS-CoV-1 (Blanco-Melo et al., 2020, Lokugamage et al., 2020, Mantlo et al., 2020, Stanifer et al., 2020).
T31	4004-4119	Sentence	denotes	However, the specific IFN-stimulated genes (ISGs) that mediate these protective effects are still being elucidated.
T32	4120-4295	Sentence	denotes	Lymphocyte antigen 6 complex locus E (LY6E) has been shown to interfere with SARS-CoV-2 spike (S) protein-mediated membrane fusion (Pfaender et al., 2020, Zhao et al., 2020c).
T33	4296-4561	Sentence	denotes	Likely, the IFN-induced transmembrane family (IFITM) proteins inhibit SARS-CoV-2 entry, as demonstrated for SARS-CoV-1 (Huang et al., 2011b), although their action in promoting infection has also been described for other CoVs (Zhao et al., 2014, Zhao et al., 2018).
T34	4563-4605	Sentence	denotes	Evasion of Innate Sensing by Coronaviruses
T35	4606-4749	Sentence	denotes	As these cytokines represent a major barrier to viral infection, CoVs have evolved several mechanisms to inhibit IFN-I induction and signaling.
T36	4750-4932	Sentence	denotes	Numerous studies have demonstrated that SARS-CoV-1 suppresses IFN release in vitro and in vivo (Cameron et al., 2012, Minakshi et al., 2009, Siu et al., 2009, Wathelet et al., 2007).
T37	4933-5136	Sentence	denotes	SARS-CoV-2 likely achieves a similar effect, as suggested by the lack of robust type I/III IFN signatures from infected cell lines, primary bronchial cells, and a ferret model (Blanco-Melo et al., 2020).
T38	5137-5286	Sentence	denotes	In fact, patients with severe COVID-19 demonstrate remarkably impaired IFN-I signatures as compared to mild or moderate cases (Hadjadj et al., 2020).
T39	5287-5496	Sentence	denotes	As is often the case, there are multiple mechanisms of evasion for CoVs, with viral factors antagonizing each step of the pathway from PRR sensing and cytokine secretion to IFN signal transduction (Figure 1 ).
T40	5497-5576	Sentence	denotes	Figure 1 Mechanisms of Host Innate Immune Response and Coronaviruses Antagonism
T41	5577-5751	Sentence	denotes	Overview of innate immune sensing (left) and interferon signaling (right), annotated with the known mechanisms by which SARS-CoV-1 and MERS-CoV antagonize the pathways (red).
T42	5752-6068	Sentence	denotes	CoV-mediated antagonism of innate immunity begins with evasion of PRR sensing. ssRNA viruses, like CoVs, form dsRNA intermediates during their replication, which can be detected by TLR3 in the endosome and RIG-I, MDA5, and PKR in the cytosol. ssRNA may also be detected by TLR7 or TLR8 and potentially RIG-I and PKR.
T43	6069-6302	Sentence	denotes	CoVs are known to avoid PRR activation by either avoiding recognition altogether or antagonizing PRR action (Bouvet et al., 2010, Chen et al., 2009, Deng et al., 2017, Hackbart et al., 2020, Ivanov et al., 2004, Knoops et al., 2008).
T44	6303-6444	Sentence	denotes	To evade PRRs, dsRNA is first shielded by membrane-bound compartments that form during viral replication of SARS-CoV-1 (Knoops et al., 2008).
T45	6445-6734	Sentence	denotes	In addition, viral RNA is guanosine-capped and methylated at the 5′ end by CoVs non-structural proteins (NSPs) 10, 13, 14, and 16 (Bouvet et al., 2010, Chen et al., 2009, Ivanov et al., 2004), thereby resembling host mRNA to promote translation, prevent degradation, and evade RLR sensing.
T46	6735-6936	Sentence	denotes	Finally, CoVs also encode an endoribonuclease, NSP15, that cleaves 5′ polyuridines formed during viral replication, which would otherwise be detected by MDA5 (Deng et al., 2017, Hackbart et al., 2020).
T47	6937-7006	Sentence	denotes	CoVs have evolved additional strategies to impede activation of PRRs.
T48	7007-7082	Sentence	denotes	SARS-CoV-1 N-protein prevents TRIM25 activation of RIG-I (Hu et al., 2017).
T49	7083-7281	Sentence	denotes	Likewise, MERS-CoV NS4a, which itself binds dsRNA, impedes PKR activation (Comar et al., 2019, Rabouw et al., 2016) and inhibits PACT, an activator of RLRs (Niemeyer et al., 2013, Siu et al., 2014).
T50	7282-7383	Sentence	denotes	Additionally, MERS-CoV NS4b antagonizes RNaseL, another activator of RLRs (Thornbrough et al., 2016).
T51	7384-7423	Sentence	denotes	The role of other PRRs remains unclear.
T52	7424-7578	Sentence	denotes	For example, SARS-CoV-1 papain-like protease (PLP) antagonizes STING, suggesting that self-DNA may also represent an important trigger (Sun et al., 2012).
T53	7579-7667	Sentence	denotes	The extent to which SARS-CoV-2 homologs overlap in these functions is currently unknown.
T54	7668-7925	Sentence	denotes	Following activation, RLR and TLRs induce signaling cascades, leading to the phosphorylation of transcription factors, such as NF-kB and the interferon-regulatory factor family (IRF), ultimately leading to transcription of IFN and proinflammatory cytokines.
T55	7926-8120	Sentence	denotes	Although no experimental studies have delineated the precise functions of SARS-CoV-2 proteins, proteomic studies have demonstrated interactions between viral proteins and PRR signaling cascades.
T56	8121-8342	Sentence	denotes	SARS-CoV-2 ORF9b indirectly interacts with the signaling adaptor MAVS via its association with Tom70 (Gordon et al., 2020), consistent with prior reports that SARS-CoV-1 ORF9b suppresses MAVS signaling (Shi et al., 2014).
T57	8343-8505	Sentence	denotes	Furthermore, SARS-CoV-2 NSP13 interacts with signaling intermediate TBK1, and NSP15 is associated with RNF41, an activator of TBK1 and IRF3 (Gordon et al., 2020).
T58	8506-8648	Sentence	denotes	Similarly, SARS-CoV-1 M protein is known to inhibit the TBK1 signaling complex (Siu et al., 2009), as does MERS-CoV ORF4b (Yang et al., 2015).
T59	8649-8818	Sentence	denotes	Other proteins, including SARS-CoV-1 PLP, N, ORF3b, and ORF6, block IRF3 phosphorylation and nuclear translocation (Devaraj et al., 2007, Kopecky-Bromberg et al., 2007).
T60	8819-8859	Sentence	denotes	NF-kB is also inhibited by CoV proteins.
T61	8860-8986	Sentence	denotes	These include SARS-CoV-1 PLP (Frieman et al., 2009) and MERS-CoV ORF4b and ORF5 (Canton et al., 2018, Menachery et al., 2017).
T62	8987-9217	Sentence	denotes	Finally, SARS-CoV-1 NSP1 (Huang et al., 2011a, Kamitani et al., 2009) and MERS-CoV NSP1 (Lokugamage et al., 2015) initiate general inhibition of host transcription and translation, thus limiting antiviral defenses nonspecifically.
T63	9218-9439	Sentence	denotes	To prevent signaling downstream of IFN release, CoV proteins inhibit several steps of the signal transduction pathway that bridge the receptor subunits (IFNAR1 and IFNAR2) to the STAT proteins that activate transcription.
T64	9440-9707	Sentence	denotes	For SARS-CoV-1, these mechanisms include IFNAR1 degradation by ORF3a (Minakshi et al., 2009), decreased STAT1 phosphorylation by NSP1 (Wathelet et al., 2007), and antagonism of STAT1 nuclear translocation by ORF6 (Frieman et al., 2007, Kopecky-Bromberg et al., 2007).
T65	9708-9830	Sentence	denotes	However, SARS-CoV-2 ORF6 shares only 69% sequence homology with SARS-CoV-1, suggesting this function may not be conserved.
T66	9831-9974	Sentence	denotes	In support of this notion, SARS-CoV-2 infection fails to limit STAT1 phosphorylation, unlike in SARS-CoV-1 infection (Lokugamage et al., 2020).
T67	9976-10033	Sentence	denotes	Imbalance between Antiviral and Proinflammatory Responses
T68	10034-10265	Sentence	denotes	Taken together, the multiplicity of strategies developed by pathogenic CoVs to escape immune sensing, particularly the IFN-I pathway, suggests a critical role played by the dysregulation of IFN-I response in COVID-19 pathogenicity.
T69	10266-10457	Sentence	denotes	Concordantly, animal models of SARS-CoV-1 and MERS-CoV infection indicate that failure to elicit an early IFN-I response correlates with the severity of disease (Channappanavar et al., 2016).
T70	10458-10655	Sentence	denotes	Perhaps more importantly, these models demonstrate that timing is key, as IFN is protective early in disease but later becomes pathologic (Channappanavar et al., 2016, Channappanavar et al., 2019).
T71	10656-10777	Sentence	denotes	Perhaps interferon-induced upregulation of ACE2 in airway epithelia may contribute to this effect (Ziegler et al., 2020).
T72	10778-10914	Sentence	denotes	Furthermore, while pathogenic CoVs block IFN signaling, they may actively promote other inflammatory pathways contributing to pathology.
T73	10915-11186	Sentence	denotes	For instance, SARS-CoV-1 ORF3a, ORF8b, and E proteins enhance inflammasome activation (Chen et al., 2019, Nieto-Torres et al., 2015, Shi et al., 2019, Siu et al., 2019), leading to secretion of IL-1β and IL-18, which are likely to contribute to pathological inflammation.
T74	11187-11347	Sentence	denotes	Similarly, SARS-CoV-2 NSP9 and NSP10 might induce IL-6 and IL-8 production, potentially by inhibition of NKRF, an endogenous NF-kB repressor (Li et al., 2020a).
T75	11348-11540	Sentence	denotes	Collectively, these proinflammatory processes likely contribute to the “cytokine storm” observed in COVID-19 patients and substantiate a role for targeted immunosuppressive treatment regimens.
T76	11541-11744	Sentence	denotes	Moving forward, a clear understanding of the delicate balance between antiviral and inflammatory innate immune programs will be essential to developing effective biomarkers and therapeutics for COVID-19.
T77	11746-11759	Sentence	denotes	Myeloid Cells
T78	11760-12029	Sentence	denotes	Mucosal immune responses to infectious agents are orchestrated and regulated by myeloid cells with specialized functions, which include conventional dendritic cells (cDCs), monocyte-derived DCs (moDCs), plasmacytoid DCs (pDCs), and macrophages (Guilliams et al., 2013).
T79	12030-12275	Sentence	denotes	A growing body of evidence points to dysregulated myeloid responses that potentially drive the COVID-19 hallmark syndromes, such as acute respiratory distress syndrome (ARDS), cytokine release syndrome (CRS) and lymphopenia (Mehta et al., 2020).
T80	12277-12313	Sentence	denotes	Myeloid Characterization in COVID-19
T81	12314-12673	Sentence	denotes	Flow cytometric analyses of peripheral blood mononuclear cells (PBMCs) from symptomatic COVID-19 patients have shown a significant influx of granulocyte-macrophage colony-stimulating factor (GM-CSF)-producing, activated CD4+ T cells and CD14+HLA-DRlo inflammatory monocytes (IMs) (Giamarellos-Bourboulis et al., 2020, Zhang et al., 2020c, Zhou et al., 2020b).
T82	12674-13118	Sentence	denotes	This matches single-cell transcriptomic (scRNA-seq) data demonstrating CD14+IL-1β+ monocytic expansion (Guo et al., 2020, Wen et al., 2020), interferon-mitogen-activated protein kinase (MAPK)-driven adaptive immune responses (Huang et al., 2020c), and IL-1β-associated inflammasome signatures (Ong et al., 2020) in peripheral blood of COVID-19 patients, although systemic levels of IL-1β detected are conspicuously low (Del Valle et al., 2020).
T83	13119-13460	Sentence	denotes	Importantly, these immune signatures track with progression of clinical disease. scRNA-seq studies performed on pulmonary tissues of patients with severe COVID-19 disease have revealed an expansion of IMs and Ficolin-1+ monocyte-derived macrophages at the expense of tissue-resident reparative alveolar macrophages (AMs) (Liao et al., 2020).
T84	13461-13634	Sentence	denotes	The aforementioned study also observed signatures of IFN signaling and monocyte recruitment that likely contribute to the rapid decline in alveolar patency and promote ARDS.
T85	13635-13880	Sentence	denotes	Although most of the clinical focus has been on pulmonary damage and mononuclear phagocyte (MNP) dysfunction therein, it is increasingly clear that COVID-19 likely presents systemic challenges in other organ sites, such as the ileum and kidneys.
T86	13881-14007	Sentence	denotes	Understanding the role of non-pulmonary myeloid cells in tissue-specific pathology associated with COVID-19 will be important.
T87	14009-14076	Sentence	denotes	Prior Knowledge from SARS-CoV-1, MERS-CoV, and Murine Coronaviruses
T88	14077-14285	Sentence	denotes	While data on COVID-19 patients continues to rapidly emerge, studies of myeloid cell dysfunction in SARS-CoV-1 and MERS-CoV can provide an important roadmap to understanding COVID-19 pathogenesis (Figure 2 ).
T89	14286-14428	Sentence	denotes	SARS-CoV-1 infection in mouse models results in an aberrant AM phenotype that limits DC trafficking and T cell activation (Zhao et al., 2009).
T90	14429-14580	Sentence	denotes	Additionally, YM1+ FIZZ1+ alternative macrophages can increase airway hypersensitivity, thus exacerbating SARS-associated fibrosis (Page et al., 2012).
T91	14581-14892	Sentence	denotes	Further, as described above, murine SARS-CoV-1 studies have demonstrated that delayed IFN-I signaling and inflammatory monocytes-macrophages promote lung cytokine and chemokine levels, vascular leakage, and impaired antigen-specific T cell responses, culminating in lethal disease (Channappanavar et al., 2016).
T92	14893-15104	Sentence	denotes	The role played by prominent IFN-producing pDCs in SARS-CoV-2 control or pathogenesis warrants investigation, as they have been shown to be critical in murine CoV (MHV) control (Cervantes-Barragan et al., 2007).
T93	15105-15456	Sentence	denotes	Longitudinal studies in SARS-CoV-2 models are awaited, but initial phenotypic studies in humanized hACE2 mice have shown the characteristic alveolar interstitial pneumonia, with infiltration of lymphocytes and monocytes and accumulation of macrophages in the alveolar lumen (Bao et al., 2020a), which recapitulates patient findings (Xu et al., 2020c).
T94	15457-15820	Sentence	denotes	Lastly, non-human primate (NHP) studies and patient data on SARS-CoV-1 have also shown that virus spike-specific immunoglobulin G (IgG) responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into proinflammatory phenotypes and enhanced recruitment of inflammatory monocyte via CCL2 and IL-8 (Clay et al., 2012, Liu et al., 2019).
T95	15821-15935	Sentence	denotes	However, the extent to which the antibody response contributes to disease pathophysiology remains to be confirmed.
T96	15936-16029	Sentence	denotes	Figure 2 SARS-CoV-2 Infection Results in Myeloid Cell Activation and Changes NK Cell Function
T97	16030-16123	Sentence	denotes	Based on data from preliminary COVID-19 studies and earlier studies in related coronaviruses.
T98	16124-16352	Sentence	denotes	IL-6, IL-1β, and IFN-I/III from infected pulmonary epithelia can induce inflammatory programs in resident (alternate) macrophages while recruiting inflammatory monocytes, as well as granulocytes and lymphocytes from circulation.
T99	16353-16445	Sentence	denotes	Sustained IL-6 and TNF-ɑ by incoming monocytes can drive several hyperinflammation cascades.
T100	16446-16568	Sentence	denotes	Inflammatory monocyte-derived macrophages can amplify dysfunctional responses in various ways (listed in top-left corner).
T101	16569-16706	Sentence	denotes	The systemic CRS- and sHLH-like inflammatory response can induce neutrophilic NETosis and microthrombosis, aggravating COVID-19 severity.
T102	16707-16803	Sentence	denotes	Other myeloid cells, such as pDCs, are purported to have an IFN-dependent role in viral control.
T103	16804-16867	Sentence	denotes	Monocyte-derived CXCL9/10/11 might recruit NK cells from blood.
T104	16868-17028	Sentence	denotes	Preliminary data suggest that the antiviral function of these NK cells might be regulated through crosstalk with SARS-infected cells and inflammatory monocytes.
T105	17029-17076	Sentence	denotes	Dashed lines indicate pathways to be confirmed.
T106	17077-17339	Sentence	denotes	Arg1, arginase 1; iNOS, inducible-nitric oxide synthase; Inflamm., inflammatory; Mono., monocytes; Macs, macrophages; Eosino, eosinophils; Neutro, neutrophils; NETosis, neutrophil extracellular trap cell death; SHLH, secondary hemophagocytic lymphohistiocytosis.
T107	17341-17394	Sentence	denotes	Myeloid Cells Contribution to Pathogenic Inflammation
T108	17395-17583	Sentence	denotes	The initial mode of viral pathogen-associated signal (PAMP) recognition by innate cells has a major impact on downstream myeloid signaling and cytokine secretion (de Marcken et al., 2019).
T109	17584-17966	Sentence	denotes	While macrophages are somewhat susceptible to MERS-CoV and SARS-CoV-1 infection (Perlman and Dandekar, 2005, Zhou et al., 2014), data do not suggest that they are infected by SARS-CoV-2, although one study reported ACE2 and SARS-CoV-2 nucleocapsid protein is expressed in lymph nodes and spleen-associated CD169+ macrophages of COVID-19 patients producing IL-6 (Chen et al., 2020h).
T110	17967-18160	Sentence	denotes	Significantly elevated systemic levels of proinflammatory cytokine IL-6 have been reported in several COVID-19 patient cohorts and shown to correlate with disease severity (Mehta et al., 2020).
T111	18161-18308	Sentence	denotes	Increased IL-6 can also be associated with higher levels of IL-2, IL-7, IFN-ɣ, and GM-CSF, as seen in secondary hemophagocytic lymphohistiocytosis.
T112	18309-18589	Sentence	denotes	In response to viral infections, MNPs drive IL and IFN-I and IFN-III production resulting in inflammasome activation, induction of pathogenic Th1 and Th17 cell responses, recruitment of effector immune cells, and CRS pathology (Prokunina-Olsson et al., 2020, Tanaka et al., 2016).
T113	18590-18820	Sentence	denotes	Independently, in vitro studies have demonstrated SARS-CoV-1 infection can induce intracellular stress pathways, resulting in NLRP3-dependent inflammasome activation and macrophage pyroptosis (Chen et al., 2019, Shi et al., 2019).
T114	18821-19033	Sentence	denotes	Functional studies are required to implicate these myeloid inflammasome pathways in COVID-19 lung pathology and to assess other immunogenic pathways such as RIPK1/3-dependent necroptosis (Nailwal and Chan, 2019).
T115	19034-19198	Sentence	denotes	In conclusion, the strength and duration of myeloid ISG)signaling potentially dictate COVID-19 disease severity, but rigorous studies are warranted to confirm this.
T116	19199-19404	Sentence	denotes	Lastly, more work is needed to ascertain the mechanistic role played by lung-resident and recruited granulocytes in SARS-CoV-2 control and pathogenesis (Camp and Jonsson, 2017, Flores-Torres et al., 2019).
T117	19405-19647	Sentence	denotes	In contrast to their early protective role, neutrophil NETosis and macrophage crosstalk can drive later-stage inflammatory cascades (Barnes et al., 2020), underscoring the overall pathogenic nature of damage-sensing host responses (Figure 2).
T118	19648-19887	Sentence	denotes	Collectively, the current knowledge of CoVs and SARS-CoV-2 infection, in particular, points to an inadvertent collusion involving myeloid cells in COVID-19 pathogenesis, despite their critical role in early sensing and antiviral responses.
T119	19889-19910	Sentence	denotes	Innate Lymphoid Cells
T120	19911-20077	Sentence	denotes	Innate lymphoid cells (ILCs) are innate immune effector cells that lack the expression of rearranged antigen receptors (T cell receptor [TCR], B cell receptor [BCR]).
T121	20078-20258	Sentence	denotes	The ILC family is divided into two main groups: the cytotoxic natural killer (NK) cells and the non-cytotoxic helper ILCs, which include ILC1, ILC2, and ILC3 (Vivier et al., 2018).
T122	20259-20413	Sentence	denotes	Conventional NK cells include CD56brightCD16− NK cells and CD56dimCD16+ cells, which are specialized in cytokine production or cytotoxicity, respectively.
T123	20415-20482	Sentence	denotes	NK Cells Are Decreased in the Peripheral Blood of COVID-19 patients
T124	20483-20715	Sentence	denotes	Multiple studies have reported reduced numbers of NK cells in the peripheral blood of COVID-19 patients, which is associated with severity of the disease (Song et al., 2020, Wang et al., 2020f, Yu et al., 2020, Zheng et al., 2020b).
T125	20716-20884	Sentence	denotes	A recent scRNA-seq analysis revealed a transcriptomic signature for NK cells that was equally represented in lungs from patients and healthy donors (Liao et al., 2020).
T126	20885-21086	Sentence	denotes	The majority of lung NK cells are non-resident (Gasteiger et al., 2015, Marquardt et al., 2017), and CXCR3 has been shown to mediate NK cell infiltration upon influenza infection (Carlin et al., 2018).
T127	21087-21301	Sentence	denotes	In vitro, CXCR3 ligands (CXCL9-11) are increased in SARS-CoV-2-infected human lung tissue (Chu et al., 2020), and CXCR3-ligand-producing monocytes are expanded in the lungs of COVID-19 patients (Liao et al., 2020).
T128	21302-21447	Sentence	denotes	This suggests that the CXCR3 pathway might facilitate NK cell recruitment from the peripheral blood to the lungs in COVID-19 patients (Figure 2).
T129	21449-21498	Sentence	denotes	NK Cell Activation Pathways in Antiviral Immunity
T130	21499-21585	Sentence	denotes	NK cells express inhibitory and activating receptors that regulate their cytotoxicity.
T131	21586-21900	Sentence	denotes	They are therefore able to induce the lysis of virus-infected cells that upregulate virus-derived proteins, as well as stress-inducible ligands, which are then recognized by NK-cell-activating receptors, such as NKp46 (Cerwenka and Lanier, 2001, Draghi et al., 2007, Duev-Cohen et al., 2016, Glasner et al., 2012).
T132	21901-22097	Sentence	denotes	Future studies should investigate the expression of NK receptor ligands on SARS-CoV-2-infected cells in order to better understand the mechanisms underlying NK cell activation in COVID-19 disease.
T133	22098-22405	Sentence	denotes	Further, secretion of IgG1 and IgG3 antibodies during SARS-CoV-2 infection (Amanat et al., 2020) may induce CD56dim CD16+ NK cell activation through Fc receptor recognition of antibodies either bound to surface antigens expressed on infected cells or to extracellular virions as immune complexes (Figure 2).
T134	22406-22618	Sentence	denotes	This interaction might trigger both cytokine production by NK cells and lysis of infected cells through antibody-mediated cellular cytotoxicity (ADCC), as shown in influenza infection (Von Holle and Moody, 2019).
T135	22619-22858	Sentence	denotes	Emerging data highlight the capacity for NK-mediated ADCC in response to naturally isolated SARS-CoV-1 anti-S IgG that crossreacts with SARS-CoV-2 S glycoprotein when transfected into Chinese hamster ovary (CHO) cells (Pinto et al., 2020).
T136	22859-23023	Sentence	denotes	These findings suggest that triggering NK cell activation may not only contribute to the resolution of infection, but also contribute to the cytokine storm in ARDS.
T137	23025-23079	Sentence	denotes	Impairment of NK Cell Function in SARS-CoV-2 Infection
T138	23080-23368	Sentence	denotes	Ex vivo NK cells from peripheral blood of COVID-19 patients have reduced intracellular expression of CD107a, Ksp37, granzyme B, and granulysin, suggesting an impaired cytotoxicity, as well as an impaired production of chemokines, IFN-ɣ, and TNF-α (Wilk et al., 2020, Zheng et al., 2020b).
T139	23369-23434	Sentence	denotes	Several pathways may contribute to the dysregulation of NK cells.
T140	23435-23677	Sentence	denotes	While influenza virus infects NK cells and induces apoptosis (Mao et al., 2009), lung NK cells do not express the entry receptor for SARS-CoV-2, ACE2, and are therefore unlikely to be directly infected by SARS-CoV-2 (Travaglini et al., 2020).
T141	23678-23995	Sentence	denotes	The majority of NK cells found in human lung display a mature CD16+KIR+CD56dim phenotype and are able to induce cell cytotoxicity in response to loss of human leukocyte antigen (HLA) class I or through Fc receptor signaling, although to a lower extent than their peripheral blood counterpart (Marquardt et al., 2017).
T142	23996-24210	Sentence	denotes	Killer-immunoglobulin receptors (KIRs) are acquired during NK cell development alongside CD16 (FcRγIIIA) and are essential for NK cell licensing and subsequent capacity for cytolytic function (Sivori et al., 2019).
T143	24211-24389	Sentence	denotes	Frequencies of NK cells expressing CD16 and/or KIRs are decreased in the blood following SARS-CoV-2 and SARS-CoV-1 infection, respectively (Xia et al., 2004, Wang et al., 2020d).
T144	24390-24597	Sentence	denotes	Collectively, the data suggest either an impaired maturation of the NK compartment or migration of the mature, circulating NK cells into the lungs or other peripheral tissues of SARS-CoV-2-infected patients.
T145	24598-24712	Sentence	denotes	The immune checkpoint NKG2A is increased on NK cells and CD8 T cells from COVID-19 patients (Zheng et al., 2020b).
T146	24713-24938	Sentence	denotes	NKG2A inhibits cell cytotoxicity by binding the non-classical HLA-E molecule (Braud et al., 1998, Brooks et al., 1997), and this interaction is strongly correlated with poor control of HIV-1 infection (Ramsuran et al., 2018).
T147	24939-25091	Sentence	denotes	Genes encoding the inhibitory receptors LAG3 and TIM3 are also upregulated in NK cells from COVID-19 patients (Wilk et al., 2020, Hadjadj et al., 2020).
T148	25092-25172	Sentence	denotes	Thus, increased immune checkpoints on NK cells might contribute to viral escape.
T149	25173-25368	Sentence	denotes	Additionally, COVID-19 patients have higher plasma concentrations of IL-6 (Huang et al., 2020b), which significantly correlate with lower NK cell numbers (Wang et al., 2020d, Wang et al., 2020f).
T150	25369-25637	Sentence	denotes	In vitro stimulation by IL-6 and soluble IL-6 receptor has previously revealed impaired cytolytic functions (perforin and granzyme B production) by healthy donor NK cells, which can be restored following addition of tocilizumab (IL-6R blockade) (Cifaldi et al., 2015).
T151	25638-25895	Sentence	denotes	TNF-α is also upregulated in the plasma of COVID-19 patients (Huang et al., 2020b), and ligand-receptor interaction analysis of peripheral blood scRNA-seq data suggests that monocyte-secreted TNF-α might bind to its receptors on NK cells (Guo et al., 2020).
T152	25896-26119	Sentence	denotes	TNF-α is known to contribute to NK cell differentiation (Lee et al., 2009), which includes downregulation of NKp46 (Ivagnès et al., 2017), though no effect of TNF-α or IL-6 on NK cell-mediated ADCC has been reported so far.
T153	26120-26377	Sentence	denotes	Collectively, these data suggest that crosstalk with monocytes might impair NK cell recognition and killing of SARS-CoV-2-infected cells, and antibodies targeting IL-6 and TNF-signaling may benefit enhanced NK cell functions in COVID-19 patients (Figure 2).
T154	26379-26428	Sentence	denotes	Relevance for Helper ILCs in SARS-CoV-2 Infection
T155	26429-26518	Sentence	denotes	No studies, to date, have reported ILC1, ILC2, or ILC3 functions in SARS-CoV-2 infection.
T156	26519-26611	Sentence	denotes	All three subsets are present in healthy lung (De Grove et al., 2016, Yudanin et al., 2019).
T157	26612-26822	Sentence	denotes	ILC2s are essential for the improvement of lung function following influenza infection in mice through amphiregulin-mediated restoration of the airway epithelium and oxygen saturation (Monticelli et al., 2011).
T158	26823-26983	Sentence	denotes	However, ILC2s also produce IL-13, contributing to the recruitment of macrophages to the lung and influenza-induced airway hyperreactivity (Chang et al., 2011).
T159	26984-27154	Sentence	denotes	Indeed, ILCs are involved in the polarization of alveolar macrophages, either toward a M1-like phenotype (ILC1 and ILC3) or a M2-like phenotype (ILC2) (Kim et al., 2019).
T160	27155-27380	Sentence	denotes	Given the increased IL-13 concentrations (Huang et al., 2020b) and the dysregulation of the macrophage compartment observed in COVID-19 patients, the role played by ILCs in SARS-CoV-2 infection warrants further investigation.
T161	27382-27398	Sentence	denotes	T Cell Responses
T162	27399-27627	Sentence	denotes	T cells play a fundamental role in viral infections: CD4 T cells provide B cell help for antibody production and orchestrate the response of other immune cells, whereas CD8 T cells kill infected cells to reduce the viral burden.
T163	27628-27697	Sentence	denotes	However, dysregulated T cell responses can result in immunopathology.
T164	27698-28038	Sentence	denotes	To better understand the role of T cell responses in SARS-CoV-2 infection, the pursuit of two major questions is imperative: (1) what is the contribution of T cells to initial virus control and tissue damage in the context of COVID-19, and (2) how do memory T cells established thereafter contribute to protective immunity upon reinfection?
T165	28039-28086	Sentence	denotes	Some tentative answers are beginning to emerge.
T166	28088-28154	Sentence	denotes	Overall Reduction of CD4 and CD8 T Cell Counts in Peripheral Blood
T167	28155-28508	Sentence	denotes	Similar to earlier observations about SARS-CoV-1 infection (He et al., 2005), several current reports emphasize the occurrence of lymphopenia with drastically reduced numbers of both CD4 and CD8 T cells in moderate and severe COVID-19 cases (Figure 3 ) (Chen et al., 2020c, Nie et al., 2020b, Wang et al., 2020d, Zeng et al., 2020, Zheng et al., 2020b).
T168	28509-28872	Sentence	denotes	The extent of lymphopenia—most striking for CD8 T cells in patients admitted to the intensive care unit (ICU)—seemingly correlates with COVID-19-associated disease severity and mortality (Chen et al., 2020c, Diao et al., 2020, Liu et al., 2020b, Liu et al., 2020c, Tan et al., 2020a, Wang et al., 2020d, Wang et al., 2020f, Zeng et al., 2020, Zhou et al., 2020c).
T169	28873-29019	Sentence	denotes	Patients with mild symptoms, however, typically present with normal or slightly higher T cell counts (Liu et al., 2020a, Thevarajan et al., 2020).
T170	29020-29271	Sentence	denotes	The cause of peripheral T cell loss in moderate to severe COVID-19, though a phenomenon also observed in other viral infections, remains elusive, and direct viral infection of T cells, in contrast to MERS-CoV (Chu et al., 2016), has not been reported.
T171	29272-29330	Sentence	denotes	Figure 3 Working Model for T Cell Responses to SARS-CoV-2:
T172	29331-29391	Sentence	denotes	Changes in Peripheral Blood T Cell Frequencies and Phenotype
T173	29392-29516	Sentence	denotes	A decrease in peripheral blood T cells associated with disease severity and inflammation is now well documented in COVID-19.
T174	29517-29801	Sentence	denotes	Several studies report increased numbers of activated CD4 and CD8 T cells, which display a trend toward an exhausted phenotype in persistent COVID-19, based on continuous and upregulated expression of inhibitory markers as well as potential reduced polyfunctionality and cytotoxicity.
T175	29802-29905	Sentence	denotes	In severe disease, production of specific inflammatory cytokines by CD4 T cells has also been reported.
T176	29906-30063	Sentence	denotes	This working model needs to be confirmed and expanded on in future studies to assess virus-specific T cell responses both in peripheral blood and in tissues.
T177	30064-30226	Sentence	denotes	In addition, larger and more defined patient cohorts with longitudinal data are required to define the relationship between disease severity and T cell phenotype.
T178	30227-30393	Sentence	denotes	IL, interleukin; IFN, interferon; TNF, tumor necrosis factor; GM-CSF, granulocyte-macrophage colony-stimulating factor; GzmA/B, granzyme A/granzyme B; Prf1, perforin.
T179	30394-30534	Sentence	denotes	Several mechanisms likely contribute to the reduced number of T cells in the blood, including effects from the inflammatory cytokine milieu.
T180	30535-30885	Sentence	denotes	Indeed, lymphopenia seems to correlate with serum IL-6, IL-10, and TNF-α (Diao et al., 2020, Wan et al., 2020a), while convalescent patients were found to have restored bulk T cell frequencies paired with overall lower proinflammatory cytokine levels (Chen et al., 2020f, Diao et al., 2020, Liu et al., 2020a, Liu et al., 2020b, Zheng et al., 2020b).
T181	30886-31078	Sentence	denotes	Cytokines such as IFN-I and TNF-α may inhibit T cell recirculation in blood by promoting retention in lymphoid organs and attachment to endothelium (Kamphuis et al., 2006, Shiow et al., 2006).
T182	31079-31345	Sentence	denotes	However, in an autopsy study examining the spleens and hilar lymph nodes of six patients who succumbed to COVID-19, Chen et al. observed extensive cell death of lymphocytes and suggested potential roles for IL-6 as well as Fas-FasL interactions (Chen et al., 2020h).
T183	31346-31516	Sentence	denotes	In support of this hypothesis, the IL-6 receptor antagonist tocilizumab was found to increase the number of circulating lymphocytes (Giamarellos-Bourboulis et al., 2020).
T184	31517-31792	Sentence	denotes	T cell recruitment to sites of infection may also reduce their presence in the peripheral blood compartment. scRNA-seq analysis of bronchoalveolar lavage (BAL) fluid of COVID-19 patients revealed an increase in CD8 T cell infiltrate with clonal expansion (Liao et al., 2020).
T185	31793-31966	Sentence	denotes	Likewise, post-mortem examination of a patient who succumbed to ARDS following SARS-CoV-2 infection showed extensive lymphocyte infiltration in the lungs (Xu et al., 2020c).
T186	31967-32111	Sentence	denotes	However, another study that examined post-mortem biopsies from four COVID-19 patients only found neutrophilic infiltration (Tian et al., 2020a).
T187	32112-32248	Sentence	denotes	Further studies are therefore needed to better determine the cause and impact of the commonly observed lymphopenia in COVID-19 patients.
T188	32250-32289	Sentence	denotes	Induction of Antiviral T Cell Responses
T189	32290-32432	Sentence	denotes	Available information about SARS-CoV-1-specific T cell immunity may serve as an orientation for further understanding of SARS-CoV-2 infection.
T190	32433-32630	Sentence	denotes	Immunogenic T cell epitopes are distributed across several SARS-CoV-1 proteins (S, N, and M, as well as ORF3), although CD4 T cell responses were more restricted to the S protein (Li et al., 2008).
T191	32631-32905	Sentence	denotes	In SARS-CoV-1 survivors, the magnitude and frequency of specific CD8 memory T cells exceeded that of CD4 memory T cells, and virus-specific T cells persisted for at least 6–11 years, suggesting that T cells may confer long-term immunity (Ng et al., 2016, Tang et al., 2011).
T192	32906-33172	Sentence	denotes	Limited data from viremic SARS patients further indicated that virus-specific CD4 T cell populations might be associated with a more severe disease course, since lethal outcomes correlated with elevated Th2 cell (IL-4, IL-5, IL-10) serum cytokines (Li et al., 2008).
T193	33173-33301	Sentence	denotes	However, the quality of CD4 T cell responses needs to be further characterized to understand associations with disease severity.
T194	33302-33391	Sentence	denotes	Few studies have thus far characterized specific T cell immunity in SARS-CoV-2 infection.
T195	33392-33790	Sentence	denotes	In 12 patients recovering from mild COVID-19, robust T cell responses specific for viral N, M, and S proteins were detected by IFN-γ ELISPOT, weakly correlated with neutralizing antibody concentrations (similar to convalescent SARS-CoV-1 patients; Li et al., 2008), and subsequently contracted with only N-specific T cells detectable in about one-third of the cases post recovery (Ni et al., 2020).
T196	33791-33966	Sentence	denotes	In a second study, PBMCs from COVID-19 patients with moderate to severe ARDS were analyzed by flow cytometry approximately 2 weeks after ICU admission (Weiskopf et al., 2020).
T197	33967-34309	Sentence	denotes	Both virus-specific CD4 and CD8 T cells were detected in all patients at average frequencies of 1.4% and 1.3%, respectively, and very limited phenotyping according to CD45RA and CCR7 expression status characterized these cells predominantly as either CD4 Tcm (central memory) or CD8 Tem (effector memory) and Temra (effector memory RA) cells.
T198	34310-34772	Sentence	denotes	This study is notable for the use of large complementary peptide pools comprising 1,095 SARS-Cov-2 epitopes (overlapping 15-mers for S protein as well as computationally predicted HLA-I- and -II-restricted epitopes for all other viral proteins) as antigen-specific stimuli that revealed a preferential specificity of both CD4 and CD8 T cells for S protein epitopes, with the former population modestly increasing over ∼10–30 days after initial onset of symptoms.
T199	34773-35025	Sentence	denotes	A caveat, however, pertains to the identification of specific T cells by induced CD69 and CD137 co-expression, since upregulation of CD137 by CD4 T cells, in contrast to CD154, may preferentially capture regulatory T cells (Treg) (Bacher et al., 2016).
T200	35026-35207	Sentence	denotes	Further analyses of S protein-specific T cells by ELISA demonstrated robust induction of IFN-γ, TNF-α, and IL-2 concomitant with lower levels of IL-5, IL-13, IL-9, IL-10, and IL-22.
T201	35208-35434	Sentence	denotes	A third report focused on S-specific CD4 T cell responses in 18 patients with mild, severe, or critical COVID-19 using overlapping peptide pools and induced CD154 and CD137 co-expression as a readout for antiviral CD4 T cells.
T202	35435-35599	Sentence	denotes	Such cells were present in 83% of cases and presented with enhanced CD38, HLA-DR, and Ki-67 expression indicative of recent in vivo activation (Braun et al., 2020).
T203	35600-35734	Sentence	denotes	Of note, the authors also detected low frequencies of S-reactive CD4 T cells in 34% of SARS-CoV-2 seronegative healthy control donors.
T204	35735-36155	Sentence	denotes	However, these CD4 T cells lacked phenotypic markers of activation and were specific for C-terminal S protein epitopes that are highly similar to endemic human CoVs, suggesting that crossreactive CD4 memory T cells in some populations (e.g., children and younger patients that experience a higher incidence of hCoV infections) may be recruited into an amplified primary SARS-CoV-2-specific response (Braun et al., 2020).
T205	36156-36279	Sentence	denotes	Similarly, endemic CoV-specific CD4 T cells were previously shown to recognize SARS-CoV1 determinants (Gioia et al., 2005).
T206	36280-36400	Sentence	denotes	How previous infections with endemic CoV may affect immune responses to SARS-CoV-2 will need to be further investigated.
T207	36401-36727	Sentence	denotes	Finally, in general accordance with the above findings on the induction of SARS-CoV-2-specific T cells, using TCR sequencing (TCR-seq), Huang et al. and Liao et al. reported greater TCR clonality of peripheral blood (Huang et al., 2020c) as well as BAL T cells (Liao et al., 2020) in patients with mild versus severe COVID-19.
T208	36728-36984	Sentence	denotes	Moving forward, a comprehensive identification of immunogenic SARS-CoV-2 epitopes recognized by T cells (Campbell et al., 2020), as well as further studies on convalescent patients who recovered from mild and severe disease, will be particularly important.
T209	36986-37035	Sentence	denotes	T Cell Contribution to COVID-19 Hyperinflammation
T210	37036-37254	Sentence	denotes	While the induction of robust T cell immunity is likely essential for efficient virus control, dysregulated T cell responses may cause immunopathology and contribute to disease severity in COVID-19 patients (Figure 3).
T211	37255-37508	Sentence	denotes	This is suggested in a study by Zhou et al., which reported a significantly increased PBMC frequency of polyclonal GM-CSF+ CD4 T cells capable of prodigious ex vivo IL-6 and IFN-γ production only in critically ill COVID-19 patients (Zhou et al., 2020c).
T212	37509-37797	Sentence	denotes	Of note, GM-CSF+ CD4 T cells have been previously implicated in inflammatory autoimmune diseases, such as multiple sclerosis or juvenile rheumatoid arthritis, and high levels of circulating GM-CSF+ CD4 T cells were found to be associated with poor outcomes in sepsis (Huang et al., 2019).
T213	37798-37931	Sentence	denotes	Additionally, two studies observed reduced frequencies of Treg cells in severe COVID-19 cases (Chen et al., 2020c, Qin et al., 2020).
T214	37932-38120	Sentence	denotes	Since Treg cells have been shown to help resolve ARDS inflammation in mouse models (Walter et al., 2018), a loss of Tregs might facilitate the development of COVID-19 lung immunopathology.
T215	38121-38378	Sentence	denotes	Similarly, a reduction of γδ-T cells, a subset of T cells with apparent protective antiviral function in influenza pneumonia (Dong et al., 2018, Zheng et al., 2013), has been reported in severely sick COVID-19 patients (Guo et al., 2020, Lei et al., 2020b).
T216	38380-38432	Sentence	denotes	Phenotype and Function of T Cell Subsets in COVID-19
T217	38433-38546	Sentence	denotes	Currently, little is known about specific phenotypical and/or functional T cell changes associated with COVID-19.
T218	38547-38889	Sentence	denotes	In the majority of preprints and peer-reviewed studies, there are reports of increased presence of activated T cells (Figure 3) characterized by expression of HLA-DR, CD38, CD69, CD25, CD44, and Ki-67 (Braun et al., 2020, Ni et al., 2020, Guo et al., 2020, Liao et al., 2020, Thevarajan et al., 2020, Yang et al., 2020a, Zheng et al., 2020a).
T219	38890-39160	Sentence	denotes	Generally, independent of COVID-19 disease severity, CD8 T cells seem to be more activated than CD4 T cells (Qin et al., 2020, Thevarajan et al., 2020, Yang et al., 2020a), a finding that echoes stronger CD8 than CD4 T cell responses during SARS-CoV-1 (Li et al., 2008).
T220	39161-39336	Sentence	denotes	Furthermore, in a case study of 10 COVID-19 patients, Diao et al. showed that levels of PD-1 increased from prodromal to symptomatic stages of the disease (Diao et al., 2020).
T221	39337-39557	Sentence	denotes	PD-1 expression is commonly associated with T cell exhaustion, but it is important to emphasize that PD-1 is primarily induced by TCR signaling; it is thus also expressed by activated effector T cells (Ahn et al., 2018).
T222	39558-39783	Sentence	denotes	In addition, several studies reported higher expression of various co-stimulatory and inhibitory molecules such as OX-40 and CD137 (Zhou et al., 2020c), CTLA-4 and TIGIT (Zheng et al., 2020a), and NKG2a (Zheng et al., 2020b).
T223	39784-39953	Sentence	denotes	Reduced numbers of CD28+ CD8 T cells (Qin et al., 2020) as well as larger frequencies of PD-1+ TIM3+ CD8 T cells in ICU patients were also reported (Zhou et al., 2020c).
T224	39954-40152	Sentence	denotes	Expression of most of these markers was found to be higher in CD8 than in CD4 T cells, and levels tended to increase in severe versus non-severe cases, which may be due to differences in viral load.
T225	40153-40530	Sentence	denotes	Cellular functionality was shown to be impaired in CD4 and CD8 T cells of critically ill patients, with reduced frequencies of polyfunctional T cells (producing more than one cytokine) as well as generally lower IFN-γ and TNF-α production following restimulation with phorbol myristate acetate (PMA) and ionomycin (Chen et al., 2020c, Zheng et al., 2020a, Zheng et al., 2020b).
T226	40531-40729	Sentence	denotes	Similarly, Zheng et al. reported that CD8 T cells in severe COVID-19 appear less cytotoxic and effector-like with reduced CD107a degranulation and granzyme B (GzmB) production (Zheng et al., 2020b).
T227	40730-40873	Sentence	denotes	In contrast, a different study found that both GzmB and perforin were increased in CD8 T cells of severely sick patients (Zheng et al., 2020a).
T228	40874-41231	Sentence	denotes	In accordance with the latter observation, when compared to a moderate disease group, convalescent patients with resolved severe SARS-CoV-1 infection had significantly higher frequencies of polyfunctional T cells, with CD4 T cells producing more IFN-γ, TNF-α, and IL-2 and CD8 T cells producing more IFN-γ, TNF-α, and CD107a, respectively (Li et al., 2008).
T229	41232-41423	Sentence	denotes	However, given the vigorous dynamics of acute T cell responses and potential differences in sample timing throughout disease course, these observations are not necessarily mutually exclusive.
T230	41424-41690	Sentence	denotes	Accordingly, RNA sequencing (RNA-seq) data by Liao et al. showed that CD8 T cells in the BAL fluid of severe COVID-19 patients express cytotoxic genes such as GZMA, GZMB, and GZMK at higher levels, while KLRC1 and XCL1 are enriched in mild cases (Liao et al., 2020).
T231	41691-41936	Sentence	denotes	In summary, T cells in severe COVID-19 seem to be more activated and may exhibit a trend toward exhaustion based on continuous expression of inhibitory markers such as PD-1 and TIM-3 as well as overall reduced polyfunctionality and cytotoxicity.
T232	41937-42240	Sentence	denotes	Conversely, recovering patients were shown to have an increase in follicular helper CD4 T cells (TFH) as well as decreasing levels of inhibitory markers along with enhanced levels of effector molecules such as Gzm A, GzmB, and perforin (Thevarajan et al., 2020, Yang et al., 2020a, Zheng et al., 2020b).
T233	42241-42475	Sentence	denotes	Collectively, these studies provide a first glimpse into T cell dynamics in acute SARS-CoV-2 infection, but any conclusions have to be tempered at this stage on account of significant limitations in many of the current investigations.
T234	42477-42493	Sentence	denotes	B Cell Responses
T235	42495-42530	Sentence	denotes	Acute B Cell and Antibody Responses
T236	42531-42680	Sentence	denotes	The humoral immune response is critical for the clearance of cytopathic viruses and is a major part of the memory response that prevents reinfection.
T237	42681-42888	Sentence	denotes	SARS-CoV-2 elicits a robust B cell response, as evidenced by the rapid and near-universal detection of virus-specific IgM, IgG and IgA, and neutralizing IgG antibodies (nAbs) in the days following infection.
T238	42889-42997	Sentence	denotes	The kinetics of the antibody response to SARS-CoV-2 are now reasonably well described (Huang et al., 2020a).
T239	42998-43367	Sentence	denotes	Similar to SARS-CoV-1 infection (Hsueh et al., 2004), seroconversion occurs in most COVID-19 patients between 7 and 14 days after the onset of symptoms, and antibody titers persist in the weeks following virus clearance (Figure 4 ) (Haveri et al., 2020, Lou et al., 2020, Okba et al., 2020, Tan et al., 2020b, Wölfel et al., 2020, Wu et al., 2020b, Zhao et al., 2020a).
T240	43368-43531	Sentence	denotes	Antibodies binding the SARS-CoV-2 internal N protein and the external S glycoprotein are commonly detected (Amanat et al., 2020, Ju et al., 2020, To et al., 2020).
T241	43532-43770	Sentence	denotes	The receptor binding domain (RBD) of the S protein is highly immunogenic, and antibodies binding this domain can be potently neutralizing, blocking virus interactions with the host entry receptor, ACE2 (Ju et al., 2020, Wu et al., 2020b).
T242	43771-43875	Sentence	denotes	Anti-RBD nAbs are detected in most tested patients (Ju et al., 2020, To et al., 2020, Wu et al., 2020b).
T243	43876-44073	Sentence	denotes	Although crossreactivity to SARS-CoV-1 S and N proteins and to MERS-CoV S protein was detected in plasma from COVID-19 patients, no crossreactivity was found to the RBD from SARS-CoV-1 or MERS-CoV.
T244	44074-44177	Sentence	denotes	In addition, plasma from COVID-19 patients did not neutralize SARS-CoV-1 or MERS-CoV (Ju et al., 2020).
T245	44178-44227	Sentence	denotes	Figure 4 Antibody-Mediated Immunity in SARS-CoV-2
T246	44228-44329	Sentence	denotes	Virus-specific IgM and IgG are detectable in serum between 7 and 14 days after the onset of symptoms.
T247	44330-44398	Sentence	denotes	Viral RNA is inversely correlated with neutralizing antibody titers.
T248	44399-44547	Sentence	denotes	Higher titers have been observed in critically ill patients, but it is unknown whether antibody responses somehow contribute to pulmonary pathology.
T249	44548-44736	Sentence	denotes	The SARS-CoV-1 humoral response is relatively short lived, and memory B cells may disappear altogether, suggesting that immunity with SARS-CoV-2 may wane 1–2 years after primary infection.
T250	44737-44906	Sentence	denotes	RBD-specific CD19+IgG+ memory B cells were single-cell sorted from a cohort of eight COVID-19 donors between days 9 and 28 after the onset of symptoms (Ju et al., 2020).
T251	44907-45003	Sentence	denotes	From their antibody gene sequences, 209 SARS-CoV-2-specific monoclonal antibodies were produced.
T252	45004-45235	Sentence	denotes	The monoclonal antibodies had a diverse repertoire, relatively low or no somatic mutations, and variable binding reactivity, with dissociation constants reaching 10−8 to 10−9, similar to antibodies isolated during acute infections.
T253	45236-45406	Sentence	denotes	Two potent neutralizing SARS-CoV-2 RBD-specific monoclonal antibodies were characterized that did not crossreact with the RBD of SARS-CoV-1 or MERS-CoV (Ju et al., 2020).
T254	45407-45555	Sentence	denotes	Together, these results demonstrate that antibody mediated neutralization is virus specific and likely driven by binding of epitopes within the RBD.
T255	45557-45571	Sentence	denotes	B Cell Memory:
T256	45572-45596	Sentence	denotes	Development and Lifespan
T257	45597-45739	Sentence	denotes	The B cell response to a virus serves not only to protect from the initial challenge, but also to offer extended immunity against reinfection.
T258	45740-45905	Sentence	denotes	Following resolution of an infection, plasma cells formed during the acute and convalescent phases continue to secrete antibodies, giving rise to serological memory.
T259	45906-46014	Sentence	denotes	Memory B cells that are also formed during the primary infection constitute the second arm of B cell memory.
T260	46015-46112	Sentence	denotes	Memory B cells can quickly respond to a reinfection by generating new high-affinity plasma cells.
T261	46113-46214	Sentence	denotes	Long-term protection is achieved through the induction of long-lived plasma cells and memory B cells.
T262	46215-46310	Sentence	denotes	There is great interest in understanding the lifespan of B cell memory responses to SARS-CoV-2.
T263	46311-46464	Sentence	denotes	Protection from reinfection has direct medical and social consequences as the world works to develop vaccination strategies and resume normal activities.
T264	46465-46706	Sentence	denotes	In COVID-19 patients, evidence of near-universal seroconversion and the lack of substantial descriptions of reinfection point to a robust antibody response, which, along with the T cell memory response, would offer protection to reinfection.
T265	46707-47065	Sentence	denotes	Indeed, a case study of a single patient described induction of CD38HiCD27Hi antibody-secreting cells (ASCs), concomitant with an increase in circulating follicular T helper cells (Tfh) cells (Thevarajan et al., 2020), and a scRNA-seq study of PBMCs from critically ill and recently recovered individuals revealed a plasma cell population (Guo et al., 2020).
T266	47066-47189	Sentence	denotes	In addition, IgG memory cells specific to the RBD have been identified in the blood of COVID-19 patients (Ju et al., 2020).
T267	47190-47446	Sentence	denotes	Consistent with the development of immunity after COVID-19 infection, a recent study of SARS-CoV-2 infection in rhesus macaques found that two macaques that had resolved the primary infection were resistant to reinfection 28 days later (Bao et al., 2020b).
T268	47447-47622	Sentence	denotes	Due to the timing of this outbreak, it is not yet possible to know the nature and extent of long-term memory responses, but lessons may again be learned from other human CoVs.
T269	47623-47839	Sentence	denotes	In the case of the human CoV 229E, specific IgG and nAbs are rapidly induced but wane in some individuals around a year after infection, with some residual protection to reinfection (Callow et al., 1990, Reed, 1984).
T270	47840-48122	Sentence	denotes	The lifespan of the humoral response following SARS-CoV-1 infection is also relatively short, with the initial specific IgG and nAb response to SARS-CoV-1 diminishing 2–3 years after infection and nearly undetectable in up to 25% of individuals (Cao et al., 2007, Liu et al., 2006).
T271	48123-48379	Sentence	denotes	A long-term study following 34 SARS-CoV-1-infected healthcare workers over a 13-year period also found that virus-specific IgG declined after several years, but the authors observed detectable virus-specific IgG 12 years after infection (Guo et al., 2020).
T272	48380-48509	Sentence	denotes	In the case of MERS-CoV, antibodies were detected in six of seven volunteers tested 3 years after infection (Payne et al., 2016).
T273	48510-48702	Sentence	denotes	IgG specific to SARS-CoV-2 trimeric spike protein was detectable in serum up to 60 days after symptom onset, but IgG titers began decreasing by 8 weeks post symptom onset (Adams et al., 2020).
T274	48703-48789	Sentence	denotes	Long-term protection from reinfection may also be mediated by reactive memory B cells.
T275	48790-49033	Sentence	denotes	A study that analyzed SARS-CoV-1 S protein-specific IgG memory cells at 2, 4, 6, and 8 months post infection found that S-specific IgG memory B cells decreased progressively about 90% from 2 to 8 months after infection (Traggiai et al., 2004).
T276	49034-49199	Sentence	denotes	A further retrospective study of 23 individuals found no evidence of circulating SARS-CoV-1-specific IgG+ memory B cells 6 years after infection (Tang et al., 2011).
T277	49200-49333	Sentence	denotes	This is in contrast to the memory T cell response, which was robustly detected based on induced IFN-γ production (Tang et al., 2011).
T278	49334-49528	Sentence	denotes	Studies of common CoVs SARS-CoV-1 and MERS-CoV indicate that virus-specific antibody responses wane over time and, in the case of common CoVs, result in only partial protection from reinfection.
T279	49529-49716	Sentence	denotes	These data suggest that immunity to SARS-CoV-2 may diminish following a primary infection, and further studies will be required to determine the degree of long-term protection (Figure 4).
T280	49718-49754	Sentence	denotes	Consequences of the B Cell Response:
T281	49755-49784	Sentence	denotes	Protection versus Enhancement
T282	49785-50064	Sentence	denotes	Several studies have demonstrated that high virus-specific antibody titers to SARS-CoV-2 are correlated with greater neutralization of virus in vitro and are inversely correlated with viral load in patients (Figure 4) (Okba et al., 2020, Wölfel et al., 2020, Zhao et al., 2020a).
T283	50065-50406	Sentence	denotes	Despite these indications of a successful neutralizing response in the majority of individuals, higher titers are also associated with more severe clinical cases (Li et al., 2020b, Okba et al., 2020, Zhao et al., 2020a, Zhou et al., 2020a), suggesting that a robust antibody response alone is insufficient to avoid severe disease (Figure 4).
T284	50407-50612	Sentence	denotes	This was also observed in the previous SARS-CoV-1 epidemic, where neutralizing titers were found to be significantly higher in deceased patients compared to patients who had recovered (Zhang et al., 2006).
T285	50613-50769	Sentence	denotes	This has led to concerns that antibody responses to these viruses may contribute to pulmonary pathology via antibody-dependent enhancement (ADE) (Figure 4).
T286	50770-51028	Sentence	denotes	This phenomenon is observed when non-neutralizing virus-specific IgG facilitate entry of virus particles into Fc-receptor (FcR) expressing cells, particularly macrophages and monocytes, leading to inflammatory activation of these cells (Taylor et al., 2015).
T287	51029-51229	Sentence	denotes	A study in SARS-CoV-1-infected rhesus macaques found that anti-S IgG contributed to severe acute lung injury (ALI) and massive accumulation of monocytes and macrophages in the lung (Liu et al., 2019).
T288	51230-51398	Sentence	denotes	Furthermore, serum containing anti-S Ig from SARS-CoV-1 patients enhanced the infection of SARS-CoV-1 in human monocyte-derived macrophages in vitro (Yip et al., 2014).
T289	51399-51506	Sentence	denotes	ADE was also reported with a monoclonal antibody isolated from a patient with MERS-CoV (Wan et al., 2020c).
T290	51507-51744	Sentence	denotes	Somewhat reassuringly, there was no evidence of ADE mediated by sera from rats vaccinated with SARS-CoV-2 RBD in vitro (Quinlan et al., 2020) nor in macaques immunized with an inactivated SARS-CoV-2 vaccine candidate (Gao et al., 2020c).
T291	51745-51892	Sentence	denotes	As of now, there is no evidence that naturally developed antibodies toward SARS-CoV-2 contribute to the pathological features observed in COVID-19.
T292	51893-52019	Sentence	denotes	However, this possibility should be considered when it comes to experimental design and development of therapeutic strategies.
T293	52020-52154	Sentence	denotes	Importantly, in all of the descriptions of ADE as it relates to CoV, the FcR was necessary to trigger the antibody-mediated pathology.
T294	52155-52414	Sentence	denotes	High-dose intravenous immunoglobulin (IVIg), which may blunt ADE, has been trialed in COVID-19 patients (Cao et al., 2020b, Shao et al., 2020), but further studies are needed to determine the extent to which IVIg is safe or beneficial in SARS-CoV-2 infection.
T295	52415-52672	Sentence	denotes	Vaccine trials will need to consider the possibility of antibody-driven pathology upon antigen rechallenge; strategies using F(ab) fragments or engineered Fc monoclonal antibodies may prove particularly beneficial in this setting (Amanat and Krammer, 2020).
T296	52674-52722	Sentence	denotes	Predictors of COVID-19 Disease Risk and Severity
T297	52723-52874	Sentence	denotes	With the rapidly growing number of cases in the first few months, numerous reports on predictors of COVID-19 severity with small cohorts were released.
T298	52875-53048	Sentence	denotes	These offered clinicians and immunologists the first understanding of the clinical course and pathological processes that are associated with the novel SARS-CoV-2 infection.
T299	53049-53188	Sentence	denotes	This section highlights key findings from those studies, with a major focus on the immune factors associated with disease risk or severity.
T300	53190-53224	Sentence	denotes	Susceptibility and Risk Biomarkers
T301	53225-53356	Sentence	denotes	There are currently limited known risk factors for susceptibility to COVID-19, although this has been evaluated in several studies.
T302	53357-53530	Sentence	denotes	Zhao et al. compared the ABO blood group distribution in a cohort of 2,173 COVID-19 patients to that of healthy controls from the corresponding regions (Zhao et al., 2020b).
T303	53531-53704	Sentence	denotes	They found blood group A to be associated with a higher risk for acquiring COVID-19 when compared to non-A blood groups; blood group O had the lowest risk for the infection.
T304	53705-53925	Sentence	denotes	Another study demonstrated an identical association (Zietz and Tatonetti, 2020), and similar results have been previously described for other viruses (Lindesmith et al., 2003), including SARS-CoV-1 (Cheng et al., 2005a).
T305	53926-54213	Sentence	denotes	Several large collaborative efforts are currently underway to generate, share, and analyze genetic data to understand the links between human genetic variation and COVID-19 susceptibility and severity, the most prominent of which is the COVID-19 Host Genetics Initiative (covid19hg.org).
T306	54214-54466	Sentence	denotes	These studies are supported by previous observations on SARS-CoV-1 that followed the 2003 outbreak, which have identified significant associations between genetic variants and immune phenotypes (Chan et al., 2007, Wang et al., 2011, Zhao et al., 2011).
T307	54467-54743	Sentence	denotes	Although identifying such polymorphisms and their associated genes and pathways for SARS-CoV-2 will require large cohorts, several studies, which remain to be tested in clinical trials, have already highlighted genetic polymorphisms that may potentially impact susceptibility.
T308	54744-55028	Sentence	denotes	These studies have focused on genetic variants that may impact the expression or function of genes important in viral entry, namely ACE2 (SARS-CoV-2 receptor) and TMPRSS2 (spike protein activator) (Asselta et al., 2020, Cao et al., 2020c, Renieri et al., 2020, Stawiski et al., 2020).
T309	55029-55263	Sentence	denotes	Cao et al. identified variants that are potentially expression quantitative trait loci (eQTL) of ACE2 (i.e., they may potentially alter ACE2 gene expression) and analyzed their frequencies in different populations (Cao et al., 2020c).
T310	55264-55458	Sentence	denotes	Stawiski et al. listed variants that may be critical in ACE2 binding and thereby its function and compared the frequencies of these variants within different populations (Stawiski et al., 2020).
T311	55459-55723	Sentence	denotes	While there are several limitations to these studies, the major question is whether the utility of these biomarkers is replicable in large populations with COVID-19 clinical outcomes data and in targeted or large-scale genomic analyses that are currently underway.
T312	55724-55869	Sentence	denotes	In addition, these studies will reveal the potential associations between genetic variants and susceptibility in a gene or loci agnostic fashion.
T313	55871-55899	Sentence	denotes	Routine Bloodwork Biomarkers
T314	55900-56108	Sentence	denotes	Several routine blood and serological parameters have been suggested to stratify patients who might be at higher risk for complications to aid in allocation of healthcare resources in the pandemic (Table 1 ).
T315	56109-56247	Sentence	denotes	Serologic markers from routine bloodwork were reported by comparing patients with mild or moderate symptoms to those with severe symptoms.
T316	56248-56377	Sentence	denotes	This includes different acute phase proteins, such as SAA (serum amyloid protein) and C-reactive protein (CRP) (Ji et al., 2020).
T317	56378-56492	Sentence	denotes	Interestingly, elevations in CRP appear to be unique to COVID-19 patients when compared to other viral infections.
T318	56493-56735	Sentence	denotes	Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels (Huang et al., 2020d), as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase (Xiang et al., 2020a).
T319	56736-56884	Sentence	denotes	Overall, inflammatory markers are common in severe cases of COVID-19 and appear to correlate with the severity of the symptoms and clinical outcome.
T320	56885-57066	Sentence	denotes	Moreover, the extensive damage that occurs in specific organs of severe COVID-19 patients is possibly related to differences in the expression of ACE2 (Figure 5 ) (Du et al., 2020).
T321	57067-57149	Sentence	denotes	Table 1 Routine Blood and Immunological Prognostic Biomarkers in COVID-19 Patients
T322	57150-57167	Sentence	denotes	Biomarker Purpose
T323	57168-57599	Sentence	denotes	Routine Bloodwork Lymphocyte count Predicted the disease severity and the outcomes of hospitalized patients (Tan et al., 2020a).Prognostic value was confirmed in numerous studies (Huang et al., 2020d, Liu et al., 2020b, Song et al., 2020, Wang et al., 2020f, Wynants et al., 2020, Yan et al., 2020b, Yang et al., 2020b, Zhang et al., 2020c, Zhao et al., 2020d).Decreased continuously in non-surviving patients (Wang et al., 2020b).
T324	57600-57873	Sentence	denotes	N/L Patients with N/L ≥3.13 were reported to be more likely to develop severe illness and to require ICU admission (Liu et al., 2020c).N/L on admission was a risk factor for short-term progression of patients with moderate pneumonia to severe pneumonia (Feng et al., 2020).
T325	57874-58003	Sentence	denotes	Confirmed to be of prognostic value in COVID-19 in several studies (Song et al., 2020, Wynants et al., 2020, Zhou et al., 2020d).
T326	58004-58080	Sentence	denotes	CRP Proposed as an early biomarker of disease progression (Ji et al., 2020).
T327	58081-58203	Sentence	denotes	Even in early stages, CRP levels were positively correlated with lung lesions and reflected disease severity (Wang, 2020).
T328	58204-58354	Sentence	denotes	Confirmed in numerous studies (Fu et al., 2020, Huang et al., 2020d, Wynants et al., 2020, Yan et al., 2020b, Zhao et al., 2020d, Zhou et al., 2020b).
T329	58355-58439	Sentence	denotes	Predicted the risk of acute myocardial injury (Liu et al., 2020g, Xu et al., 2020a).
T330	58440-58508	Sentence	denotes	LDH Higher in severe cases than in mild cases (Xiang et al., 2020a).
T331	58509-58645	Sentence	denotes	Widely proposed to have prognostic value in COVID-19 (Huang et al., 2020d, Wynants et al., 2020, Yan et al., 2020b, Zhao et al., 2020d).
T332	58646-58756	Sentence	denotes	D-dimer (and coagulation parameters) Predicted severity independently of other variables (Zhou et al., 2020d).
T333	58757-58864	Sentence	denotes	Elevated levels and disseminated intravascular coagulation are found in non-survivors (Wang et al., 2020b).
T334	58865-58938	Sentence	denotes	Identified patients at risk for acute cardiac injury (Liu et al., 2020g).
T335	58939-59142	Sentence	denotes	Other coagulation parameters, such as fibrin degradation product levels, longer prothrombin time, and activated partial thromboplastin time, were also associated with poor prognosis (Tang et al., 2020a).
T336	59143-59289	Sentence	denotes	SAA SAA was proposed to be used as an auxiliary index for diagnosis as it was elevated in 80% of the patients in a small cohort (Ji et al., 2020).
T337	59290-59459	Sentence	denotes	NT-proBNP (N-terminal pro B type natriuretic peptide) NT-proBNP was an independent risk factor of in-hospital death in patients with severe COVID-19 (Gao et al., 2020b).
T338	59460-59561	Sentence	denotes	Platelet count High platelet-to-lymphocyte ratio was associated with worse outcome (Qu et al., 2020).
T339	59562-59702	Sentence	denotes	Thrombocytopenia was associated with poor outcome and with incidence of myocardial injury in COVID-19 (Liu et al., 2020h, Shi et al., 2020).
T340	59703-59845	Sentence	denotes	Immunological CD4+, CD8+, and NK cell counts Lower CD4+, CD8+, and NK cells in PBMCs correlated with severity of COVID-19 (Nie et al., 2020b).
T341	59846-59917	Sentence	denotes	Validated by several studies (Wang et al., 2020f, Zheng et al., 2020b).
T342	59918-60109	Sentence	denotes	PD-1 and Tim-3 expression on T cells Increasing PD-1 and Tim-3 expression on T cells could be detected as patients progressed from prodromal to overtly symptomatic stages (Diao et al., 2020).
T343	60110-60261	Sentence	denotes	Expression was higher in infected patients versus healthy controls and in ICU versus non-ICU patients in both CD4 and CD8 T cells (Zhou et al., 2020b).
T344	60262-60586	Sentence	denotes	phenotypic changes in peripheral blood monocytes The presence of a distinct population of monocytes with high forward scatter (CD11b+, CD14+, CD16+, CD68+, CD80+, CD163+, and CD206+, which secrete IL-6, IL-10, and TNF-α) was identified in patients requiring prolonged hospitalization and ICU admission (Zhang et al., 2020c).
T345	60587-60664	Sentence	denotes	CD14+CD16+IL-6+ monocytes are increased in ICU patients (Zhou et al., 2020b).
T346	60665-60881	Sentence	denotes	IP-10, MCP-3, and IL-1ra IP-10, MCP-3, and IL-1ra were, among 48 examined cytokines, the only ones that closely associated with disease severity and outcome of COVID-19 in a study by Yang et al. (Yang et al., 2020b).
T347	60882-61075	Sentence	denotes	IL-6 Associated with disease severity (hospitalization and ICU admission) and poor prognosis (Chen et al., 2020g, Huang et al., 2020b, Liu et al., 2020b, Liu et al., 2020f, Wang et al., 2020b).
T348	61076-61169	Sentence	denotes	Increased levels were associated with higher risk of respiratory failure (Yao et al., 2020b).
T349	61170-61310	Sentence	denotes	IL-8 Positively correlated with disease severity (Chen et al., 2020e, Gong et al., 2020), with severe cases showing the highest IL-8 levels.
T350	61311-61528	Sentence	denotes	IL-10 Increased in severe or critical patients as compared to mild patients (Gong et al., 2020, Zhou et al., 2020d) without a statistically significant difference between severe and critical cases (Gong et al., 2020).
T351	61529-61722	Sentence	denotes	IL-2R Associated with disease severity in a study that, among other cytokines, also associated ferroprotein levels, PCT levels, and eosinophil counts with COVID-19 severity (Gong et al., 2020).
T352	61723-61902	Sentence	denotes	IL-1β CD14+IL-1β+ monocytes are abundant in early-recovery patients as shown in a single-cell RNA-seq analysis and thought to be associated with cytokine storm (Wen et al., 2020).
T353	61903-62037	Sentence	denotes	IL-1β did not correlate with disease severity in a cross-sectional study with mild, severe, and critical patients (Gong et al., 2020).
T354	62038-62182	Sentence	denotes	IL-4 IL-4 was associated with impaired lung lesions (Fu et al., 2020), but some reports point to a potential mediator effect (Wen et al., 2020).
T355	62183-62414	Sentence	denotes	IL-18 In modeling immune cell interaction between DCs and B cells in late recovery COVID-19 patients, IL-18 was found to be important in B cell production of antibodies, which suggests its importance in recovery (Wen et al., 2020).
T356	62415-62487	Sentence	denotes	GM-CSF GM-CSF+IFN-γ+ T cells are higher in ICU than in non-ICU patients.
T357	62488-62601	Sentence	denotes	CD14+CD16+GM-CSF+ monocytes are higher in COVID-19 patients as compared to healthy controls (Zhou et al., 2020b).
T358	62602-62702	Sentence	denotes	IL-2 and IFN-γ IL-2 and IFN-γ levels were shown to be increased in severe cases (Liu et al., 2020b).
T359	62703-62848	Sentence	denotes	anti-SARS-CoV-2 antibody levels Prolonged SARS-CoV-2 IgM positivity could be utilized as a predictive factor for poor recovery (Fu et al., 2020).
T360	62849-62961	Sentence	denotes	Higher anti-SARS-CoV-2 IgG levels and higher N/L were more commonly found in severe cases (Zhang et al., 2020a).
T361	62962-63061	Sentence	denotes	Figure 5 ACE2 Expression in Organs and Systems Most Frequently Implicated in COVID-19 Complications
T362	63062-63144	Sentence	denotes	The gastrointestinal tract, kidneys, and testis have the highest ACE2 expressions.
T363	63145-63503	Sentence	denotes	In some organs, different cell types have remarkably distinct expressions; e.g., in the lungs, alveolar epithelial cells have higher ACE2 expression levels than bronchial epithelial cells; in the liver, ACE2 is not expressed in hepatocytes, Kupffer cells, or endothelial cells but is detected in cholangiocytes, which can explain liver injury to some extent.
T364	63504-63605	Sentence	denotes	Furthermore, ACE2 expression is enriched on enterocytes of the small intestine compared to the colon.
T365	63606-63823	Sentence	denotes	ACE2, angiotensin-converting enzyme 2; BNP, B-type natriuretic peptide; CRP, C-reactive protein; IL, interleukin; N/L, neutrophil-to-lymphocyte ratio; PT, prothrombin time; aPTT, activated partial thromboplastin time.
T366	63824-64000	Sentence	denotes	Lymphopenia is the most frequently described prognostic marker in COVID-19 (Table 1), and it appears to predict morbidity and mortality even at early stages (Fei et al., 2020).
T367	64001-64256	Sentence	denotes	Tan et al. proposed a prognostic model based on lymphocyte counts at two time points: patients with less than 20% lymphocytes at days 10–12 from the onset of symptoms and less than 5% at days 17–19 had the worst outcomes in this study (Tan et al., 2020a).
T368	64257-64509	Sentence	denotes	Wynants et al. compared predictors of disease severity across seven studies (>1,330 patients), highlighting CRP, neutrophil-to-lymphocyte ratio (N/L), and lactate dehydrogenase (LDH) as the most significant predictive biomarkers (Wynants et al., 2020).
T369	64510-64683	Sentence	denotes	Furthermore, a meta-analysis of 30 COVID-19 studies with a total of 53,000 patients also attempted to identify early-stage patients with poor prognosis (Zhao et al., 2020d).
T370	64684-64887	Sentence	denotes	The most consistent findings across the different studies were elevated levels of CRP, LDH, and D-dimer, as well as decreased blood platelet and lymphocyte counts (Yan et al., 2020b, Zhou et al., 2020d).
T371	64888-65286	Sentence	denotes	Systemic and pulmonary thrombi have been reported with activation of the extrinsic coagulation cascade, involving dysfunctional endothelium and monocytic infiltration (Poor et al., 2020, Varga et al., 2020); thrombocytopenia and elevated D-dimer levels may be indicative of these coagulopathies in COVID-19 patients with important therapeutic implications (Fogarty et al., 2020, Poor et al., 2020).
T372	65288-65336	Sentence	denotes	Immunological Biomarkers in the Peripheral Blood
T373	65337-65489	Sentence	denotes	Immunological biomarkers are particularly important, as immunopathology has been suggested as a primary driver of morbidity and mortality with COVID-19.
T374	65490-65595	Sentence	denotes	Several cytokines and other immunologic parameters have been correlated with COVID-19 severity (Table 1).
T375	65596-65866	Sentence	denotes	Most notably, elevated IL-6 levels were detected in hospitalized patients, especially critically ill patients, in several studies and are associated with ICU admission, respiratory failure, and poor prognosis (Chen et al., 2020g, Huang et al., 2020b, Liu et al., 2020f).
T376	65867-66117	Sentence	denotes	Increased IL-2R, IL-8, IL-10, and GM-CSF have been associated with disease severity as well, but studies are limited, and further studies with larger cohorts of patients are needed to indicate predictive power (Gong et al., 2020, Zhou et al., 2020b).
T377	66118-66237	Sentence	denotes	Conflicting results regarding IL-1β and IL-4 have been reported (Fu et al., 2020, Gong et al., 2020, Wen et al., 2020).
T378	66238-66529	Sentence	denotes	Although elevated cytokine concentrations have been widely described in COVID-19 patients, the vast majority (including IL-6, IL-10, IL-18, CTACK, and IFN-γ) do not seem to have prognostic value, because they do not always differentiate moderate cases from severe cases (Yang et al., 2020b).
T379	66530-66593	Sentence	denotes	This stratification was possible with IP-10, MCP-3, and IL-1ra.
T380	66594-66921	Sentence	denotes	While there are reports that levels of IL-6 at first assessment might predict respiratory failure (Herold et al., 2020), other publications with longitudinal analyses demonstrated that IL-6 increases fairly late during the disease’s course, consequently compromising its prognostic value at earlier stages (Zhou et al., 2020a).
T381	66922-67219	Sentence	denotes	Liu et al. developed a web-based tool using k-means clustering to predict prognosis in terms of death or hospital discharge of COVID-19 patients using age, comorbidities (binary), and baseline log helper T cell count (TH), log suppressor T cell count (TS), and log TH/TS ratio (Liu et al., 2020e).
T382	67220-67428	Sentence	denotes	Total T cell, helper T cell, and suppressor T cell counts were significantly lower and the TH/TS ratio was significantly higher in patients who died from infection as compared to patients who were discharged.
T383	67429-67679	Sentence	denotes	Importantly, most serological and immunological changes observed in severe cases are associated with disease severity but cannot necessarily serve as predictive factors, as they may not have utility in early identification of patients at higher risk.
T384	67680-67888	Sentence	denotes	Discovery of truly predictive biomarkers and potential drivers of hyperinflammatory processes requires comprehensive profiling of asymptomatic and mild cases and longitudinal studies that are limited to date.
T385	67889-67998	Sentence	denotes	Confounding variables including age, gender, and comorbidities may dramatically affect associations observed.
T386	67999-68274	Sentence	denotes	In addition, direct correlation with patient viral load will be important to provide a greater understanding of underlying causes of morbidity and mortality in COVID-19 and the contribution of viral infectivity, hyperinflammation, and host tolerance (Medzhitov et al., 2012).
T387	68275-68482	Sentence	denotes	In summary, lymphopenia, increases in proinflammatory markers and cytokines, and potential blood hypercoagulability characterize severe COVID-19 cases with features reminiscent of cytokine release syndromes.
T388	68483-68587	Sentence	denotes	This correlates with a diverse clinical spectrum ranging from asymptomatic to severe and critical cases.
T389	68588-68712	Sentence	denotes	During the incubation period and early phase of the disease, leukocyte and lymphocyte counts are normal or slightly reduced.
T390	68713-68876	Sentence	denotes	After SARS-CoV-2 binds to ACE2 overexpressing organs, such as the gastrointestinal tracts and kidneys, increases in non-specific inflammation markers are observed.
T391	68877-69111	Sentence	denotes	In more severe cases, a marked systemic release of inflammatory mediators and cytokines occurs, with corresponding worsening of lymphopenia and potential atrophy of lymphoid organs, impairing lymphocyte turnover (Terpos et al., 2020).
T392	69113-69123	Sentence	denotes	Antivirals
T393	69124-69238	Sentence	denotes	Antivirals are a class of small molecules that function as inhibitors of one or more stages of a virus life cycle.
T394	69239-69378	Sentence	denotes	Because of similarities between different virus replication mechanisms, some antivirals can be repurposed against various viral infections.
T395	69379-69554	Sentence	denotes	Currently, most of the available antiviral drugs tested against SARS-CoV-2 are small molecules previously developed against SARS-CoV-1, MERS-CoV, or other RNA and DNA viruses.
T396	69556-69581	Sentence	denotes	Broad-Spectrum Antivirals
T397	69582-69728	Sentence	denotes	A number of small molecules with known antiviral activity against other human RNA viruses are being evaluated for efficacy in treating SARS-CoV-2.
T398	69729-69920	Sentence	denotes	The ribonucleoside analog β-D-N4-hydroxycytidine (NHC) reduced viral titers and lung injury in mice infected with SARS-CoV-2 via introduction of mutations in viral RNA (Sheahan et al., 2017).
T399	69921-70147	Sentence	denotes	Further, an inhibitor of host DHODH, a rate-limiting enzyme in pyrimidine synthesis, was able to inhibit SARS-CoV-2 growth in vitro with greater efficacy than remdesivir or chloroquine (Wang et al., 2020e, Xiong et al., 2020).
T400	70148-70369	Sentence	denotes	Merimepodib, a non-competitive inhibitor of the enzyme inosine-5′-monophosphate dehydrogenase (IMPDH), involved in host guanosine biosynthesis, is able to suppress SARS-CoV-2 replication in vitro (Bukreyeva et al., 2020).
T401	70370-70667	Sentence	denotes	Finally, N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride (HTCC), which was previously shown to efficiently reduce infection by the less-pathogenic human CoV HCoV-NL63, was also found to inhibit MERS-CoV and pseudotyped SARS-CoV-2 in human airway epithelial cells (Milewska et al., 2020).
T402	70669-70688	Sentence	denotes	Protease Inhibitors
T403	70689-70833	Sentence	denotes	Much of the antiviral computational and experimental data currently available for SARS-CoV-2 focus on targeting the 3CL or Main protease (Mpro).
T404	70834-70993	Sentence	denotes	Two prominent drug candidates targeting the SARS-CoV-2 Mpro were designed and synthesized by analyzing the substrate binding pocket of Mpro (Dai et al., 2020).
T405	70994-71102	Sentence	denotes	The X-ray crystal structures of the novel inhibitors in complex with SARS-CoV-2 Mpro were resolved at 1.5 Å.
T406	71103-71227	Sentence	denotes	Both compounds showed good pharmacokinetic activity in vitro, and one exhibited limited toxicity in vivo (Dai et al., 2020).
T407	71228-71317	Sentence	denotes	Multiple studies also aimed to repurpose protease inhibitors to reduce SARS-CoV-2 titers.
T408	71318-71640	Sentence	denotes	Nine existing HIV protease inhibitors (nelfinavir, lopinavir, ritonavir, saquinavir, atazanavir, tipranavir, amprenavir, darunavir, and indinavir) were evaluated for their antiviral activity in Vero cells infected with SARS-CoV-2 (Yamamoto et al., 2020), and nelfinavir was the most potent at inhibiting viral replication.
T409	71642-71657	Sentence	denotes	RdRp Inhibitors
T410	71658-71846	Sentence	denotes	The CoV RNA-dependent RNA polymerase (RdRp) catalyzes the synthesis of viral RNA (Gao et al., 2020a), making it essential for viral replication and a prime target for antiviral inhibitors.
T411	71847-72070	Sentence	denotes	Remdesivir, an adenosine triphosphate analog, inhibits RdRp by binding to RNA strands and preventing additional nucleotides from being added, thereby terminating viral RNA transcription (Figure 6 A) (Agostini et al., 2018).
T412	72071-72228	Sentence	denotes	Remdesivir has been previously shown to be effective against MERS-CoV and SARS-CoV-1 infections in animal models (Sheahan et al., 2017, de Wit et al., 2020).
T413	72229-72374	Sentence	denotes	Similarly, a study investigated the efficacy of remdesivir treatments on 12 rhesus macaques with SARS-CoV-2 infections (Williamson et al., 2020).
T414	72375-72505	Sentence	denotes	Macaques treated with remdesivir showed a reduction in lung viral loads and pneumonia symptoms but no reduction in virus shedding.
T415	72506-72636	Sentence	denotes	This study does provide evidence that if administered early enough, remdesivir may be effective at treating SARS-CoV-2 infections.
T416	72637-72741	Sentence	denotes	Figure 6 Available Therapeutic Options to Manage COVID-19 Immunopathology and to Deter Viral Propagation
T417	72742-72956	Sentence	denotes	(A) Rdrp inhibitors (remdesivir, favipiravir), protease inhibitors (lopinavir/ritonavir), and antifusion inhibitors (arbidol) are currently being investigated in their efficacy in controlling SARS-CoV-2 infections.
T418	72957-73064	Sentence	denotes	(B) CQ and HCQ increase the pH within lysosomes, impairing viral transit through the endolysosomal pathway.
T419	73065-73213	Sentence	denotes	Reduced proteolytic function within lysosomes augments antigen processing for presentation on MHC complexes and increases CTLA4 expression on Tregs.
T420	73214-73349	Sentence	denotes	(C) Antagonism of IL-6 signaling pathway and of other cytokine-/chemokine-associated targets has been proposed to control COVID-19 CRS.
T421	73350-73470	Sentence	denotes	These include secreted factors like GM-CSF that contribute to the recruitment of inflammatory monocytes and macrophages.
T422	73471-73687	Sentence	denotes	(D) Several potential sources of SARS-CoV-2 neutralizing antibodies are currently under investigation, including monoclonal antibodies, polyclonal antibodies, and convalescent plasma from recovered COVID-19 patients.
T423	73688-73823	Sentence	denotes	GM-CSF, granulocyte-macrophage colony-stimulating factor; CQ, chloroquine; HCQ, hydroxychloroquine; RdRp, RNA-dependent RNA polymerase.
T424	73825-73850	Sentence	denotes	Antiviral Clinical Trials
T425	73851-73943	Sentence	denotes	A large number of clinical trials using experimental antiviral drugs are currently underway.
T426	73944-74305	Sentence	denotes	A small proportion of them are aimed at repurposing existing antivirals, including arbidol (umifenovir), a broad-spectrum antiviral that blocks viral fusion; lopinavir/ritonavir (LPV/r), a combination of anti-HIV protease inhibitors; favipiravir, an RdRp inhibitor used to treat severe influenza infections (Hayden and Shindo, 2019); and remdesivir (Figure 6A).
T427	74306-74471	Sentence	denotes	Chen et al. conducted a multicenter, randomized priority trial on 240 patients with confirmed COVID-19 infection to test favipiravir or arbidol (Chen et al., 2020b).
T428	74472-74538	Sentence	denotes	Favipiravir was suggested to significantly improve symptom relief.
T429	74539-74721	Sentence	denotes	However, the interpretation of this study is limited by a short clinical recovery window of 7 days, only 100 of 236 patients with confirmed COVID-19, and the lack of a control group.
T430	74722-74865	Sentence	denotes	LPV/r has previously shown efficacy in treating SARS-Cov-1 (Chu et al., 2004), prompting an early SARS-Cov-2 clinical trial (Li et al., 2020c).
T431	74866-75049	Sentence	denotes	44 patients were enrolled in a trial investigating the efficacy and safety of LPV/r (n = 21 patients), arbidol (n = 16), or control (n = 7) as treatment for mild to moderate COVID-19.
T432	75050-75253	Sentence	denotes	At day 14 of treatment, 76.2%, 62.4%, and 71.4% of patients had a positive to negative conversion in the LPV/r, arbidol, and control groups, respectively, with no statistical significance between groups.
T433	75254-75398	Sentence	denotes	A randomized controlled trial (RCT) with 200 severe COVID-19 patients did not observe a significant benefit of LPV/r either (Cao et al., 2020a).
T434	75399-75618	Sentence	denotes	However, a study that looked at the impact of earlier administration of LPV/r treatment showed that when treatment of LPV/r was started within 10 days of symptom onset, a shorter duration of virus shedding was observed.
T435	75619-75708	Sentence	denotes	Thus, timing of LPV/r administration may be critical to its efficacy (Yan et al., 2020a).
T436	75709-75915	Sentence	denotes	In a multicenter clinical study assessing the compassionate use of remdesivir in severe COVID-19 patients, 53 patients across several countries were treated with remdesivir for 10 days (Grein et al., 2020).
T437	75916-76047	Sentence	denotes	68% of the 53 patients who received remdesivir showed clinical improvement assessed through improved oxygen support or extubations.
T438	76048-76172	Sentence	denotes	Without a proper control group, limited conclusions can be drawn with regards to the efficacy of remdesivir from this study.
T439	76173-76325	Sentence	denotes	The measured 68% clinical improvement may be in line with average clinical improvement across patients treated with standard of care (Li et al., 2020c).
T440	76326-76514	Sentence	denotes	A small RCT in China with 237 severe COVID-19 patients randomized 2:1 to remdesivir versus placebo demonstrated no significant benefit in time to clinical improvement (Wang et al., 2020g).
T441	76515-76746	Sentence	denotes	Almost simultaneously, preliminary results from a larger National Institute of Allergy and Infectious Diseases (NIAID) RCT with more than 1,000 patients were announced with remdesevir to be associated with quicker time to recovery:
T442	76747-76793	Sentence	denotes	11 days compared with 15 days (Ledford, 2020).
T443	76794-76930	Sentence	denotes	A non-significant benefit in mortality was also noted, and the trial was stopped early to allow access to remdesivir in the placebo arm.
T444	76931-77132	Sentence	denotes	Complete safety data and full publication are awaited, but this study offers encouraging results and has resulted in an FDA emergency use authorization for remdesivir in hospitalized COVID-19 patients.
T445	77134-77185	Sentence	denotes	Therapeutic Immunomodulation for COVID-19 Treatment
T446	77187-77199	Sentence	denotes	Chloroquine:
T447	77200-77240	Sentence	denotes	Modes of Action and Immunological Impact
T448	77241-77361	Sentence	denotes	Chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) have gained traction as possible therapeutics for COVID-19.
T449	77362-77466	Sentence	denotes	Both drugs are used as antimalarial agents and as immunomodulatory therapies for rheumatologic diseases.
T450	77467-77654	Sentence	denotes	However, the application of CQ and HCQ to COVID-19 stems from their past use as antivirals (Savarino et al., 2003), including for SARS-CoV-1 (Keyaerts et al., 2004, Vincent et al., 2005).
T451	77655-77756	Sentence	denotes	CQ and HCQ interfere with lysosomal activity and have been reported to have immunomodulatory effects.
T452	77757-78030	Sentence	denotes	CQ augments antigen processing for MHC class I and II presentation, directly inhibits endosomal TLR7 and TLR9, and enhances the activity of regulatory T cells (Garulli et al., 2008, Lo et al., 2015, Schrezenmeier and Dörner, 2020, Thomé et al., 2013a, Thomé et al., 2013b).
T453	78031-78259	Sentence	denotes	Early studies involving in vitro infection of host cells with SARS-CoV-2 demonstrated that both CQ and HCQ significantly impact endosomal maturation, resulting in increased sequestration of virion particles within endolysosomes.
T454	78260-78422	Sentence	denotes	However, there has been conflicting evidence whether CQ is more potent than HCQ in reducing viral load (Liu et al., 2020d, Wang et al., 2020b, Yao et al., 2020a).
T455	78423-78665	Sentence	denotes	Notably, one group reported that treatment of infected cells with HCQ before and during infection significantly reduced viral load, suggesting that combined prophylactic and therapeutic HCQ use yields maximum efficacy (Clementi et al., 2020).
T456	78666-79021	Sentence	denotes	To better understand host immune responses to treatment, one group compared bulk transcriptomic changes in primary PBMCs treated with HCQ for 24 h to PBMCs from confirmed SARS-CoV-2 positive patients and controls, followed by a comparison of HCQ-treated primary macrophages to BAL and postmortem lung biopsies from COVID-19 patients (Corley et al., 2020).
T457	79022-79158	Sentence	denotes	Across all comparisons, there was minimal overlap between host differential gene expression and genes altered by in vitro HCQ treatment.
T458	79159-79257	Sentence	denotes	Thus, the potential mechanistic action of HCQ in the context of SARS-CoV-2 remains poorly defined.
T459	79259-79304	Sentence	denotes	Evaluation of HCQ Efficacy in Clinical Trials
T460	79305-79526	Sentence	denotes	Despite the apparent widespread use of HCQ and CQ to treat COVID-19 (Figure 6B), few controlled clinical trials have been performed so far and thus the potential benefits of these drugs for COVID-19 remains controversial.
T461	79527-79650	Sentence	denotes	One of the earliest trials (2020-000890-25) was a single-arm, open-label trial of 600 mg daily HCQ in 20 COVID-19 patients.
T462	79651-79790	Sentence	denotes	They reported that HCQ alone, or in combination with the antibiotic azithromycin (AZ), reduced viral load by day 6 (Gautret et al., 2020a).
T463	79791-79981	Sentence	denotes	A follow-up trial in 80 patients treated with HCQ and AZ reported that 93% of patients had a negative PCR result on day 8 of treatment, and 81.3% were discharged within 10 days of treatment.
T464	79982-80076	Sentence	denotes	However, it is important to note that both trials had no control arms (Gautret et al., 2020b).
T465	80077-80262	Sentence	denotes	Rigorous statistical analyses by others that accounted for the patients excluded from the original analysis found limited evidence for HCQ monotherapy (Hulme et al., 2020, Lover, 2020).
T466	80263-80381	Sentence	denotes	A double-blind RCT assessed HCQ monotherapy in the treatment of mild COVID-19 (ChiCTR2000029559) (Chen et al., 2020i).
T467	80382-80476	Sentence	denotes	A total of 62 patients were enrolled; the treatment arm received 400 mg HCQ daily over 5 days.
T468	80477-80663	Sentence	denotes	By day 6, patients who received HCQ had clinical resolution on average 1 day earlier than controls; no patients progressed to severe disease compared to four patients in the control arm.
T469	80664-81033	Sentence	denotes	In a smaller RCT that treated 30 patients with mild COVID-19 (NCT04261517) with 400 mg HCQ for 7 days, there were no significant differences in the number of patients with negative PCR results on day 7 (all but one positive), median duration of hospitalization, time to fever resolution, or progression of disease on chest computed tomography (CT) (Chen et al., 2020d).
T470	81034-81187	Sentence	denotes	The largest RCT to date enrolled 150 patients with mild COVID-19 across 16 centers in an open-label trial of HCQ and standard of care (ChiCTR2000029868).
T471	81188-81611	Sentence	denotes	There were no significant differences between groups in conversion to negative SARS-CoV-2 RT-PCR result on day 28 or rate of symptom resolution; there were significantly more adverse events in the HCQ arm, though largely non-serious; they reported some evidence for faster normalization of C-reactive protein in the patients who received HCQ plus standard of care, but this finding was not significant (Tang et al., 2020b).
T472	81612-81786	Sentence	denotes	A meta-analysis including most of the studies described here found no clinical benefits to patients receiving standard of care plus an HCQ regimen (Shamshirian et al., 2020).
T473	81787-81845	Sentence	denotes	Two studies have assessed HCQ efficacy in severe COVID-19.
T474	81846-82095	Sentence	denotes	In a prospective study of 11 patients who had received 600 mg HCQ over 10 days with AZ on days 1–5, there were several patients with worsening clinical status and one death; 8 of 10 patients had a positive PCR result on day 10 (Molina et al., 2020).
T475	82096-82319	Sentence	denotes	An ongoing double-blind RCT of patients with severe COVID-19 (NCT04323527) randomized 81 patients into high-dose HCQ (600 mg 2× per day for 10 days) or low-dose (450 mg/day for 5 days) treatment groups (Borba et al., 2020).
T476	82320-82406	Sentence	denotes	Recruitment into the high-dose arm was halted prematurely due to poor safety outcomes.
T477	82407-82520	Sentence	denotes	There was no significant difference in negative PCR results on day 4 or need for mechanical ventilation on day 6.
T478	82521-82715	Sentence	denotes	Taken together, the clinical trials performed thus far to evaluate the efficacy of HCQ ± AZ for COVID-19 have not demonstrated clear evidence of clinical benefit in patients with severe disease.
T479	82716-82809	Sentence	denotes	A search of ClinicalTrials.gov on April 27, 2020 found 140 clinical trials investigating HCQ.
T480	82810-82950	Sentence	denotes	This number is rapidly growing, indicating the heightened interest in this therapeutic and pressing need for evidence-based recommendations.
T481	82952-82988	Sentence	denotes	Corticosteroids for COVID-19 Therapy
T482	82989-83108	Sentence	denotes	Because of their anti-inflammatory activity, corticosteroids (CSs) are an adjuvant therapy for ARDS and cytokine storm.
T483	83109-83286	Sentence	denotes	However, the broad immunosuppression mediated by CS does raise the possibility that treatment could interfere with the development of a proper immune response against the virus.
T484	83287-83459	Sentence	denotes	A meta-analysis of 5,270 patients with MERS-CoV, SARS-CoV-1, or SARS-CoV-2 infection found that CS treatment was associated with higher mortality rate (Yang et al., 2020c).
T485	83460-83677	Sentence	denotes	A more recent meta-analysis of only SARS-CoV-2 infection assessed 2,636 patients and found no mortality difference associated with CS treatment, including in a subset of patients with ARDS (Gangopadhyay et al., 2020).
T486	83678-83825	Sentence	denotes	Other studies have reported associations with delayed viral clearance and increased complications in SARS and MERS patients (Sanders et al., 2020).
T487	83826-83990	Sentence	denotes	In fact, the interim guidelines updated by the WHO on March 13, 2020 advise against giving systemic corticosteroids for COVID-19 (World Health Organization, 2020a).
T488	83991-84035	Sentence	denotes	Yet, new data from COVID-19 are conflicting.
T489	84036-84254	Sentence	denotes	One group reported no significant difference in time to viral clearance between patients who received methylprednisolone orally (mild disease) or intravenously (i.v.) (severe) and those who did not (Fang et al., 2020).
T490	84255-84516	Sentence	denotes	Retrospective studies from groups in China report that patients who were transferred to the ICU were less likely to have received CSs (Wang et al., 2020b) and that patients with ARDS who received methylprednisolone had reduced mortality risk (Wu et al., 2020a).
T491	84517-84761	Sentence	denotes	In contrast, another retrospective analysis found that patients who received CSs were more likely to have either been admitted to the ICU or perished, although the CS-treated group also had significantly more comorbidities (Wang et al., 2020c).
T492	84762-84954	Sentence	denotes	A smaller observational study of 31 patients found no association between corticosteroid treatment and time to viral clearance, length of hospital stay, or symptom duration (Zha et al., 2020).
T493	84955-85198	Sentence	denotes	A larger study of adjuvant CSs in 244 patients with critical COVID-19 found no association with 28-day mortality; subgroup analysis of patients with ARDS found no association between treatment with CSs and clinical outcomes (Lu et al., 2020b).
T494	85199-85296	Sentence	denotes	They also found that increased dosage was significantly associated with increased mortality risk.
T495	85297-85552	Sentence	denotes	A retrospective review of 46 patients, of whom 26 received i.v. methylprednisolone, found that early, low-dose administration significantly improved SpO2 and chest CT, time to fever resolution, and time on supplemental oxygen therapy (Wang et al., 2020h).
T496	85553-85740	Sentence	denotes	Others have published perspectives in support of early (Lee et al., 2020) and short-term, low-dose administration (Shang et al., 2020) based on anecdotal evidence but not clinical trials.
T497	85741-85887	Sentence	denotes	Most of the current data on CS use in COVID-19 are from observational studies and support either modest clinical benefit or no meaningful effects.
T498	85888-86087	Sentence	denotes	Larger RCTs are necessary to understand the risks and benefits of CSs for these patients; there are 22 trials evaluating various corticosteroids registered on ClinicalTrials.gov as of April 27, 2020.
T499	86089-86126	Sentence	denotes	Cytokine-Directed Therapy in COVID-19
T500	86128-86169	Sentence	denotes	Recombinant IFN as an Antiviral Treatment
T501	86170-86289	Sentence	denotes	One of the first defenses of the human body against RNA viruses like SARS-CoV-2 is the release of types I and III IFNs.
T502	86290-86520	Sentence	denotes	It is important to note that type I IFN (IFNα/β) receptors are ubiquitously expressed, so IFNα/β signaling can result in not only antiviral effects, but also the activation of immune cells that potentially exacerbate pathogenesis.
T503	86521-86652	Sentence	denotes	In contrast, type III IFN (also known as IFNλ) signals mainly in epithelial cells, as well as in a restricted pool of immune cells.
T504	86653-86866	Sentence	denotes	Because type III IFNs have immunomodulatory functions, subsequent signaling could induce a potent antiviral effect without enhancing pathogenic inflammation (Andreakos et al., 2017, Prokunina-Olsson et al., 2020).
T505	86867-87011	Sentence	denotes	Recently, there has been a growing interest in the potential therapeutic impact of modulating the IFN response to disable COVID-19 pathogenesis.
T506	87012-87114	Sentence	denotes	Before the current pandemic, groups have studied the role of IFNs in other betacoronavirus infections.
T507	87115-87268	Sentence	denotes	One study of 40 patients with SARS-CoV-1 infection described unresolved elevated type I IFNs and ISGs in those with poor outcomes (Cameron et al., 2007).
T508	87269-87548	Sentence	denotes	Others report that exogenous type I IFN does not improve outcomes when given with ribavirin in patients with MERS-CoV infection (Arabi et al., 2020), suggesting that the role of IFN as a therapeutic or prophylactic option may be strain or species specific (Sheahan et al., 2020).
T509	87549-87799	Sentence	denotes	Interestingly, a recent study by Mount Sinai virology groups revealed that type I IFN signaling is impaired in the early response to SARS-CoV-2; in vitro, SARS-CoV-2 may be more susceptible to type I IFN than SARS-CoV-1 is (Blanco-Melo et al., 2020).

T10

0-9

Sentence

denotes

Main Text

T11

11-23

Sentence

denotes

Introduction

T12

24-310

Sentence

denotes

The recent emergence and rapid global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting coronavirus disease 2019 (COVID-19) poses an unprecedented health crisis that was declared a pandemic by the World Health Organization (WHO) on March 11, 2020.

T13

311-522

Sentence

denotes

The origin of SARS-CoV-2 was traced to the city of Wuhan in the province of Hubei, China, where a cluster of viral pneumonia cases was first detected, many in connection with the Huanan Seafood Wholesale Market.

T14

523-842

Sentence

denotes

China reported this outbreak to the WHO on December 31, 2019 and soon after identified the causative pathogen as a betacoronavirus with high sequence homology to bat coronaviruses (CoVs) using angiotensin-converting enzyme 2 (ACE2) receptor as the dominant mechanism of cell entry (Lu et al., 2020a, Wan et al., 2020b).

T15

843-1069

Sentence

denotes

Following a likely zoonotic spillover, human-to-human transmission events were confirmed with clinical presentations ranging from no symptoms to mild fever, cough, and dyspnea to cytokine storm, respiratory failure, and death.

T16

1070-1300

Sentence

denotes

SARS-CoV-2 is also closely related to SARS (retrospectively named SARS-CoV-1) and Middle Eastern respiratory syndrome (MERS) CoVs, causing zoonotic epidemic and local outbreaks in 2003 and 2012, respectively (de Wit et al., 2016).

T17

1301-1539

Sentence

denotes

While SARS-CoV-2 is not as lethal as SARS-CoV-1 or MERS-CoV (Fauci et al., 2020), the considerable spread of the current pandemic has brought tremendous pressure and disastrous consequences for public health and medical systems worldwide.

T18

1540-1764

Sentence

denotes

The scientific response to the crisis has been extraordinary, with a plethora of COVID-19 studies posted in preprint servers in an attempt to rapidly unravel the pathogenesis of COVID-19 and potential therapeutic strategies.

T19

1765-2173

Sentence

denotes

In response, trainees and faculty members of the Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai (PrIISM) have initiated an institutional effort to critically review the preprint literature (Vabret et al., 2020), together with peer-reviewed articles published in traditional journals, and summarize the current state of science on the fast-evolving field of COVID-19 immunology.

T20

2174-2411

Sentence

denotes

We thematically focus on the innate and adaptive immune responses to SARS-CoV-2 and related CoVs, clinical studies and prognostic laboratory correlates, current therapeutic strategies, prospective clinical trials, and vaccine approaches.

T21

2413-2448

Sentence

denotes

Innate Immune Sensing of SARS-CoV-2

T22

2449-2558

Sentence

denotes

Innate immune sensing serves as the first line of antiviral defense and is essential for immunity to viruses.

T23

2559-2660

Sentence

denotes

To date, our understanding of the specific innate immune response to SARS-CoV-2 is extremely limited.

T24

2661-2884

Sentence

denotes

However, the virus-host interactions involving SARS-CoV-2 are likely to recapitulate many of those involving other CoVs, given the shared sequence homology among CoVs and the conserved mechanisms of innate immune signaling.

T25

2885-3194

Sentence

denotes

In the case of RNA viruses such as SARS-CoV-2, these pathways are initiated through the engagement of pattern-recognition receptors (PRRs) by viral single-stranded RNA (ssRNA) and double-stranded RNA (dsRNA) via cytosolic RIG-I like receptors (RLRs) and extracellular and endosomal Toll-like receptors (TLRs).

T26

3195-3281

Sentence

denotes

Upon PRR activation, downstream signaling cascades trigger the secretion of cytokines.

T27

3282-3524

Sentence

denotes

Among these, type I/III interferons (IFNs) are considered the most important for antiviral defense, but other cytokines, such as proinflammatory tumor necrosis factor alpha (TNF-α), and interleukin-1 (IL-1), IL-6, and IL-18 are also released.

T28

3525-3626

Sentence

denotes

Together, they induce antiviral programs in target cells and potentiate the adaptive immune response.

T29

3627-3769

Sentence

denotes

If present early and properly localized, IFN-I can effectively limit CoV infection (Channappanavar et al., 2016, Channappanavar et al., 2019).

T30

3770-4003

Sentence

denotes

Early evidence demonstrated that SARS-CoV-2 is sensitive to IFN-I/III pretreatment in vitro, perhaps to a greater degree than SARS-CoV-1 (Blanco-Melo et al., 2020, Lokugamage et al., 2020, Mantlo et al., 2020, Stanifer et al., 2020).

T31

4004-4119

Sentence

denotes

However, the specific IFN-stimulated genes (ISGs) that mediate these protective effects are still being elucidated.

T32

4120-4295

Sentence

denotes

Lymphocyte antigen 6 complex locus E (LY6E) has been shown to interfere with SARS-CoV-2 spike (S) protein-mediated membrane fusion (Pfaender et al., 2020, Zhao et al., 2020c).

T33

4296-4561

Sentence

denotes

Likely, the IFN-induced transmembrane family (IFITM) proteins inhibit SARS-CoV-2 entry, as demonstrated for SARS-CoV-1 (Huang et al., 2011b), although their action in promoting infection has also been described for other CoVs (Zhao et al., 2014, Zhao et al., 2018).

T34

4563-4605

Sentence

denotes

Evasion of Innate Sensing by Coronaviruses

T35

4606-4749

Sentence

denotes

As these cytokines represent a major barrier to viral infection, CoVs have evolved several mechanisms to inhibit IFN-I induction and signaling.

T36

4750-4932

Sentence

denotes

Numerous studies have demonstrated that SARS-CoV-1 suppresses IFN release in vitro and in vivo (Cameron et al., 2012, Minakshi et al., 2009, Siu et al., 2009, Wathelet et al., 2007).

T37

4933-5136

Sentence

denotes

SARS-CoV-2 likely achieves a similar effect, as suggested by the lack of robust type I/III IFN signatures from infected cell lines, primary bronchial cells, and a ferret model (Blanco-Melo et al., 2020).

T38

5137-5286

Sentence

denotes

In fact, patients with severe COVID-19 demonstrate remarkably impaired IFN-I signatures as compared to mild or moderate cases (Hadjadj et al., 2020).

T39

5287-5496

Sentence

denotes

As is often the case, there are multiple mechanisms of evasion for CoVs, with viral factors antagonizing each step of the pathway from PRR sensing and cytokine secretion to IFN signal transduction (Figure 1 ).

T40

5497-5576

Sentence

denotes

Figure 1 Mechanisms of Host Innate Immune Response and Coronaviruses Antagonism

T41

5577-5751

Sentence

denotes

Overview of innate immune sensing (left) and interferon signaling (right), annotated with the known mechanisms by which SARS-CoV-1 and MERS-CoV antagonize the pathways (red).

T42

5752-6068

Sentence

denotes

CoV-mediated antagonism of innate immunity begins with evasion of PRR sensing. ssRNA viruses, like CoVs, form dsRNA intermediates during their replication, which can be detected by TLR3 in the endosome and RIG-I, MDA5, and PKR in the cytosol. ssRNA may also be detected by TLR7 or TLR8 and potentially RIG-I and PKR.

T43

6069-6302

Sentence

denotes

CoVs are known to avoid PRR activation by either avoiding recognition altogether or antagonizing PRR action (Bouvet et al., 2010, Chen et al., 2009, Deng et al., 2017, Hackbart et al., 2020, Ivanov et al., 2004, Knoops et al., 2008).

T44

6303-6444

Sentence

denotes

To evade PRRs, dsRNA is first shielded by membrane-bound compartments that form during viral replication of SARS-CoV-1 (Knoops et al., 2008).

T45

6445-6734

Sentence

denotes

In addition, viral RNA is guanosine-capped and methylated at the 5′ end by CoVs non-structural proteins (NSPs) 10, 13, 14, and 16 (Bouvet et al., 2010, Chen et al., 2009, Ivanov et al., 2004), thereby resembling host mRNA to promote translation, prevent degradation, and evade RLR sensing.

T46

6735-6936

Sentence

denotes

Finally, CoVs also encode an endoribonuclease, NSP15, that cleaves 5′ polyuridines formed during viral replication, which would otherwise be detected by MDA5 (Deng et al., 2017, Hackbart et al., 2020).

T47

6937-7006

Sentence

denotes

CoVs have evolved additional strategies to impede activation of PRRs.

T48

7007-7082

Sentence

denotes

SARS-CoV-1 N-protein prevents TRIM25 activation of RIG-I (Hu et al., 2017).

T49

7083-7281

Sentence

denotes

Likewise, MERS-CoV NS4a, which itself binds dsRNA, impedes PKR activation (Comar et al., 2019, Rabouw et al., 2016) and inhibits PACT, an activator of RLRs (Niemeyer et al., 2013, Siu et al., 2014).

T50

7282-7383

Sentence

denotes

Additionally, MERS-CoV NS4b antagonizes RNaseL, another activator of RLRs (Thornbrough et al., 2016).

T51

7384-7423

Sentence

denotes

The role of other PRRs remains unclear.

T52

7424-7578

Sentence

denotes

For example, SARS-CoV-1 papain-like protease (PLP) antagonizes STING, suggesting that self-DNA may also represent an important trigger (Sun et al., 2012).

T53

7579-7667

Sentence

denotes

The extent to which SARS-CoV-2 homologs overlap in these functions is currently unknown.

T54

7668-7925

Sentence

denotes

Following activation, RLR and TLRs induce signaling cascades, leading to the phosphorylation of transcription factors, such as NF-kB and the interferon-regulatory factor family (IRF), ultimately leading to transcription of IFN and proinflammatory cytokines.

T55

7926-8120

Sentence

denotes

Although no experimental studies have delineated the precise functions of SARS-CoV-2 proteins, proteomic studies have demonstrated interactions between viral proteins and PRR signaling cascades.

T56

8121-8342

Sentence

denotes

SARS-CoV-2 ORF9b indirectly interacts with the signaling adaptor MAVS via its association with Tom70 (Gordon et al., 2020), consistent with prior reports that SARS-CoV-1 ORF9b suppresses MAVS signaling (Shi et al., 2014).

T57

8343-8505

Sentence

denotes

Furthermore, SARS-CoV-2 NSP13 interacts with signaling intermediate TBK1, and NSP15 is associated with RNF41, an activator of TBK1 and IRF3 (Gordon et al., 2020).

T58

8506-8648

Sentence

denotes

Similarly, SARS-CoV-1 M protein is known to inhibit the TBK1 signaling complex (Siu et al., 2009), as does MERS-CoV ORF4b (Yang et al., 2015).

T59

8649-8818

Sentence

denotes

Other proteins, including SARS-CoV-1 PLP, N, ORF3b, and ORF6, block IRF3 phosphorylation and nuclear translocation (Devaraj et al., 2007, Kopecky-Bromberg et al., 2007).

T60

8819-8859

Sentence

denotes

NF-kB is also inhibited by CoV proteins.

T61

8860-8986

Sentence

denotes

These include SARS-CoV-1 PLP (Frieman et al., 2009) and MERS-CoV ORF4b and ORF5 (Canton et al., 2018, Menachery et al., 2017).

T62

8987-9217

Sentence

denotes

Finally, SARS-CoV-1 NSP1 (Huang et al., 2011a, Kamitani et al., 2009) and MERS-CoV NSP1 (Lokugamage et al., 2015) initiate general inhibition of host transcription and translation, thus limiting antiviral defenses nonspecifically.

T63

9218-9439

Sentence

denotes

To prevent signaling downstream of IFN release, CoV proteins inhibit several steps of the signal transduction pathway that bridge the receptor subunits (IFNAR1 and IFNAR2) to the STAT proteins that activate transcription.

T64

9440-9707

Sentence

denotes

For SARS-CoV-1, these mechanisms include IFNAR1 degradation by ORF3a (Minakshi et al., 2009), decreased STAT1 phosphorylation by NSP1 (Wathelet et al., 2007), and antagonism of STAT1 nuclear translocation by ORF6 (Frieman et al., 2007, Kopecky-Bromberg et al., 2007).

T65

9708-9830

Sentence

denotes

However, SARS-CoV-2 ORF6 shares only 69% sequence homology with SARS-CoV-1, suggesting this function may not be conserved.

T66

9831-9974

Sentence

denotes

In support of this notion, SARS-CoV-2 infection fails to limit STAT1 phosphorylation, unlike in SARS-CoV-1 infection (Lokugamage et al., 2020).

T67

9976-10033

Sentence

denotes

Imbalance between Antiviral and Proinflammatory Responses

T68

10034-10265

Sentence

denotes

Taken together, the multiplicity of strategies developed by pathogenic CoVs to escape immune sensing, particularly the IFN-I pathway, suggests a critical role played by the dysregulation of IFN-I response in COVID-19 pathogenicity.

T69

10266-10457

Sentence

denotes

Concordantly, animal models of SARS-CoV-1 and MERS-CoV infection indicate that failure to elicit an early IFN-I response correlates with the severity of disease (Channappanavar et al., 2016).

T70

10458-10655

Sentence

denotes

Perhaps more importantly, these models demonstrate that timing is key, as IFN is protective early in disease but later becomes pathologic (Channappanavar et al., 2016, Channappanavar et al., 2019).

T71

10656-10777

Sentence

denotes

Perhaps interferon-induced upregulation of ACE2 in airway epithelia may contribute to this effect (Ziegler et al., 2020).

T72

10778-10914

Sentence

denotes

Furthermore, while pathogenic CoVs block IFN signaling, they may actively promote other inflammatory pathways contributing to pathology.

T73

10915-11186

Sentence

denotes

For instance, SARS-CoV-1 ORF3a, ORF8b, and E proteins enhance inflammasome activation (Chen et al., 2019, Nieto-Torres et al., 2015, Shi et al., 2019, Siu et al., 2019), leading to secretion of IL-1β and IL-18, which are likely to contribute to pathological inflammation.

T74

11187-11347

Sentence

denotes

Similarly, SARS-CoV-2 NSP9 and NSP10 might induce IL-6 and IL-8 production, potentially by inhibition of NKRF, an endogenous NF-kB repressor (Li et al., 2020a).

T75

11348-11540

Sentence

denotes

Collectively, these proinflammatory processes likely contribute to the “cytokine storm” observed in COVID-19 patients and substantiate a role for targeted immunosuppressive treatment regimens.

T76

11541-11744

Sentence

denotes

Moving forward, a clear understanding of the delicate balance between antiviral and inflammatory innate immune programs will be essential to developing effective biomarkers and therapeutics for COVID-19.

T77

11746-11759

Sentence

denotes

Myeloid Cells

T78

11760-12029

Sentence

denotes

Mucosal immune responses to infectious agents are orchestrated and regulated by myeloid cells with specialized functions, which include conventional dendritic cells (cDCs), monocyte-derived DCs (moDCs), plasmacytoid DCs (pDCs), and macrophages (Guilliams et al., 2013).

T79

12030-12275

Sentence

denotes

A growing body of evidence points to dysregulated myeloid responses that potentially drive the COVID-19 hallmark syndromes, such as acute respiratory distress syndrome (ARDS), cytokine release syndrome (CRS) and lymphopenia (Mehta et al., 2020).

T80

12277-12313

Sentence

denotes

Myeloid Characterization in COVID-19

T81

12314-12673

Sentence

denotes

Flow cytometric analyses of peripheral blood mononuclear cells (PBMCs) from symptomatic COVID-19 patients have shown a significant influx of granulocyte-macrophage colony-stimulating factor (GM-CSF)-producing, activated CD4+ T cells and CD14+HLA-DRlo inflammatory monocytes (IMs) (Giamarellos-Bourboulis et al., 2020, Zhang et al., 2020c, Zhou et al., 2020b).

T82

12674-13118

Sentence

denotes

This matches single-cell transcriptomic (scRNA-seq) data demonstrating CD14+IL-1β+ monocytic expansion (Guo et al., 2020, Wen et al., 2020), interferon-mitogen-activated protein kinase (MAPK)-driven adaptive immune responses (Huang et al., 2020c), and IL-1β-associated inflammasome signatures (Ong et al., 2020) in peripheral blood of COVID-19 patients, although systemic levels of IL-1β detected are conspicuously low (Del Valle et al., 2020).

T83

13119-13460

Sentence

denotes

Importantly, these immune signatures track with progression of clinical disease. scRNA-seq studies performed on pulmonary tissues of patients with severe COVID-19 disease have revealed an expansion of IMs and Ficolin-1+ monocyte-derived macrophages at the expense of tissue-resident reparative alveolar macrophages (AMs) (Liao et al., 2020).

T84

13461-13634

Sentence

denotes

The aforementioned study also observed signatures of IFN signaling and monocyte recruitment that likely contribute to the rapid decline in alveolar patency and promote ARDS.

T85

13635-13880

Sentence

denotes

Although most of the clinical focus has been on pulmonary damage and mononuclear phagocyte (MNP) dysfunction therein, it is increasingly clear that COVID-19 likely presents systemic challenges in other organ sites, such as the ileum and kidneys.

T86

13881-14007

Sentence

denotes

Understanding the role of non-pulmonary myeloid cells in tissue-specific pathology associated with COVID-19 will be important.

T87

14009-14076

Sentence

denotes

Prior Knowledge from SARS-CoV-1, MERS-CoV, and Murine Coronaviruses

T88

14077-14285

Sentence

denotes

While data on COVID-19 patients continues to rapidly emerge, studies of myeloid cell dysfunction in SARS-CoV-1 and MERS-CoV can provide an important roadmap to understanding COVID-19 pathogenesis (Figure 2 ).

T89

14286-14428

Sentence

denotes

SARS-CoV-1 infection in mouse models results in an aberrant AM phenotype that limits DC trafficking and T cell activation (Zhao et al., 2009).

T90

14429-14580

Sentence

denotes

Additionally, YM1+ FIZZ1+ alternative macrophages can increase airway hypersensitivity, thus exacerbating SARS-associated fibrosis (Page et al., 2012).

T91

14581-14892

Sentence

denotes

Further, as described above, murine SARS-CoV-1 studies have demonstrated that delayed IFN-I signaling and inflammatory monocytes-macrophages promote lung cytokine and chemokine levels, vascular leakage, and impaired antigen-specific T cell responses, culminating in lethal disease (Channappanavar et al., 2016).

T92

14893-15104

Sentence

denotes

The role played by prominent IFN-producing pDCs in SARS-CoV-2 control or pathogenesis warrants investigation, as they have been shown to be critical in murine CoV (MHV) control (Cervantes-Barragan et al., 2007).

T93

15105-15456

Sentence

denotes

Longitudinal studies in SARS-CoV-2 models are awaited, but initial phenotypic studies in humanized hACE2 mice have shown the characteristic alveolar interstitial pneumonia, with infiltration of lymphocytes and monocytes and accumulation of macrophages in the alveolar lumen (Bao et al., 2020a), which recapitulates patient findings (Xu et al., 2020c).

T94

15457-15820

Sentence

denotes

Lastly, non-human primate (NHP) studies and patient data on SARS-CoV-1 have also shown that virus spike-specific immunoglobulin G (IgG) responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into proinflammatory phenotypes and enhanced recruitment of inflammatory monocyte via CCL2 and IL-8 (Clay et al., 2012, Liu et al., 2019).

T95

15821-15935

Sentence

denotes

However, the extent to which the antibody response contributes to disease pathophysiology remains to be confirmed.

T96

15936-16029

Sentence

denotes

Figure 2 SARS-CoV-2 Infection Results in Myeloid Cell Activation and Changes NK Cell Function

T97

16030-16123

Sentence

denotes

Based on data from preliminary COVID-19 studies and earlier studies in related coronaviruses.

T98

16124-16352

Sentence

denotes

IL-6, IL-1β, and IFN-I/III from infected pulmonary epithelia can induce inflammatory programs in resident (alternate) macrophages while recruiting inflammatory monocytes, as well as granulocytes and lymphocytes from circulation.

T99

16353-16445

Sentence

denotes

Sustained IL-6 and TNF-ɑ by incoming monocytes can drive several hyperinflammation cascades.

T100

16446-16568

Sentence

denotes

Inflammatory monocyte-derived macrophages can amplify dysfunctional responses in various ways (listed in top-left corner).

T101

16569-16706

Sentence

denotes

The systemic CRS- and sHLH-like inflammatory response can induce neutrophilic NETosis and microthrombosis, aggravating COVID-19 severity.

T102

16707-16803

Sentence

denotes

Other myeloid cells, such as pDCs, are purported to have an IFN-dependent role in viral control.

T103

16804-16867

Sentence

denotes

Monocyte-derived CXCL9/10/11 might recruit NK cells from blood.

T104

16868-17028

Sentence

denotes

Preliminary data suggest that the antiviral function of these NK cells might be regulated through crosstalk with SARS-infected cells and inflammatory monocytes.

T105

17029-17076

Sentence

denotes

Dashed lines indicate pathways to be confirmed.

T106

17077-17339

Sentence

denotes

Arg1, arginase 1; iNOS, inducible-nitric oxide synthase; Inflamm., inflammatory; Mono., monocytes; Macs, macrophages; Eosino, eosinophils; Neutro, neutrophils; NETosis, neutrophil extracellular trap cell death; SHLH, secondary hemophagocytic lymphohistiocytosis.

T107

17341-17394

Sentence

denotes

Myeloid Cells Contribution to Pathogenic Inflammation

T108

17395-17583

Sentence

denotes

The initial mode of viral pathogen-associated signal (PAMP) recognition by innate cells has a major impact on downstream myeloid signaling and cytokine secretion (de Marcken et al., 2019).

T109

17584-17966

Sentence

denotes

While macrophages are somewhat susceptible to MERS-CoV and SARS-CoV-1 infection (Perlman and Dandekar, 2005, Zhou et al., 2014), data do not suggest that they are infected by SARS-CoV-2, although one study reported ACE2 and SARS-CoV-2 nucleocapsid protein is expressed in lymph nodes and spleen-associated CD169+ macrophages of COVID-19 patients producing IL-6 (Chen et al., 2020h).

T110

17967-18160

Sentence

denotes

Significantly elevated systemic levels of proinflammatory cytokine IL-6 have been reported in several COVID-19 patient cohorts and shown to correlate with disease severity (Mehta et al., 2020).

T111

18161-18308

Sentence

denotes

Increased IL-6 can also be associated with higher levels of IL-2, IL-7, IFN-ɣ, and GM-CSF, as seen in secondary hemophagocytic lymphohistiocytosis.

T112

18309-18589

Sentence

denotes

In response to viral infections, MNPs drive IL and IFN-I and IFN-III production resulting in inflammasome activation, induction of pathogenic Th1 and Th17 cell responses, recruitment of effector immune cells, and CRS pathology (Prokunina-Olsson et al., 2020, Tanaka et al., 2016).

T113

18590-18820

Sentence

denotes

Independently, in vitro studies have demonstrated SARS-CoV-1 infection can induce intracellular stress pathways, resulting in NLRP3-dependent inflammasome activation and macrophage pyroptosis (Chen et al., 2019, Shi et al., 2019).

T114

18821-19033

Sentence

denotes

Functional studies are required to implicate these myeloid inflammasome pathways in COVID-19 lung pathology and to assess other immunogenic pathways such as RIPK1/3-dependent necroptosis (Nailwal and Chan, 2019).

T115

19034-19198

Sentence

denotes

In conclusion, the strength and duration of myeloid ISG)signaling potentially dictate COVID-19 disease severity, but rigorous studies are warranted to confirm this.

T116

19199-19404

Sentence

denotes

Lastly, more work is needed to ascertain the mechanistic role played by lung-resident and recruited granulocytes in SARS-CoV-2 control and pathogenesis (Camp and Jonsson, 2017, Flores-Torres et al., 2019).

T117

19405-19647

Sentence

denotes

In contrast to their early protective role, neutrophil NETosis and macrophage crosstalk can drive later-stage inflammatory cascades (Barnes et al., 2020), underscoring the overall pathogenic nature of damage-sensing host responses (Figure 2).

T118

19648-19887

Sentence

denotes

Collectively, the current knowledge of CoVs and SARS-CoV-2 infection, in particular, points to an inadvertent collusion involving myeloid cells in COVID-19 pathogenesis, despite their critical role in early sensing and antiviral responses.

T119

19889-19910

Sentence

denotes

Innate Lymphoid Cells

T120

19911-20077

Sentence

denotes

Innate lymphoid cells (ILCs) are innate immune effector cells that lack the expression of rearranged antigen receptors (T cell receptor [TCR], B cell receptor [BCR]).

T121

20078-20258

Sentence

denotes

The ILC family is divided into two main groups: the cytotoxic natural killer (NK) cells and the non-cytotoxic helper ILCs, which include ILC1, ILC2, and ILC3 (Vivier et al., 2018).

T122

20259-20413

Sentence

denotes

Conventional NK cells include CD56brightCD16− NK cells and CD56dimCD16+ cells, which are specialized in cytokine production or cytotoxicity, respectively.

T123

20415-20482

Sentence

denotes

NK Cells Are Decreased in the Peripheral Blood of COVID-19 patients

T124

20483-20715

Sentence

denotes

Multiple studies have reported reduced numbers of NK cells in the peripheral blood of COVID-19 patients, which is associated with severity of the disease (Song et al., 2020, Wang et al., 2020f, Yu et al., 2020, Zheng et al., 2020b).

T125

20716-20884

Sentence

denotes

A recent scRNA-seq analysis revealed a transcriptomic signature for NK cells that was equally represented in lungs from patients and healthy donors (Liao et al., 2020).

T126

20885-21086

Sentence

denotes

The majority of lung NK cells are non-resident (Gasteiger et al., 2015, Marquardt et al., 2017), and CXCR3 has been shown to mediate NK cell infiltration upon influenza infection (Carlin et al., 2018).

T127

21087-21301

Sentence

denotes

In vitro, CXCR3 ligands (CXCL9-11) are increased in SARS-CoV-2-infected human lung tissue (Chu et al., 2020), and CXCR3-ligand-producing monocytes are expanded in the lungs of COVID-19 patients (Liao et al., 2020).

T128

21302-21447

Sentence

denotes

This suggests that the CXCR3 pathway might facilitate NK cell recruitment from the peripheral blood to the lungs in COVID-19 patients (Figure 2).

T129

21449-21498

Sentence

denotes

NK Cell Activation Pathways in Antiviral Immunity

T130

21499-21585

Sentence

denotes

NK cells express inhibitory and activating receptors that regulate their cytotoxicity.

T131

21586-21900

Sentence

denotes

They are therefore able to induce the lysis of virus-infected cells that upregulate virus-derived proteins, as well as stress-inducible ligands, which are then recognized by NK-cell-activating receptors, such as NKp46 (Cerwenka and Lanier, 2001, Draghi et al., 2007, Duev-Cohen et al., 2016, Glasner et al., 2012).

T132

21901-22097

Sentence

denotes

Future studies should investigate the expression of NK receptor ligands on SARS-CoV-2-infected cells in order to better understand the mechanisms underlying NK cell activation in COVID-19 disease.

T133

22098-22405

Sentence

denotes

Further, secretion of IgG1 and IgG3 antibodies during SARS-CoV-2 infection (Amanat et al., 2020) may induce CD56dim CD16+ NK cell activation through Fc receptor recognition of antibodies either bound to surface antigens expressed on infected cells or to extracellular virions as immune complexes (Figure 2).

T134

22406-22618

Sentence

denotes

This interaction might trigger both cytokine production by NK cells and lysis of infected cells through antibody-mediated cellular cytotoxicity (ADCC), as shown in influenza infection (Von Holle and Moody, 2019).

T135

22619-22858

Sentence

denotes

Emerging data highlight the capacity for NK-mediated ADCC in response to naturally isolated SARS-CoV-1 anti-S IgG that crossreacts with SARS-CoV-2 S glycoprotein when transfected into Chinese hamster ovary (CHO) cells (Pinto et al., 2020).

T136

22859-23023

Sentence

denotes

These findings suggest that triggering NK cell activation may not only contribute to the resolution of infection, but also contribute to the cytokine storm in ARDS.

T137

23025-23079

Sentence

denotes

Impairment of NK Cell Function in SARS-CoV-2 Infection

T138

23080-23368

Sentence

denotes

Ex vivo NK cells from peripheral blood of COVID-19 patients have reduced intracellular expression of CD107a, Ksp37, granzyme B, and granulysin, suggesting an impaired cytotoxicity, as well as an impaired production of chemokines, IFN-ɣ, and TNF-α (Wilk et al., 2020, Zheng et al., 2020b).

T139

23369-23434

Sentence

denotes

Several pathways may contribute to the dysregulation of NK cells.

T140

23435-23677

Sentence

denotes

While influenza virus infects NK cells and induces apoptosis (Mao et al., 2009), lung NK cells do not express the entry receptor for SARS-CoV-2, ACE2, and are therefore unlikely to be directly infected by SARS-CoV-2 (Travaglini et al., 2020).

T141

23678-23995

Sentence

denotes

The majority of NK cells found in human lung display a mature CD16+KIR+CD56dim phenotype and are able to induce cell cytotoxicity in response to loss of human leukocyte antigen (HLA) class I or through Fc receptor signaling, although to a lower extent than their peripheral blood counterpart (Marquardt et al., 2017).

T142

23996-24210

Sentence

denotes

Killer-immunoglobulin receptors (KIRs) are acquired during NK cell development alongside CD16 (FcRγIIIA) and are essential for NK cell licensing and subsequent capacity for cytolytic function (Sivori et al., 2019).

T143

24211-24389

Sentence

denotes

Frequencies of NK cells expressing CD16 and/or KIRs are decreased in the blood following SARS-CoV-2 and SARS-CoV-1 infection, respectively (Xia et al., 2004, Wang et al., 2020d).

T144

24390-24597

Sentence

denotes

Collectively, the data suggest either an impaired maturation of the NK compartment or migration of the mature, circulating NK cells into the lungs or other peripheral tissues of SARS-CoV-2-infected patients.

T145

24598-24712

Sentence

denotes

The immune checkpoint NKG2A is increased on NK cells and CD8 T cells from COVID-19 patients (Zheng et al., 2020b).

T146

24713-24938

Sentence

denotes

NKG2A inhibits cell cytotoxicity by binding the non-classical HLA-E molecule (Braud et al., 1998, Brooks et al., 1997), and this interaction is strongly correlated with poor control of HIV-1 infection (Ramsuran et al., 2018).

T147

24939-25091

Sentence

denotes

Genes encoding the inhibitory receptors LAG3 and TIM3 are also upregulated in NK cells from COVID-19 patients (Wilk et al., 2020, Hadjadj et al., 2020).

T148

25092-25172

Sentence

denotes

Thus, increased immune checkpoints on NK cells might contribute to viral escape.

T149

25173-25368

Sentence

denotes

Additionally, COVID-19 patients have higher plasma concentrations of IL-6 (Huang et al., 2020b), which significantly correlate with lower NK cell numbers (Wang et al., 2020d, Wang et al., 2020f).

T150

25369-25637

Sentence

denotes

In vitro stimulation by IL-6 and soluble IL-6 receptor has previously revealed impaired cytolytic functions (perforin and granzyme B production) by healthy donor NK cells, which can be restored following addition of tocilizumab (IL-6R blockade) (Cifaldi et al., 2015).

T151

25638-25895

Sentence

denotes

TNF-α is also upregulated in the plasma of COVID-19 patients (Huang et al., 2020b), and ligand-receptor interaction analysis of peripheral blood scRNA-seq data suggests that monocyte-secreted TNF-α might bind to its receptors on NK cells (Guo et al., 2020).

T152

25896-26119

Sentence

denotes

TNF-α is known to contribute to NK cell differentiation (Lee et al., 2009), which includes downregulation of NKp46 (Ivagnès et al., 2017), though no effect of TNF-α or IL-6 on NK cell-mediated ADCC has been reported so far.

T153

26120-26377

Sentence

denotes

Collectively, these data suggest that crosstalk with monocytes might impair NK cell recognition and killing of SARS-CoV-2-infected cells, and antibodies targeting IL-6 and TNF-signaling may benefit enhanced NK cell functions in COVID-19 patients (Figure 2).

T154

26379-26428

Sentence

denotes

Relevance for Helper ILCs in SARS-CoV-2 Infection

T155

26429-26518

Sentence

denotes

No studies, to date, have reported ILC1, ILC2, or ILC3 functions in SARS-CoV-2 infection.

T156

26519-26611

Sentence

denotes

All three subsets are present in healthy lung (De Grove et al., 2016, Yudanin et al., 2019).

T157

26612-26822

Sentence

denotes

ILC2s are essential for the improvement of lung function following influenza infection in mice through amphiregulin-mediated restoration of the airway epithelium and oxygen saturation (Monticelli et al., 2011).

T158

26823-26983

Sentence

denotes

However, ILC2s also produce IL-13, contributing to the recruitment of macrophages to the lung and influenza-induced airway hyperreactivity (Chang et al., 2011).

T159

26984-27154

Sentence

denotes

Indeed, ILCs are involved in the polarization of alveolar macrophages, either toward a M1-like phenotype (ILC1 and ILC3) or a M2-like phenotype (ILC2) (Kim et al., 2019).

T160

27155-27380

Sentence

denotes

Given the increased IL-13 concentrations (Huang et al., 2020b) and the dysregulation of the macrophage compartment observed in COVID-19 patients, the role played by ILCs in SARS-CoV-2 infection warrants further investigation.

T161

27382-27398

Sentence

denotes

T Cell Responses

T162

27399-27627

Sentence

denotes

T cells play a fundamental role in viral infections: CD4 T cells provide B cell help for antibody production and orchestrate the response of other immune cells, whereas CD8 T cells kill infected cells to reduce the viral burden.

T163

27628-27697

Sentence

denotes

However, dysregulated T cell responses can result in immunopathology.

T164

27698-28038

Sentence

denotes

To better understand the role of T cell responses in SARS-CoV-2 infection, the pursuit of two major questions is imperative: (1) what is the contribution of T cells to initial virus control and tissue damage in the context of COVID-19, and (2) how do memory T cells established thereafter contribute to protective immunity upon reinfection?

T165

28039-28086

Sentence

denotes

Some tentative answers are beginning to emerge.

T166

28088-28154

Sentence

denotes

Overall Reduction of CD4 and CD8 T Cell Counts in Peripheral Blood

T167

28155-28508

Sentence

denotes

Similar to earlier observations about SARS-CoV-1 infection (He et al., 2005), several current reports emphasize the occurrence of lymphopenia with drastically reduced numbers of both CD4 and CD8 T cells in moderate and severe COVID-19 cases (Figure 3 ) (Chen et al., 2020c, Nie et al., 2020b, Wang et al., 2020d, Zeng et al., 2020, Zheng et al., 2020b).

T168

28509-28872

Sentence

denotes

The extent of lymphopenia—most striking for CD8 T cells in patients admitted to the intensive care unit (ICU)—seemingly correlates with COVID-19-associated disease severity and mortality (Chen et al., 2020c, Diao et al., 2020, Liu et al., 2020b, Liu et al., 2020c, Tan et al., 2020a, Wang et al., 2020d, Wang et al., 2020f, Zeng et al., 2020, Zhou et al., 2020c).

T169

28873-29019

Sentence

denotes

Patients with mild symptoms, however, typically present with normal or slightly higher T cell counts (Liu et al., 2020a, Thevarajan et al., 2020).

T170

29020-29271

Sentence

denotes

The cause of peripheral T cell loss in moderate to severe COVID-19, though a phenomenon also observed in other viral infections, remains elusive, and direct viral infection of T cells, in contrast to MERS-CoV (Chu et al., 2016), has not been reported.

T171

29272-29330

Sentence

denotes

Figure 3 Working Model for T Cell Responses to SARS-CoV-2:

T172

29331-29391

Sentence

denotes

Changes in Peripheral Blood T Cell Frequencies and Phenotype

T173

29392-29516

Sentence

denotes

A decrease in peripheral blood T cells associated with disease severity and inflammation is now well documented in COVID-19.

T174

29517-29801

Sentence

denotes

Several studies report increased numbers of activated CD4 and CD8 T cells, which display a trend toward an exhausted phenotype in persistent COVID-19, based on continuous and upregulated expression of inhibitory markers as well as potential reduced polyfunctionality and cytotoxicity.

T175

29802-29905

Sentence

denotes

In severe disease, production of specific inflammatory cytokines by CD4 T cells has also been reported.

T176

29906-30063

Sentence

denotes

This working model needs to be confirmed and expanded on in future studies to assess virus-specific T cell responses both in peripheral blood and in tissues.

T177

30064-30226

Sentence

denotes

In addition, larger and more defined patient cohorts with longitudinal data are required to define the relationship between disease severity and T cell phenotype.

T178

30227-30393

Sentence

denotes

IL, interleukin; IFN, interferon; TNF, tumor necrosis factor; GM-CSF, granulocyte-macrophage colony-stimulating factor; GzmA/B, granzyme A/granzyme B; Prf1, perforin.

T179

30394-30534

Sentence

denotes

Several mechanisms likely contribute to the reduced number of T cells in the blood, including effects from the inflammatory cytokine milieu.

T180

30535-30885

Sentence

denotes

Indeed, lymphopenia seems to correlate with serum IL-6, IL-10, and TNF-α (Diao et al., 2020, Wan et al., 2020a), while convalescent patients were found to have restored bulk T cell frequencies paired with overall lower proinflammatory cytokine levels (Chen et al., 2020f, Diao et al., 2020, Liu et al., 2020a, Liu et al., 2020b, Zheng et al., 2020b).

T181

30886-31078

Sentence

denotes

Cytokines such as IFN-I and TNF-α may inhibit T cell recirculation in blood by promoting retention in lymphoid organs and attachment to endothelium (Kamphuis et al., 2006, Shiow et al., 2006).

T182

31079-31345

Sentence

denotes

However, in an autopsy study examining the spleens and hilar lymph nodes of six patients who succumbed to COVID-19, Chen et al. observed extensive cell death of lymphocytes and suggested potential roles for IL-6 as well as Fas-FasL interactions (Chen et al., 2020h).

T183

31346-31516

Sentence

denotes

In support of this hypothesis, the IL-6 receptor antagonist tocilizumab was found to increase the number of circulating lymphocytes (Giamarellos-Bourboulis et al., 2020).

T184

31517-31792

Sentence

denotes

T cell recruitment to sites of infection may also reduce their presence in the peripheral blood compartment. scRNA-seq analysis of bronchoalveolar lavage (BAL) fluid of COVID-19 patients revealed an increase in CD8 T cell infiltrate with clonal expansion (Liao et al., 2020).

T185

31793-31966

Sentence

denotes

Likewise, post-mortem examination of a patient who succumbed to ARDS following SARS-CoV-2 infection showed extensive lymphocyte infiltration in the lungs (Xu et al., 2020c).

T186

31967-32111

Sentence

denotes

However, another study that examined post-mortem biopsies from four COVID-19 patients only found neutrophilic infiltration (Tian et al., 2020a).

T187

32112-32248

Sentence

denotes

Further studies are therefore needed to better determine the cause and impact of the commonly observed lymphopenia in COVID-19 patients.

T188

32250-32289

Sentence

denotes

Induction of Antiviral T Cell Responses

T189

32290-32432

Sentence

denotes

Available information about SARS-CoV-1-specific T cell immunity may serve as an orientation for further understanding of SARS-CoV-2 infection.

T190

32433-32630

Sentence

denotes

Immunogenic T cell epitopes are distributed across several SARS-CoV-1 proteins (S, N, and M, as well as ORF3), although CD4 T cell responses were more restricted to the S protein (Li et al., 2008).

T191

32631-32905

Sentence

denotes

In SARS-CoV-1 survivors, the magnitude and frequency of specific CD8 memory T cells exceeded that of CD4 memory T cells, and virus-specific T cells persisted for at least 6–11 years, suggesting that T cells may confer long-term immunity (Ng et al., 2016, Tang et al., 2011).

T192

32906-33172

Sentence

denotes

Limited data from viremic SARS patients further indicated that virus-specific CD4 T cell populations might be associated with a more severe disease course, since lethal outcomes correlated with elevated Th2 cell (IL-4, IL-5, IL-10) serum cytokines (Li et al., 2008).

T193

33173-33301

Sentence

denotes

However, the quality of CD4 T cell responses needs to be further characterized to understand associations with disease severity.

T194

33302-33391

Sentence

denotes

Few studies have thus far characterized specific T cell immunity in SARS-CoV-2 infection.

T195

33392-33790

Sentence

denotes

In 12 patients recovering from mild COVID-19, robust T cell responses specific for viral N, M, and S proteins were detected by IFN-γ ELISPOT, weakly correlated with neutralizing antibody concentrations (similar to convalescent SARS-CoV-1 patients; Li et al., 2008), and subsequently contracted with only N-specific T cells detectable in about one-third of the cases post recovery (Ni et al., 2020).

T196

33791-33966

Sentence

denotes

In a second study, PBMCs from COVID-19 patients with moderate to severe ARDS were analyzed by flow cytometry approximately 2 weeks after ICU admission (Weiskopf et al., 2020).

T197

33967-34309

Sentence

denotes

Both virus-specific CD4 and CD8 T cells were detected in all patients at average frequencies of 1.4% and 1.3%, respectively, and very limited phenotyping according to CD45RA and CCR7 expression status characterized these cells predominantly as either CD4 Tcm (central memory) or CD8 Tem (effector memory) and Temra (effector memory RA) cells.

T198

34310-34772

Sentence

denotes

This study is notable for the use of large complementary peptide pools comprising 1,095 SARS-Cov-2 epitopes (overlapping 15-mers for S protein as well as computationally predicted HLA-I- and -II-restricted epitopes for all other viral proteins) as antigen-specific stimuli that revealed a preferential specificity of both CD4 and CD8 T cells for S protein epitopes, with the former population modestly increasing over ∼10–30 days after initial onset of symptoms.

T199

34773-35025

Sentence

denotes

A caveat, however, pertains to the identification of specific T cells by induced CD69 and CD137 co-expression, since upregulation of CD137 by CD4 T cells, in contrast to CD154, may preferentially capture regulatory T cells (Treg) (Bacher et al., 2016).

T200

35026-35207

Sentence

denotes

Further analyses of S protein-specific T cells by ELISA demonstrated robust induction of IFN-γ, TNF-α, and IL-2 concomitant with lower levels of IL-5, IL-13, IL-9, IL-10, and IL-22.

T201

35208-35434

Sentence

denotes

A third report focused on S-specific CD4 T cell responses in 18 patients with mild, severe, or critical COVID-19 using overlapping peptide pools and induced CD154 and CD137 co-expression as a readout for antiviral CD4 T cells.

T202

35435-35599

Sentence

denotes

Such cells were present in 83% of cases and presented with enhanced CD38, HLA-DR, and Ki-67 expression indicative of recent in vivo activation (Braun et al., 2020).

T203

35600-35734

Sentence

denotes

Of note, the authors also detected low frequencies of S-reactive CD4 T cells in 34% of SARS-CoV-2 seronegative healthy control donors.

T204

35735-36155

Sentence

denotes

However, these CD4 T cells lacked phenotypic markers of activation and were specific for C-terminal S protein epitopes that are highly similar to endemic human CoVs, suggesting that crossreactive CD4 memory T cells in some populations (e.g., children and younger patients that experience a higher incidence of hCoV infections) may be recruited into an amplified primary SARS-CoV-2-specific response (Braun et al., 2020).

T205

36156-36279

Sentence

denotes

Similarly, endemic CoV-specific CD4 T cells were previously shown to recognize SARS-CoV1 determinants (Gioia et al., 2005).

T206

36280-36400

Sentence

denotes

How previous infections with endemic CoV may affect immune responses to SARS-CoV-2 will need to be further investigated.

T207

36401-36727

Sentence

denotes

Finally, in general accordance with the above findings on the induction of SARS-CoV-2-specific T cells, using TCR sequencing (TCR-seq), Huang et al. and Liao et al. reported greater TCR clonality of peripheral blood (Huang et al., 2020c) as well as BAL T cells (Liao et al., 2020) in patients with mild versus severe COVID-19.

T208

36728-36984

Sentence

denotes

Moving forward, a comprehensive identification of immunogenic SARS-CoV-2 epitopes recognized by T cells (Campbell et al., 2020), as well as further studies on convalescent patients who recovered from mild and severe disease, will be particularly important.

T209

36986-37035

Sentence

denotes

T Cell Contribution to COVID-19 Hyperinflammation

T210

37036-37254

Sentence

denotes

While the induction of robust T cell immunity is likely essential for efficient virus control, dysregulated T cell responses may cause immunopathology and contribute to disease severity in COVID-19 patients (Figure 3).

T211

37255-37508

Sentence

denotes

This is suggested in a study by Zhou et al., which reported a significantly increased PBMC frequency of polyclonal GM-CSF+ CD4 T cells capable of prodigious ex vivo IL-6 and IFN-γ production only in critically ill COVID-19 patients (Zhou et al., 2020c).

T212

37509-37797

Sentence

denotes

Of note, GM-CSF+ CD4 T cells have been previously implicated in inflammatory autoimmune diseases, such as multiple sclerosis or juvenile rheumatoid arthritis, and high levels of circulating GM-CSF+ CD4 T cells were found to be associated with poor outcomes in sepsis (Huang et al., 2019).

T213

37798-37931

Sentence

denotes

Additionally, two studies observed reduced frequencies of Treg cells in severe COVID-19 cases (Chen et al., 2020c, Qin et al., 2020).

T214

37932-38120

Sentence

denotes

Since Treg cells have been shown to help resolve ARDS inflammation in mouse models (Walter et al., 2018), a loss of Tregs might facilitate the development of COVID-19 lung immunopathology.

T215

38121-38378

Sentence

denotes

Similarly, a reduction of γδ-T cells, a subset of T cells with apparent protective antiviral function in influenza pneumonia (Dong et al., 2018, Zheng et al., 2013), has been reported in severely sick COVID-19 patients (Guo et al., 2020, Lei et al., 2020b).

T216

38380-38432

Sentence

denotes

Phenotype and Function of T Cell Subsets in COVID-19

T217

38433-38546

Sentence

denotes

Currently, little is known about specific phenotypical and/or functional T cell changes associated with COVID-19.

T218

38547-38889

Sentence

denotes

In the majority of preprints and peer-reviewed studies, there are reports of increased presence of activated T cells (Figure 3) characterized by expression of HLA-DR, CD38, CD69, CD25, CD44, and Ki-67 (Braun et al., 2020, Ni et al., 2020, Guo et al., 2020, Liao et al., 2020, Thevarajan et al., 2020, Yang et al., 2020a, Zheng et al., 2020a).

T219

38890-39160

Sentence

denotes

Generally, independent of COVID-19 disease severity, CD8 T cells seem to be more activated than CD4 T cells (Qin et al., 2020, Thevarajan et al., 2020, Yang et al., 2020a), a finding that echoes stronger CD8 than CD4 T cell responses during SARS-CoV-1 (Li et al., 2008).

T220

39161-39336

Sentence

denotes

Furthermore, in a case study of 10 COVID-19 patients, Diao et al. showed that levels of PD-1 increased from prodromal to symptomatic stages of the disease (Diao et al., 2020).

T221

39337-39557

Sentence

denotes

PD-1 expression is commonly associated with T cell exhaustion, but it is important to emphasize that PD-1 is primarily induced by TCR signaling; it is thus also expressed by activated effector T cells (Ahn et al., 2018).

T222

39558-39783

Sentence

denotes

In addition, several studies reported higher expression of various co-stimulatory and inhibitory molecules such as OX-40 and CD137 (Zhou et al., 2020c), CTLA-4 and TIGIT (Zheng et al., 2020a), and NKG2a (Zheng et al., 2020b).

T223

39784-39953

Sentence

denotes

Reduced numbers of CD28+ CD8 T cells (Qin et al., 2020) as well as larger frequencies of PD-1+ TIM3+ CD8 T cells in ICU patients were also reported (Zhou et al., 2020c).

T224

39954-40152

Sentence

denotes

Expression of most of these markers was found to be higher in CD8 than in CD4 T cells, and levels tended to increase in severe versus non-severe cases, which may be due to differences in viral load.

T225

40153-40530

Sentence

denotes

Cellular functionality was shown to be impaired in CD4 and CD8 T cells of critically ill patients, with reduced frequencies of polyfunctional T cells (producing more than one cytokine) as well as generally lower IFN-γ and TNF-α production following restimulation with phorbol myristate acetate (PMA) and ionomycin (Chen et al., 2020c, Zheng et al., 2020a, Zheng et al., 2020b).

T226

40531-40729

Sentence

denotes

Similarly, Zheng et al. reported that CD8 T cells in severe COVID-19 appear less cytotoxic and effector-like with reduced CD107a degranulation and granzyme B (GzmB) production (Zheng et al., 2020b).

T227

40730-40873

Sentence

denotes

In contrast, a different study found that both GzmB and perforin were increased in CD8 T cells of severely sick patients (Zheng et al., 2020a).

T228

40874-41231

Sentence

denotes

In accordance with the latter observation, when compared to a moderate disease group, convalescent patients with resolved severe SARS-CoV-1 infection had significantly higher frequencies of polyfunctional T cells, with CD4 T cells producing more IFN-γ, TNF-α, and IL-2 and CD8 T cells producing more IFN-γ, TNF-α, and CD107a, respectively (Li et al., 2008).

T229

41232-41423

Sentence

denotes

However, given the vigorous dynamics of acute T cell responses and potential differences in sample timing throughout disease course, these observations are not necessarily mutually exclusive.

T230

41424-41690

Sentence

denotes

Accordingly, RNA sequencing (RNA-seq) data by Liao et al. showed that CD8 T cells in the BAL fluid of severe COVID-19 patients express cytotoxic genes such as GZMA, GZMB, and GZMK at higher levels, while KLRC1 and XCL1 are enriched in mild cases (Liao et al., 2020).

T231

41691-41936

Sentence

denotes

In summary, T cells in severe COVID-19 seem to be more activated and may exhibit a trend toward exhaustion based on continuous expression of inhibitory markers such as PD-1 and TIM-3 as well as overall reduced polyfunctionality and cytotoxicity.

T232

41937-42240

Sentence

denotes

Conversely, recovering patients were shown to have an increase in follicular helper CD4 T cells (TFH) as well as decreasing levels of inhibitory markers along with enhanced levels of effector molecules such as Gzm A, GzmB, and perforin (Thevarajan et al., 2020, Yang et al., 2020a, Zheng et al., 2020b).

T233

42241-42475

Sentence

denotes

Collectively, these studies provide a first glimpse into T cell dynamics in acute SARS-CoV-2 infection, but any conclusions have to be tempered at this stage on account of significant limitations in many of the current investigations.

T234

42477-42493

Sentence

denotes

B Cell Responses

T235

42495-42530

Sentence

denotes

Acute B Cell and Antibody Responses

T236

42531-42680

Sentence

denotes

The humoral immune response is critical for the clearance of cytopathic viruses and is a major part of the memory response that prevents reinfection.

T237

42681-42888

Sentence

denotes

SARS-CoV-2 elicits a robust B cell response, as evidenced by the rapid and near-universal detection of virus-specific IgM, IgG and IgA, and neutralizing IgG antibodies (nAbs) in the days following infection.

T238

42889-42997

Sentence

denotes

The kinetics of the antibody response to SARS-CoV-2 are now reasonably well described (Huang et al., 2020a).

T239

42998-43367

Sentence

denotes

Similar to SARS-CoV-1 infection (Hsueh et al., 2004), seroconversion occurs in most COVID-19 patients between 7 and 14 days after the onset of symptoms, and antibody titers persist in the weeks following virus clearance (Figure 4 ) (Haveri et al., 2020, Lou et al., 2020, Okba et al., 2020, Tan et al., 2020b, Wölfel et al., 2020, Wu et al., 2020b, Zhao et al., 2020a).

T240

43368-43531

Sentence

denotes

Antibodies binding the SARS-CoV-2 internal N protein and the external S glycoprotein are commonly detected (Amanat et al., 2020, Ju et al., 2020, To et al., 2020).

T241

43532-43770

Sentence

denotes

The receptor binding domain (RBD) of the S protein is highly immunogenic, and antibodies binding this domain can be potently neutralizing, blocking virus interactions with the host entry receptor, ACE2 (Ju et al., 2020, Wu et al., 2020b).

T242

43771-43875

Sentence

denotes

Anti-RBD nAbs are detected in most tested patients (Ju et al., 2020, To et al., 2020, Wu et al., 2020b).

T243

43876-44073

Sentence

denotes

Although crossreactivity to SARS-CoV-1 S and N proteins and to MERS-CoV S protein was detected in plasma from COVID-19 patients, no crossreactivity was found to the RBD from SARS-CoV-1 or MERS-CoV.

T244

44074-44177

Sentence

denotes

In addition, plasma from COVID-19 patients did not neutralize SARS-CoV-1 or MERS-CoV (Ju et al., 2020).

T245

44178-44227

Sentence

denotes

Figure 4 Antibody-Mediated Immunity in SARS-CoV-2

T246

44228-44329

Sentence

denotes

Virus-specific IgM and IgG are detectable in serum between 7 and 14 days after the onset of symptoms.

T247

44330-44398

Sentence

denotes

Viral RNA is inversely correlated with neutralizing antibody titers.

T248

44399-44547

Sentence

denotes

Higher titers have been observed in critically ill patients, but it is unknown whether antibody responses somehow contribute to pulmonary pathology.

T249

44548-44736

Sentence

denotes

The SARS-CoV-1 humoral response is relatively short lived, and memory B cells may disappear altogether, suggesting that immunity with SARS-CoV-2 may wane 1–2 years after primary infection.

T250

44737-44906

Sentence

denotes

RBD-specific CD19+IgG+ memory B cells were single-cell sorted from a cohort of eight COVID-19 donors between days 9 and 28 after the onset of symptoms (Ju et al., 2020).

T251

44907-45003

Sentence

denotes

From their antibody gene sequences, 209 SARS-CoV-2-specific monoclonal antibodies were produced.

T252

45004-45235

Sentence

denotes

The monoclonal antibodies had a diverse repertoire, relatively low or no somatic mutations, and variable binding reactivity, with dissociation constants reaching 10−8 to 10−9, similar to antibodies isolated during acute infections.

T253

45236-45406

Sentence

denotes

Two potent neutralizing SARS-CoV-2 RBD-specific monoclonal antibodies were characterized that did not crossreact with the RBD of SARS-CoV-1 or MERS-CoV (Ju et al., 2020).

T254

45407-45555

Sentence

denotes

Together, these results demonstrate that antibody mediated neutralization is virus specific and likely driven by binding of epitopes within the RBD.

T255

45557-45571

Sentence

denotes

B Cell Memory:

T256

45572-45596

Sentence

denotes

Development and Lifespan

T257

45597-45739

Sentence

denotes

The B cell response to a virus serves not only to protect from the initial challenge, but also to offer extended immunity against reinfection.

T258

45740-45905

Sentence

denotes

Following resolution of an infection, plasma cells formed during the acute and convalescent phases continue to secrete antibodies, giving rise to serological memory.

T259

45906-46014

Sentence

denotes

Memory B cells that are also formed during the primary infection constitute the second arm of B cell memory.

T260

46015-46112

Sentence

denotes

Memory B cells can quickly respond to a reinfection by generating new high-affinity plasma cells.

T261

46113-46214

Sentence

denotes

Long-term protection is achieved through the induction of long-lived plasma cells and memory B cells.

T262

46215-46310

Sentence

denotes

There is great interest in understanding the lifespan of B cell memory responses to SARS-CoV-2.

T263

46311-46464

Sentence

denotes

Protection from reinfection has direct medical and social consequences as the world works to develop vaccination strategies and resume normal activities.

T264

46465-46706

Sentence

denotes

In COVID-19 patients, evidence of near-universal seroconversion and the lack of substantial descriptions of reinfection point to a robust antibody response, which, along with the T cell memory response, would offer protection to reinfection.

T265

46707-47065

Sentence

denotes

Indeed, a case study of a single patient described induction of CD38HiCD27Hi antibody-secreting cells (ASCs), concomitant with an increase in circulating follicular T helper cells (Tfh) cells (Thevarajan et al., 2020), and a scRNA-seq study of PBMCs from critically ill and recently recovered individuals revealed a plasma cell population (Guo et al., 2020).

T266

47066-47189

Sentence

denotes

In addition, IgG memory cells specific to the RBD have been identified in the blood of COVID-19 patients (Ju et al., 2020).

T267

47190-47446

Sentence

denotes

Consistent with the development of immunity after COVID-19 infection, a recent study of SARS-CoV-2 infection in rhesus macaques found that two macaques that had resolved the primary infection were resistant to reinfection 28 days later (Bao et al., 2020b).

T268

47447-47622

Sentence

denotes

Due to the timing of this outbreak, it is not yet possible to know the nature and extent of long-term memory responses, but lessons may again be learned from other human CoVs.

T269

47623-47839

Sentence

denotes

In the case of the human CoV 229E, specific IgG and nAbs are rapidly induced but wane in some individuals around a year after infection, with some residual protection to reinfection (Callow et al., 1990, Reed, 1984).

T270

47840-48122

Sentence

denotes

The lifespan of the humoral response following SARS-CoV-1 infection is also relatively short, with the initial specific IgG and nAb response to SARS-CoV-1 diminishing 2–3 years after infection and nearly undetectable in up to 25% of individuals (Cao et al., 2007, Liu et al., 2006).

T271

48123-48379

Sentence

denotes

A long-term study following 34 SARS-CoV-1-infected healthcare workers over a 13-year period also found that virus-specific IgG declined after several years, but the authors observed detectable virus-specific IgG 12 years after infection (Guo et al., 2020).

T272

48380-48509

Sentence

denotes

In the case of MERS-CoV, antibodies were detected in six of seven volunteers tested 3 years after infection (Payne et al., 2016).

T273

48510-48702

Sentence

denotes

IgG specific to SARS-CoV-2 trimeric spike protein was detectable in serum up to 60 days after symptom onset, but IgG titers began decreasing by 8 weeks post symptom onset (Adams et al., 2020).

T274

48703-48789

Sentence

denotes

Long-term protection from reinfection may also be mediated by reactive memory B cells.

T275

48790-49033

Sentence

denotes

A study that analyzed SARS-CoV-1 S protein-specific IgG memory cells at 2, 4, 6, and 8 months post infection found that S-specific IgG memory B cells decreased progressively about 90% from 2 to 8 months after infection (Traggiai et al., 2004).

T276

49034-49199

Sentence

denotes

A further retrospective study of 23 individuals found no evidence of circulating SARS-CoV-1-specific IgG+ memory B cells 6 years after infection (Tang et al., 2011).

T277

49200-49333

Sentence

denotes

This is in contrast to the memory T cell response, which was robustly detected based on induced IFN-γ production (Tang et al., 2011).

T278

49334-49528

Sentence

denotes

Studies of common CoVs SARS-CoV-1 and MERS-CoV indicate that virus-specific antibody responses wane over time and, in the case of common CoVs, result in only partial protection from reinfection.

T279

49529-49716

Sentence

denotes

These data suggest that immunity to SARS-CoV-2 may diminish following a primary infection, and further studies will be required to determine the degree of long-term protection (Figure 4).

T280

49718-49754

Sentence

denotes

Consequences of the B Cell Response:

T281

49755-49784

Sentence

denotes

Protection versus Enhancement

T282

49785-50064

Sentence

denotes

Several studies have demonstrated that high virus-specific antibody titers to SARS-CoV-2 are correlated with greater neutralization of virus in vitro and are inversely correlated with viral load in patients (Figure 4) (Okba et al., 2020, Wölfel et al., 2020, Zhao et al., 2020a).

T283

50065-50406

Sentence

denotes

Despite these indications of a successful neutralizing response in the majority of individuals, higher titers are also associated with more severe clinical cases (Li et al., 2020b, Okba et al., 2020, Zhao et al., 2020a, Zhou et al., 2020a), suggesting that a robust antibody response alone is insufficient to avoid severe disease (Figure 4).

T284

50407-50612

Sentence

denotes

This was also observed in the previous SARS-CoV-1 epidemic, where neutralizing titers were found to be significantly higher in deceased patients compared to patients who had recovered (Zhang et al., 2006).

T285

50613-50769

Sentence

denotes

This has led to concerns that antibody responses to these viruses may contribute to pulmonary pathology via antibody-dependent enhancement (ADE) (Figure 4).

T286

50770-51028

Sentence

denotes

This phenomenon is observed when non-neutralizing virus-specific IgG facilitate entry of virus particles into Fc-receptor (FcR) expressing cells, particularly macrophages and monocytes, leading to inflammatory activation of these cells (Taylor et al., 2015).

T287

51029-51229

Sentence

denotes

A study in SARS-CoV-1-infected rhesus macaques found that anti-S IgG contributed to severe acute lung injury (ALI) and massive accumulation of monocytes and macrophages in the lung (Liu et al., 2019).

T288

51230-51398

Sentence

denotes

Furthermore, serum containing anti-S Ig from SARS-CoV-1 patients enhanced the infection of SARS-CoV-1 in human monocyte-derived macrophages in vitro (Yip et al., 2014).

T289

51399-51506

Sentence

denotes

ADE was also reported with a monoclonal antibody isolated from a patient with MERS-CoV (Wan et al., 2020c).

T290

51507-51744

Sentence

denotes

Somewhat reassuringly, there was no evidence of ADE mediated by sera from rats vaccinated with SARS-CoV-2 RBD in vitro (Quinlan et al., 2020) nor in macaques immunized with an inactivated SARS-CoV-2 vaccine candidate (Gao et al., 2020c).

T291

51745-51892

Sentence

denotes

As of now, there is no evidence that naturally developed antibodies toward SARS-CoV-2 contribute to the pathological features observed in COVID-19.

T292

51893-52019

Sentence

denotes

However, this possibility should be considered when it comes to experimental design and development of therapeutic strategies.

T293

52020-52154

Sentence

denotes

Importantly, in all of the descriptions of ADE as it relates to CoV, the FcR was necessary to trigger the antibody-mediated pathology.

T294

52155-52414

Sentence

denotes

High-dose intravenous immunoglobulin (IVIg), which may blunt ADE, has been trialed in COVID-19 patients (Cao et al., 2020b, Shao et al., 2020), but further studies are needed to determine the extent to which IVIg is safe or beneficial in SARS-CoV-2 infection.

T295

52415-52672

Sentence

denotes

Vaccine trials will need to consider the possibility of antibody-driven pathology upon antigen rechallenge; strategies using F(ab) fragments or engineered Fc monoclonal antibodies may prove particularly beneficial in this setting (Amanat and Krammer, 2020).

T296

52674-52722

Sentence

denotes

Predictors of COVID-19 Disease Risk and Severity

T297

52723-52874

Sentence

denotes

With the rapidly growing number of cases in the first few months, numerous reports on predictors of COVID-19 severity with small cohorts were released.

T298

52875-53048

Sentence

denotes

These offered clinicians and immunologists the first understanding of the clinical course and pathological processes that are associated with the novel SARS-CoV-2 infection.

T299

53049-53188

Sentence

denotes

This section highlights key findings from those studies, with a major focus on the immune factors associated with disease risk or severity.

T300

53190-53224

Sentence

denotes

Susceptibility and Risk Biomarkers

T301

53225-53356

Sentence

denotes

There are currently limited known risk factors for susceptibility to COVID-19, although this has been evaluated in several studies.

T302

53357-53530

Sentence

denotes

Zhao et al. compared the ABO blood group distribution in a cohort of 2,173 COVID-19 patients to that of healthy controls from the corresponding regions (Zhao et al., 2020b).

T303

53531-53704

Sentence

denotes

They found blood group A to be associated with a higher risk for acquiring COVID-19 when compared to non-A blood groups; blood group O had the lowest risk for the infection.

T304

53705-53925

Sentence

denotes

Another study demonstrated an identical association (Zietz and Tatonetti, 2020), and similar results have been previously described for other viruses (Lindesmith et al., 2003), including SARS-CoV-1 (Cheng et al., 2005a).

T305

53926-54213

Sentence

denotes

Several large collaborative efforts are currently underway to generate, share, and analyze genetic data to understand the links between human genetic variation and COVID-19 susceptibility and severity, the most prominent of which is the COVID-19 Host Genetics Initiative (covid19hg.org).

T306

54214-54466

Sentence

denotes

These studies are supported by previous observations on SARS-CoV-1 that followed the 2003 outbreak, which have identified significant associations between genetic variants and immune phenotypes (Chan et al., 2007, Wang et al., 2011, Zhao et al., 2011).

T307

54467-54743

Sentence

denotes

Although identifying such polymorphisms and their associated genes and pathways for SARS-CoV-2 will require large cohorts, several studies, which remain to be tested in clinical trials, have already highlighted genetic polymorphisms that may potentially impact susceptibility.

T308

54744-55028

Sentence

denotes

These studies have focused on genetic variants that may impact the expression or function of genes important in viral entry, namely ACE2 (SARS-CoV-2 receptor) and TMPRSS2 (spike protein activator) (Asselta et al., 2020, Cao et al., 2020c, Renieri et al., 2020, Stawiski et al., 2020).

T309

55029-55263

Sentence

denotes

Cao et al. identified variants that are potentially expression quantitative trait loci (eQTL) of ACE2 (i.e., they may potentially alter ACE2 gene expression) and analyzed their frequencies in different populations (Cao et al., 2020c).

T310

55264-55458

Sentence

denotes

Stawiski et al. listed variants that may be critical in ACE2 binding and thereby its function and compared the frequencies of these variants within different populations (Stawiski et al., 2020).

T311

55459-55723

Sentence

denotes

While there are several limitations to these studies, the major question is whether the utility of these biomarkers is replicable in large populations with COVID-19 clinical outcomes data and in targeted or large-scale genomic analyses that are currently underway.

T312

55724-55869

Sentence

denotes

In addition, these studies will reveal the potential associations between genetic variants and susceptibility in a gene or loci agnostic fashion.

T313

55871-55899

Sentence

denotes

Routine Bloodwork Biomarkers

T314

55900-56108

Sentence

denotes

Several routine blood and serological parameters have been suggested to stratify patients who might be at higher risk for complications to aid in allocation of healthcare resources in the pandemic (Table 1 ).

T315

56109-56247

Sentence

denotes

Serologic markers from routine bloodwork were reported by comparing patients with mild or moderate symptoms to those with severe symptoms.

T316

56248-56377

Sentence

denotes

This includes different acute phase proteins, such as SAA (serum amyloid protein) and C-reactive protein (CRP) (Ji et al., 2020).

T317

56378-56492

Sentence

denotes

Interestingly, elevations in CRP appear to be unique to COVID-19 patients when compared to other viral infections.

T318

56493-56735

Sentence

denotes

Other consistently reported markers in non-survivors are increased procalcitonin (PCT) and IL-6 levels (Huang et al., 2020d), as well as increased serum urea, creatinine, cystatin C, direct bilirubin, and cholinesterase (Xiang et al., 2020a).

T319

56736-56884

Sentence

denotes

Overall, inflammatory markers are common in severe cases of COVID-19 and appear to correlate with the severity of the symptoms and clinical outcome.

T320

56885-57066

Sentence

denotes

Moreover, the extensive damage that occurs in specific organs of severe COVID-19 patients is possibly related to differences in the expression of ACE2 (Figure 5 ) (Du et al., 2020).

T321

57067-57149

Sentence

denotes

Table 1 Routine Blood and Immunological Prognostic Biomarkers in COVID-19 Patients

T322

57150-57167

Sentence

denotes

Biomarker Purpose

T323

57168-57599

Sentence

denotes

Routine Bloodwork Lymphocyte count Predicted the disease severity and the outcomes of hospitalized patients (Tan et al., 2020a).Prognostic value was confirmed in numerous studies (Huang et al., 2020d, Liu et al., 2020b, Song et al., 2020, Wang et al., 2020f, Wynants et al., 2020, Yan et al., 2020b, Yang et al., 2020b, Zhang et al., 2020c, Zhao et al., 2020d).Decreased continuously in non-surviving patients (Wang et al., 2020b).

T324

57600-57873

Sentence

denotes

N/L Patients with N/L ≥3.13 were reported to be more likely to develop severe illness and to require ICU admission (Liu et al., 2020c).N/L on admission was a risk factor for short-term progression of patients with moderate pneumonia to severe pneumonia (Feng et al., 2020).

T325

57874-58003

Sentence

denotes

Confirmed to be of prognostic value in COVID-19 in several studies (Song et al., 2020, Wynants et al., 2020, Zhou et al., 2020d).

T326

58004-58080

Sentence

denotes

CRP Proposed as an early biomarker of disease progression (Ji et al., 2020).

T327

58081-58203

Sentence

denotes

Even in early stages, CRP levels were positively correlated with lung lesions and reflected disease severity (Wang, 2020).

T328

58204-58354

Sentence

denotes

Confirmed in numerous studies (Fu et al., 2020, Huang et al., 2020d, Wynants et al., 2020, Yan et al., 2020b, Zhao et al., 2020d, Zhou et al., 2020b).

T329

58355-58439

Sentence

denotes

Predicted the risk of acute myocardial injury (Liu et al., 2020g, Xu et al., 2020a).

T330

58440-58508

Sentence

denotes

LDH Higher in severe cases than in mild cases (Xiang et al., 2020a).

T331

58509-58645

Sentence

denotes

Widely proposed to have prognostic value in COVID-19 (Huang et al., 2020d, Wynants et al., 2020, Yan et al., 2020b, Zhao et al., 2020d).

T332

58646-58756

Sentence

denotes

D-dimer (and coagulation parameters) Predicted severity independently of other variables (Zhou et al., 2020d).

T333

58757-58864

Sentence

denotes

Elevated levels and disseminated intravascular coagulation are found in non-survivors (Wang et al., 2020b).

T334

58865-58938

Sentence

denotes

Identified patients at risk for acute cardiac injury (Liu et al., 2020g).

T335

58939-59142

Sentence

denotes

Other coagulation parameters, such as fibrin degradation product levels, longer prothrombin time, and activated partial thromboplastin time, were also associated with poor prognosis (Tang et al., 2020a).

T336

59143-59289

Sentence

denotes

SAA SAA was proposed to be used as an auxiliary index for diagnosis as it was elevated in 80% of the patients in a small cohort (Ji et al., 2020).

T337

59290-59459

Sentence

denotes

NT-proBNP (N-terminal pro B type natriuretic peptide) NT-proBNP was an independent risk factor of in-hospital death in patients with severe COVID-19 (Gao et al., 2020b).

T338

59460-59561

Sentence

denotes

Platelet count High platelet-to-lymphocyte ratio was associated with worse outcome (Qu et al., 2020).

T339

59562-59702

Sentence

denotes

Thrombocytopenia was associated with poor outcome and with incidence of myocardial injury in COVID-19 (Liu et al., 2020h, Shi et al., 2020).

T340

59703-59845

Sentence

denotes

Immunological CD4+, CD8+, and NK cell counts Lower CD4+, CD8+, and NK cells in PBMCs correlated with severity of COVID-19 (Nie et al., 2020b).

T341

59846-59917

Sentence

denotes

Validated by several studies (Wang et al., 2020f, Zheng et al., 2020b).

T342

59918-60109

Sentence

denotes

PD-1 and Tim-3 expression on T cells Increasing PD-1 and Tim-3 expression on T cells could be detected as patients progressed from prodromal to overtly symptomatic stages (Diao et al., 2020).

T343

60110-60261

Sentence

denotes

Expression was higher in infected patients versus healthy controls and in ICU versus non-ICU patients in both CD4 and CD8 T cells (Zhou et al., 2020b).

T344

60262-60586

Sentence

denotes

phenotypic changes in peripheral blood monocytes The presence of a distinct population of monocytes with high forward scatter (CD11b+, CD14+, CD16+, CD68+, CD80+, CD163+, and CD206+, which secrete IL-6, IL-10, and TNF-α) was identified in patients requiring prolonged hospitalization and ICU admission (Zhang et al., 2020c).

T345

60587-60664

Sentence

denotes

CD14+CD16+IL-6+ monocytes are increased in ICU patients (Zhou et al., 2020b).

T346

60665-60881

Sentence

denotes

IP-10, MCP-3, and IL-1ra IP-10, MCP-3, and IL-1ra were, among 48 examined cytokines, the only ones that closely associated with disease severity and outcome of COVID-19 in a study by Yang et al. (Yang et al., 2020b).

T347

60882-61075

Sentence

denotes

IL-6 Associated with disease severity (hospitalization and ICU admission) and poor prognosis (Chen et al., 2020g, Huang et al., 2020b, Liu et al., 2020b, Liu et al., 2020f, Wang et al., 2020b).

T348

61076-61169

Sentence

denotes

Increased levels were associated with higher risk of respiratory failure (Yao et al., 2020b).

T349

61170-61310

Sentence

denotes

IL-8 Positively correlated with disease severity (Chen et al., 2020e, Gong et al., 2020), with severe cases showing the highest IL-8 levels.

T350

61311-61528

Sentence

denotes

IL-10 Increased in severe or critical patients as compared to mild patients (Gong et al., 2020, Zhou et al., 2020d) without a statistically significant difference between severe and critical cases (Gong et al., 2020).

T351

61529-61722

Sentence

denotes

IL-2R Associated with disease severity in a study that, among other cytokines, also associated ferroprotein levels, PCT levels, and eosinophil counts with COVID-19 severity (Gong et al., 2020).

T352

61723-61902

Sentence

denotes

IL-1β CD14+IL-1β+ monocytes are abundant in early-recovery patients as shown in a single-cell RNA-seq analysis and thought to be associated with cytokine storm (Wen et al., 2020).

T353

61903-62037

Sentence

denotes

IL-1β did not correlate with disease severity in a cross-sectional study with mild, severe, and critical patients (Gong et al., 2020).

T354

62038-62182

Sentence

denotes

IL-4 IL-4 was associated with impaired lung lesions (Fu et al., 2020), but some reports point to a potential mediator effect (Wen et al., 2020).

T355

62183-62414

Sentence

denotes

IL-18 In modeling immune cell interaction between DCs and B cells in late recovery COVID-19 patients, IL-18 was found to be important in B cell production of antibodies, which suggests its importance in recovery (Wen et al., 2020).

T356

62415-62487

Sentence

denotes

GM-CSF GM-CSF+IFN-γ+ T cells are higher in ICU than in non-ICU patients.

T357

62488-62601

Sentence

denotes

CD14+CD16+GM-CSF+ monocytes are higher in COVID-19 patients as compared to healthy controls (Zhou et al., 2020b).

T358

62602-62702

Sentence

denotes

IL-2 and IFN-γ IL-2 and IFN-γ levels were shown to be increased in severe cases (Liu et al., 2020b).

T359

62703-62848

Sentence

denotes

anti-SARS-CoV-2 antibody levels Prolonged SARS-CoV-2 IgM positivity could be utilized as a predictive factor for poor recovery (Fu et al., 2020).

T360

62849-62961

Sentence

denotes

Higher anti-SARS-CoV-2 IgG levels and higher N/L were more commonly found in severe cases (Zhang et al., 2020a).

T361

62962-63061

Sentence

denotes

Figure 5 ACE2 Expression in Organs and Systems Most Frequently Implicated in COVID-19 Complications

T362

63062-63144

Sentence

denotes

The gastrointestinal tract, kidneys, and testis have the highest ACE2 expressions.

T363

63145-63503

Sentence

denotes

In some organs, different cell types have remarkably distinct expressions; e.g., in the lungs, alveolar epithelial cells have higher ACE2 expression levels than bronchial epithelial cells; in the liver, ACE2 is not expressed in hepatocytes, Kupffer cells, or endothelial cells but is detected in cholangiocytes, which can explain liver injury to some extent.

T364

63504-63605

Sentence

denotes

Furthermore, ACE2 expression is enriched on enterocytes of the small intestine compared to the colon.

T365

63606-63823

Sentence

denotes

ACE2, angiotensin-converting enzyme 2; BNP, B-type natriuretic peptide; CRP, C-reactive protein; IL, interleukin; N/L, neutrophil-to-lymphocyte ratio; PT, prothrombin time; aPTT, activated partial thromboplastin time.

T366

63824-64000

Sentence

denotes

Lymphopenia is the most frequently described prognostic marker in COVID-19 (Table 1), and it appears to predict morbidity and mortality even at early stages (Fei et al., 2020).

T367

64001-64256

Sentence

denotes

Tan et al. proposed a prognostic model based on lymphocyte counts at two time points: patients with less than 20% lymphocytes at days 10–12 from the onset of symptoms and less than 5% at days 17–19 had the worst outcomes in this study (Tan et al., 2020a).

T368

64257-64509

Sentence

denotes

Wynants et al. compared predictors of disease severity across seven studies (>1,330 patients), highlighting CRP, neutrophil-to-lymphocyte ratio (N/L), and lactate dehydrogenase (LDH) as the most significant predictive biomarkers (Wynants et al., 2020).

T369

64510-64683

Sentence

denotes

Furthermore, a meta-analysis of 30 COVID-19 studies with a total of 53,000 patients also attempted to identify early-stage patients with poor prognosis (Zhao et al., 2020d).

T370

64684-64887

Sentence

denotes

The most consistent findings across the different studies were elevated levels of CRP, LDH, and D-dimer, as well as decreased blood platelet and lymphocyte counts (Yan et al., 2020b, Zhou et al., 2020d).

T371

64888-65286

Sentence

denotes

Systemic and pulmonary thrombi have been reported with activation of the extrinsic coagulation cascade, involving dysfunctional endothelium and monocytic infiltration (Poor et al., 2020, Varga et al., 2020); thrombocytopenia and elevated D-dimer levels may be indicative of these coagulopathies in COVID-19 patients with important therapeutic implications (Fogarty et al., 2020, Poor et al., 2020).

T372

65288-65336

Sentence

denotes

Immunological Biomarkers in the Peripheral Blood

T373

65337-65489

Sentence

denotes

Immunological biomarkers are particularly important, as immunopathology has been suggested as a primary driver of morbidity and mortality with COVID-19.

T374

65490-65595

Sentence

denotes

Several cytokines and other immunologic parameters have been correlated with COVID-19 severity (Table 1).

T375

65596-65866

Sentence

denotes

Most notably, elevated IL-6 levels were detected in hospitalized patients, especially critically ill patients, in several studies and are associated with ICU admission, respiratory failure, and poor prognosis (Chen et al., 2020g, Huang et al., 2020b, Liu et al., 2020f).

T376

65867-66117

Sentence

denotes

Increased IL-2R, IL-8, IL-10, and GM-CSF have been associated with disease severity as well, but studies are limited, and further studies with larger cohorts of patients are needed to indicate predictive power (Gong et al., 2020, Zhou et al., 2020b).

T377

66118-66237

Sentence

denotes

Conflicting results regarding IL-1β and IL-4 have been reported (Fu et al., 2020, Gong et al., 2020, Wen et al., 2020).

T378

66238-66529

Sentence

denotes

Although elevated cytokine concentrations have been widely described in COVID-19 patients, the vast majority (including IL-6, IL-10, IL-18, CTACK, and IFN-γ) do not seem to have prognostic value, because they do not always differentiate moderate cases from severe cases (Yang et al., 2020b).

T379

66530-66593

Sentence

denotes

This stratification was possible with IP-10, MCP-3, and IL-1ra.

T380

66594-66921

Sentence

denotes

While there are reports that levels of IL-6 at first assessment might predict respiratory failure (Herold et al., 2020), other publications with longitudinal analyses demonstrated that IL-6 increases fairly late during the disease’s course, consequently compromising its prognostic value at earlier stages (Zhou et al., 2020a).

T381

66922-67219

Sentence

denotes

Liu et al. developed a web-based tool using k-means clustering to predict prognosis in terms of death or hospital discharge of COVID-19 patients using age, comorbidities (binary), and baseline log helper T cell count (TH), log suppressor T cell count (TS), and log TH/TS ratio (Liu et al., 2020e).

T382

67220-67428

Sentence

denotes

Total T cell, helper T cell, and suppressor T cell counts were significantly lower and the TH/TS ratio was significantly higher in patients who died from infection as compared to patients who were discharged.

T383

67429-67679

Sentence

denotes

Importantly, most serological and immunological changes observed in severe cases are associated with disease severity but cannot necessarily serve as predictive factors, as they may not have utility in early identification of patients at higher risk.

T384

67680-67888

Sentence

denotes

Discovery of truly predictive biomarkers and potential drivers of hyperinflammatory processes requires comprehensive profiling of asymptomatic and mild cases and longitudinal studies that are limited to date.

T385

67889-67998

Sentence

denotes

Confounding variables including age, gender, and comorbidities may dramatically affect associations observed.

T386

67999-68274

Sentence

denotes

In addition, direct correlation with patient viral load will be important to provide a greater understanding of underlying causes of morbidity and mortality in COVID-19 and the contribution of viral infectivity, hyperinflammation, and host tolerance (Medzhitov et al., 2012).

T387

68275-68482

Sentence

denotes

In summary, lymphopenia, increases in proinflammatory markers and cytokines, and potential blood hypercoagulability characterize severe COVID-19 cases with features reminiscent of cytokine release syndromes.

T388

68483-68587

Sentence

denotes

This correlates with a diverse clinical spectrum ranging from asymptomatic to severe and critical cases.

T389

68588-68712

Sentence

denotes

During the incubation period and early phase of the disease, leukocyte and lymphocyte counts are normal or slightly reduced.

T390

68713-68876

Sentence

denotes

After SARS-CoV-2 binds to ACE2 overexpressing organs, such as the gastrointestinal tracts and kidneys, increases in non-specific inflammation markers are observed.

T391

68877-69111

Sentence

denotes

In more severe cases, a marked systemic release of inflammatory mediators and cytokines occurs, with corresponding worsening of lymphopenia and potential atrophy of lymphoid organs, impairing lymphocyte turnover (Terpos et al., 2020).

T392

69113-69123

Sentence

denotes

Antivirals

T393

69124-69238

Sentence

denotes

Antivirals are a class of small molecules that function as inhibitors of one or more stages of a virus life cycle.

T394

69239-69378

Sentence

denotes

Because of similarities between different virus replication mechanisms, some antivirals can be repurposed against various viral infections.

T395

69379-69554

Sentence

denotes

Currently, most of the available antiviral drugs tested against SARS-CoV-2 are small molecules previously developed against SARS-CoV-1, MERS-CoV, or other RNA and DNA viruses.

T396

69556-69581

Sentence

denotes

Broad-Spectrum Antivirals

T397

69582-69728

Sentence

denotes

A number of small molecules with known antiviral activity against other human RNA viruses are being evaluated for efficacy in treating SARS-CoV-2.

T398

69729-69920

Sentence

denotes

The ribonucleoside analog β-D-N4-hydroxycytidine (NHC) reduced viral titers and lung injury in mice infected with SARS-CoV-2 via introduction of mutations in viral RNA (Sheahan et al., 2017).

T399

69921-70147

Sentence

denotes

Further, an inhibitor of host DHODH, a rate-limiting enzyme in pyrimidine synthesis, was able to inhibit SARS-CoV-2 growth in vitro with greater efficacy than remdesivir or chloroquine (Wang et al., 2020e, Xiong et al., 2020).

T400

70148-70369

Sentence

denotes

Merimepodib, a non-competitive inhibitor of the enzyme inosine-5′-monophosphate dehydrogenase (IMPDH), involved in host guanosine biosynthesis, is able to suppress SARS-CoV-2 replication in vitro (Bukreyeva et al., 2020).

T401

70370-70667

Sentence

denotes

Finally, N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride (HTCC), which was previously shown to efficiently reduce infection by the less-pathogenic human CoV HCoV-NL63, was also found to inhibit MERS-CoV and pseudotyped SARS-CoV-2 in human airway epithelial cells (Milewska et al., 2020).

T402

70669-70688

Sentence

denotes

Protease Inhibitors

T403

70689-70833

Sentence

denotes

Much of the antiviral computational and experimental data currently available for SARS-CoV-2 focus on targeting the 3CL or Main protease (Mpro).

T404

70834-70993

Sentence

denotes

Two prominent drug candidates targeting the SARS-CoV-2 Mpro were designed and synthesized by analyzing the substrate binding pocket of Mpro (Dai et al., 2020).

T405

70994-71102

Sentence

denotes

The X-ray crystal structures of the novel inhibitors in complex with SARS-CoV-2 Mpro were resolved at 1.5 Å.

T406

71103-71227

Sentence

denotes

Both compounds showed good pharmacokinetic activity in vitro, and one exhibited limited toxicity in vivo (Dai et al., 2020).

T407

71228-71317

Sentence

denotes

Multiple studies also aimed to repurpose protease inhibitors to reduce SARS-CoV-2 titers.

T408

71318-71640

Sentence

denotes

Nine existing HIV protease inhibitors (nelfinavir, lopinavir, ritonavir, saquinavir, atazanavir, tipranavir, amprenavir, darunavir, and indinavir) were evaluated for their antiviral activity in Vero cells infected with SARS-CoV-2 (Yamamoto et al., 2020), and nelfinavir was the most potent at inhibiting viral replication.

T409

71642-71657

Sentence

denotes

RdRp Inhibitors

T410

71658-71846

Sentence

denotes

The CoV RNA-dependent RNA polymerase (RdRp) catalyzes the synthesis of viral RNA (Gao et al., 2020a), making it essential for viral replication and a prime target for antiviral inhibitors.

T411

71847-72070

Sentence

denotes

Remdesivir, an adenosine triphosphate analog, inhibits RdRp by binding to RNA strands and preventing additional nucleotides from being added, thereby terminating viral RNA transcription (Figure 6 A) (Agostini et al., 2018).

T412

72071-72228

Sentence

denotes

Remdesivir has been previously shown to be effective against MERS-CoV and SARS-CoV-1 infections in animal models (Sheahan et al., 2017, de Wit et al., 2020).

T413

72229-72374

Sentence

denotes

Similarly, a study investigated the efficacy of remdesivir treatments on 12 rhesus macaques with SARS-CoV-2 infections (Williamson et al., 2020).

T414

72375-72505

Sentence

denotes

Macaques treated with remdesivir showed a reduction in lung viral loads and pneumonia symptoms but no reduction in virus shedding.

T415

72506-72636

Sentence

denotes

This study does provide evidence that if administered early enough, remdesivir may be effective at treating SARS-CoV-2 infections.

T416

72637-72741

Sentence

denotes

Figure 6 Available Therapeutic Options to Manage COVID-19 Immunopathology and to Deter Viral Propagation

T417

72742-72956

Sentence

denotes

(A) Rdrp inhibitors (remdesivir, favipiravir), protease inhibitors (lopinavir/ritonavir), and antifusion inhibitors (arbidol) are currently being investigated in their efficacy in controlling SARS-CoV-2 infections.

T418

72957-73064

Sentence

denotes

(B) CQ and HCQ increase the pH within lysosomes, impairing viral transit through the endolysosomal pathway.

T419

73065-73213

Sentence

denotes

Reduced proteolytic function within lysosomes augments antigen processing for presentation on MHC complexes and increases CTLA4 expression on Tregs.

T420

73214-73349

Sentence

denotes

(C) Antagonism of IL-6 signaling pathway and of other cytokine-/chemokine-associated targets has been proposed to control COVID-19 CRS.

T421

73350-73470

Sentence

denotes

These include secreted factors like GM-CSF that contribute to the recruitment of inflammatory monocytes and macrophages.

T422

73471-73687

Sentence

denotes

(D) Several potential sources of SARS-CoV-2 neutralizing antibodies are currently under investigation, including monoclonal antibodies, polyclonal antibodies, and convalescent plasma from recovered COVID-19 patients.

T423

73688-73823

Sentence

denotes

GM-CSF, granulocyte-macrophage colony-stimulating factor; CQ, chloroquine; HCQ, hydroxychloroquine; RdRp, RNA-dependent RNA polymerase.

T424

73825-73850

Sentence

denotes

Antiviral Clinical Trials

T425

73851-73943

Sentence

denotes

A large number of clinical trials using experimental antiviral drugs are currently underway.

T426

73944-74305

Sentence

denotes

A small proportion of them are aimed at repurposing existing antivirals, including arbidol (umifenovir), a broad-spectrum antiviral that blocks viral fusion; lopinavir/ritonavir (LPV/r), a combination of anti-HIV protease inhibitors; favipiravir, an RdRp inhibitor used to treat severe influenza infections (Hayden and Shindo, 2019); and remdesivir (Figure 6A).

T427

74306-74471

Sentence

denotes

Chen et al. conducted a multicenter, randomized priority trial on 240 patients with confirmed COVID-19 infection to test favipiravir or arbidol (Chen et al., 2020b).

T428

74472-74538

Sentence

denotes

Favipiravir was suggested to significantly improve symptom relief.

T429

74539-74721

Sentence

denotes

However, the interpretation of this study is limited by a short clinical recovery window of 7 days, only 100 of 236 patients with confirmed COVID-19, and the lack of a control group.

T430

74722-74865

Sentence

denotes

LPV/r has previously shown efficacy in treating SARS-Cov-1 (Chu et al., 2004), prompting an early SARS-Cov-2 clinical trial (Li et al., 2020c).

T431

74866-75049

Sentence

denotes

44 patients were enrolled in a trial investigating the efficacy and safety of LPV/r (n = 21 patients), arbidol (n = 16), or control (n = 7) as treatment for mild to moderate COVID-19.

T432

75050-75253

Sentence

denotes

At day 14 of treatment, 76.2%, 62.4%, and 71.4% of patients had a positive to negative conversion in the LPV/r, arbidol, and control groups, respectively, with no statistical significance between groups.

T433

75254-75398

Sentence

denotes

A randomized controlled trial (RCT) with 200 severe COVID-19 patients did not observe a significant benefit of LPV/r either (Cao et al., 2020a).

T434

75399-75618

Sentence

denotes

However, a study that looked at the impact of earlier administration of LPV/r treatment showed that when treatment of LPV/r was started within 10 days of symptom onset, a shorter duration of virus shedding was observed.

T435

75619-75708

Sentence

denotes

Thus, timing of LPV/r administration may be critical to its efficacy (Yan et al., 2020a).

T436

75709-75915

Sentence

denotes

In a multicenter clinical study assessing the compassionate use of remdesivir in severe COVID-19 patients, 53 patients across several countries were treated with remdesivir for 10 days (Grein et al., 2020).

T437

75916-76047

Sentence

denotes

68% of the 53 patients who received remdesivir showed clinical improvement assessed through improved oxygen support or extubations.

T438

76048-76172

Sentence

denotes

Without a proper control group, limited conclusions can be drawn with regards to the efficacy of remdesivir from this study.

T439

76173-76325

Sentence

denotes

The measured 68% clinical improvement may be in line with average clinical improvement across patients treated with standard of care (Li et al., 2020c).

T440

76326-76514

Sentence

denotes

A small RCT in China with 237 severe COVID-19 patients randomized 2:1 to remdesivir versus placebo demonstrated no significant benefit in time to clinical improvement (Wang et al., 2020g).

T441

76515-76746

Sentence

denotes

Almost simultaneously, preliminary results from a larger National Institute of Allergy and Infectious Diseases (NIAID) RCT with more than 1,000 patients were announced with remdesevir to be associated with quicker time to recovery:

T442

76747-76793

Sentence

denotes

11 days compared with 15 days (Ledford, 2020).

T443

76794-76930

Sentence

denotes

A non-significant benefit in mortality was also noted, and the trial was stopped early to allow access to remdesivir in the placebo arm.

T444

76931-77132

Sentence

denotes

Complete safety data and full publication are awaited, but this study offers encouraging results and has resulted in an FDA emergency use authorization for remdesivir in hospitalized COVID-19 patients.

T445

77134-77185

Sentence

denotes

Therapeutic Immunomodulation for COVID-19 Treatment

T446

77187-77199

Sentence

denotes

Chloroquine:

T447

77200-77240

Sentence

denotes

Modes of Action and Immunological Impact

T448

77241-77361

Sentence

denotes

Chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) have gained traction as possible therapeutics for COVID-19.

T449

77362-77466

Sentence

denotes

Both drugs are used as antimalarial agents and as immunomodulatory therapies for rheumatologic diseases.

T450

77467-77654

Sentence

denotes

However, the application of CQ and HCQ to COVID-19 stems from their past use as antivirals (Savarino et al., 2003), including for SARS-CoV-1 (Keyaerts et al., 2004, Vincent et al., 2005).

T451

77655-77756

Sentence

denotes

CQ and HCQ interfere with lysosomal activity and have been reported to have immunomodulatory effects.

T452

77757-78030

Sentence

denotes

CQ augments antigen processing for MHC class I and II presentation, directly inhibits endosomal TLR7 and TLR9, and enhances the activity of regulatory T cells (Garulli et al., 2008, Lo et al., 2015, Schrezenmeier and Dörner, 2020, Thomé et al., 2013a, Thomé et al., 2013b).

T453

78031-78259

Sentence

denotes

Early studies involving in vitro infection of host cells with SARS-CoV-2 demonstrated that both CQ and HCQ significantly impact endosomal maturation, resulting in increased sequestration of virion particles within endolysosomes.

T454

78260-78422

Sentence

denotes

However, there has been conflicting evidence whether CQ is more potent than HCQ in reducing viral load (Liu et al., 2020d, Wang et al., 2020b, Yao et al., 2020a).

T455

78423-78665

Sentence

denotes

Notably, one group reported that treatment of infected cells with HCQ before and during infection significantly reduced viral load, suggesting that combined prophylactic and therapeutic HCQ use yields maximum efficacy (Clementi et al., 2020).

T456

78666-79021

Sentence

denotes

To better understand host immune responses to treatment, one group compared bulk transcriptomic changes in primary PBMCs treated with HCQ for 24 h to PBMCs from confirmed SARS-CoV-2 positive patients and controls, followed by a comparison of HCQ-treated primary macrophages to BAL and postmortem lung biopsies from COVID-19 patients (Corley et al., 2020).

T457

79022-79158

Sentence

denotes

Across all comparisons, there was minimal overlap between host differential gene expression and genes altered by in vitro HCQ treatment.

T458

79159-79257

Sentence

denotes

Thus, the potential mechanistic action of HCQ in the context of SARS-CoV-2 remains poorly defined.

T459

79259-79304

Sentence

denotes

Evaluation of HCQ Efficacy in Clinical Trials

T460

79305-79526

Sentence

denotes

Despite the apparent widespread use of HCQ and CQ to treat COVID-19 (Figure 6B), few controlled clinical trials have been performed so far and thus the potential benefits of these drugs for COVID-19 remains controversial.

T461

79527-79650

Sentence

denotes

One of the earliest trials (2020-000890-25) was a single-arm, open-label trial of 600 mg daily HCQ in 20 COVID-19 patients.

T462

79651-79790

Sentence

denotes

They reported that HCQ alone, or in combination with the antibiotic azithromycin (AZ), reduced viral load by day 6 (Gautret et al., 2020a).

T463

79791-79981

Sentence

denotes

A follow-up trial in 80 patients treated with HCQ and AZ reported that 93% of patients had a negative PCR result on day 8 of treatment, and 81.3% were discharged within 10 days of treatment.

T464

79982-80076

Sentence

denotes

However, it is important to note that both trials had no control arms (Gautret et al., 2020b).

T465

80077-80262

Sentence

denotes

Rigorous statistical analyses by others that accounted for the patients excluded from the original analysis found limited evidence for HCQ monotherapy (Hulme et al., 2020, Lover, 2020).

T466

80263-80381

Sentence

denotes

A double-blind RCT assessed HCQ monotherapy in the treatment of mild COVID-19 (ChiCTR2000029559) (Chen et al., 2020i).

T467

80382-80476

Sentence

denotes

A total of 62 patients were enrolled; the treatment arm received 400 mg HCQ daily over 5 days.

T468

80477-80663

Sentence

denotes

By day 6, patients who received HCQ had clinical resolution on average 1 day earlier than controls; no patients progressed to severe disease compared to four patients in the control arm.

T469

80664-81033

Sentence

denotes

In a smaller RCT that treated 30 patients with mild COVID-19 (NCT04261517) with 400 mg HCQ for 7 days, there were no significant differences in the number of patients with negative PCR results on day 7 (all but one positive), median duration of hospitalization, time to fever resolution, or progression of disease on chest computed tomography (CT) (Chen et al., 2020d).

T470

81034-81187

Sentence

denotes

The largest RCT to date enrolled 150 patients with mild COVID-19 across 16 centers in an open-label trial of HCQ and standard of care (ChiCTR2000029868).

T471

81188-81611

Sentence

denotes

There were no significant differences between groups in conversion to negative SARS-CoV-2 RT-PCR result on day 28 or rate of symptom resolution; there were significantly more adverse events in the HCQ arm, though largely non-serious; they reported some evidence for faster normalization of C-reactive protein in the patients who received HCQ plus standard of care, but this finding was not significant (Tang et al., 2020b).

T472

81612-81786

Sentence

denotes

A meta-analysis including most of the studies described here found no clinical benefits to patients receiving standard of care plus an HCQ regimen (Shamshirian et al., 2020).

T473

81787-81845

Sentence

denotes

Two studies have assessed HCQ efficacy in severe COVID-19.

T474

81846-82095

Sentence

denotes

In a prospective study of 11 patients who had received 600 mg HCQ over 10 days with AZ on days 1–5, there were several patients with worsening clinical status and one death; 8 of 10 patients had a positive PCR result on day 10 (Molina et al., 2020).

T475

82096-82319

Sentence

denotes

An ongoing double-blind RCT of patients with severe COVID-19 (NCT04323527) randomized 81 patients into high-dose HCQ (600 mg 2× per day for 10 days) or low-dose (450 mg/day for 5 days) treatment groups (Borba et al., 2020).

T476

82320-82406

Sentence

denotes

Recruitment into the high-dose arm was halted prematurely due to poor safety outcomes.

T477

82407-82520

Sentence

denotes

There was no significant difference in negative PCR results on day 4 or need for mechanical ventilation on day 6.

T478

82521-82715

Sentence

denotes

Taken together, the clinical trials performed thus far to evaluate the efficacy of HCQ ± AZ for COVID-19 have not demonstrated clear evidence of clinical benefit in patients with severe disease.

T479

82716-82809

Sentence

denotes

A search of ClinicalTrials.gov on April 27, 2020 found 140 clinical trials investigating HCQ.

T480

82810-82950

Sentence

denotes

This number is rapidly growing, indicating the heightened interest in this therapeutic and pressing need for evidence-based recommendations.

T481

82952-82988

Sentence

denotes

Corticosteroids for COVID-19 Therapy

T482

82989-83108

Sentence

denotes

Because of their anti-inflammatory activity, corticosteroids (CSs) are an adjuvant therapy for ARDS and cytokine storm.

T483

83109-83286

Sentence

denotes

However, the broad immunosuppression mediated by CS does raise the possibility that treatment could interfere with the development of a proper immune response against the virus.

T484

83287-83459

Sentence

denotes

A meta-analysis of 5,270 patients with MERS-CoV, SARS-CoV-1, or SARS-CoV-2 infection found that CS treatment was associated with higher mortality rate (Yang et al., 2020c).

T485

83460-83677

Sentence

denotes

A more recent meta-analysis of only SARS-CoV-2 infection assessed 2,636 patients and found no mortality difference associated with CS treatment, including in a subset of patients with ARDS (Gangopadhyay et al., 2020).

T486

83678-83825

Sentence

denotes

Other studies have reported associations with delayed viral clearance and increased complications in SARS and MERS patients (Sanders et al., 2020).

T487

83826-83990

Sentence

denotes

In fact, the interim guidelines updated by the WHO on March 13, 2020 advise against giving systemic corticosteroids for COVID-19 (World Health Organization, 2020a).

T488

83991-84035

Sentence

denotes

Yet, new data from COVID-19 are conflicting.

T489

84036-84254

Sentence

denotes

One group reported no significant difference in time to viral clearance between patients who received methylprednisolone orally (mild disease) or intravenously (i.v.) (severe) and those who did not (Fang et al., 2020).

T490

84255-84516

Sentence

denotes

Retrospective studies from groups in China report that patients who were transferred to the ICU were less likely to have received CSs (Wang et al., 2020b) and that patients with ARDS who received methylprednisolone had reduced mortality risk (Wu et al., 2020a).

T491

84517-84761

Sentence

denotes

In contrast, another retrospective analysis found that patients who received CSs were more likely to have either been admitted to the ICU or perished, although the CS-treated group also had significantly more comorbidities (Wang et al., 2020c).

T492

84762-84954

Sentence

denotes

A smaller observational study of 31 patients found no association between corticosteroid treatment and time to viral clearance, length of hospital stay, or symptom duration (Zha et al., 2020).

T493

84955-85198

Sentence

denotes

A larger study of adjuvant CSs in 244 patients with critical COVID-19 found no association with 28-day mortality; subgroup analysis of patients with ARDS found no association between treatment with CSs and clinical outcomes (Lu et al., 2020b).

T494

85199-85296

Sentence

denotes

They also found that increased dosage was significantly associated with increased mortality risk.

T495

85297-85552

Sentence

denotes

A retrospective review of 46 patients, of whom 26 received i.v. methylprednisolone, found that early, low-dose administration significantly improved SpO2 and chest CT, time to fever resolution, and time on supplemental oxygen therapy (Wang et al., 2020h).

T496

85553-85740

Sentence

denotes

Others have published perspectives in support of early (Lee et al., 2020) and short-term, low-dose administration (Shang et al., 2020) based on anecdotal evidence but not clinical trials.

T497

85741-85887

Sentence

denotes

Most of the current data on CS use in COVID-19 are from observational studies and support either modest clinical benefit or no meaningful effects.

T498

85888-86087

Sentence

denotes

Larger RCTs are necessary to understand the risks and benefits of CSs for these patients; there are 22 trials evaluating various corticosteroids registered on ClinicalTrials.gov as of April 27, 2020.

T499

86089-86126

Sentence

denotes

Cytokine-Directed Therapy in COVID-19

T500

86128-86169

Sentence

denotes

Recombinant IFN as an Antiviral Treatment

T501

86170-86289

Sentence

denotes

One of the first defenses of the human body against RNA viruses like SARS-CoV-2 is the release of types I and III IFNs.

T502

86290-86520

Sentence

denotes

It is important to note that type I IFN (IFNα/β) receptors are ubiquitously expressed, so IFNα/β signaling can result in not only antiviral effects, but also the activation of immune cells that potentially exacerbate pathogenesis.

T503

86521-86652

Sentence

denotes

In contrast, type III IFN (also known as IFNλ) signals mainly in epithelial cells, as well as in a restricted pool of immune cells.

T504

86653-86866

Sentence

denotes

Because type III IFNs have immunomodulatory functions, subsequent signaling could induce a potent antiviral effect without enhancing pathogenic inflammation (Andreakos et al., 2017, Prokunina-Olsson et al., 2020).

T505

86867-87011

Sentence

denotes

Recently, there has been a growing interest in the potential therapeutic impact of modulating the IFN response to disable COVID-19 pathogenesis.

T506

87012-87114

Sentence

denotes

Before the current pandemic, groups have studied the role of IFNs in other betacoronavirus infections.

T507

87115-87268

Sentence

denotes

One study of 40 patients with SARS-CoV-1 infection described unresolved elevated type I IFNs and ISGs in those with poor outcomes (Cameron et al., 2007).

T508

87269-87548

Sentence

denotes

Others report that exogenous type I IFN does not improve outcomes when given with ribavirin in patients with MERS-CoV infection (Arabi et al., 2020), suggesting that the role of IFN as a therapeutic or prophylactic option may be strain or species specific (Sheahan et al., 2020).

T509

87549-87799

Sentence

denotes

Interestingly, a recent study by Mount Sinai virology groups revealed that type I IFN signaling is impaired in the early response to SARS-CoV-2; in vitro, SARS-CoV-2 may be more susceptible to type I IFN than SARS-CoV-1 is (Blanco-Melo et al., 2020).

T510

87800-88086

Sentence

denotes

Based on additional evidence that IFN responses to betacoronaviruses are altered as compared to other respiratory viruses (Blanco-Melo et al., 2020, Channappanavar et al., 2016, Okabayashi et al., 2006), trials of IFN-I/III administration have been initiated (NCT04343976, NCT04331899).

T511

88088-88105

Sentence

denotes

Cytokine Blockade

T512

88106-88380

Sentence

denotes

Hyperinflammatory responses and elevated levels of inflammatory cytokines, including IL-6, -8, and -10, have been shown to correlate with COVID-19 severity (Chen et al., 2020h, Diao et al., 2020, Gong et al., 2020, Moore and June, 2020, Wan et al., 2020a, Xu et al., 2020b).

T513

88381-88538

Sentence

denotes

The drivers of this cytokine storm remain to be established, but they are likely triggered initially by a combination of viral PAMPs and host danger signals.

T514

88539-88697

Sentence

denotes

The heterogeneous response between patients suggests other factors are involved, possibly including the SARS-CoV-2 receptor, ACE2 (Hirano and Murakami, 2020).

T515

88698-88829

Sentence

denotes

Several studies have begun to report the cellular programs that may contribute to the cytokine storm detected in COVID-19 patients.

T516

88830-89084

Sentence

denotes

One group reported that in the context of generalized lymphopenia, certain subsets of CD4 T cells that express GM-CSF and IL-6 are more abundant in severe COVID-19 patients than in COVID-19 patients who do not require intensive care (Zhou et al., 2020b).

T517

89085-89323

Sentence

denotes

Reports that other major proinflammatory cytokines (TNF-α, IFN-ɣ, IL-2) and chemokines (CCL2, CCL3, CCL4) are elevated underscore a potentially pathogenic TH1/2 program in COVID-19 (Diao et al., 2020, Giamarellos-Bourboulis et al., 2020).

T518

89324-89594

Sentence

denotes

Histological and single-cell analyses identified monocytes and macrophages as other potent sources of inflammatory cytokines in COVID-19 cytokine storm (Chen et al., 2020h, Giamarellos-Bourboulis et al., 2020, Law et al., 2005, Moore and June, 2020, Zhou et al., 2020b).

T519

89595-89973

Sentence

denotes

Studies of other betacoronavirus infections, including SARS-CoV-1 and MERS-CoV, have also identified similar hyperactivation of monocytes, macrophages, and DCs as a driver of cytokine-mediated immunopathology in humans (Cheung et al., 2005, Chien et al., 2006, Huang et al., 2020c, Konig et al., 2020, Wang et al., 2005, Wong et al., 2004, Xu et al., 2020b, Zhou et al., 2020b).

T520

89974-90204

Sentence

denotes

Following preliminary reports of IL-6 as a critical cytokine in COVID-19-associated CRS, monoclonal antibodies that target the IL-6 signaling pathway have been proposed as therapeutic candidates (Moore and June, 2020) (Figure 6C).

T521

90205-90450

Sentence

denotes

The commercial anti-IL-6R antibodies tocilizumab (Actemra) and sarilumab (Kevzara) and the anti-IL-6 antibody siltuximab (Sylvant) are now being tested for efficacy in managing COVID-19 CRS and pneumonia in 13 ongoing clinical trials (Table 2 ).

T522

90451-90713

Sentence

denotes

To date, only one group has reported preliminary results from a cohort of 20 COVID-19 patients treated with a single administration of tocilizumab (400 mg, i.v.), along with lopinavir, methylprednisolone, and oxygen therapy (ChiCTR2000029765) (Xu et al., 2020b).

T523

90714-90901

Sentence

denotes

The single observation study found recuperated lymphocyte counts in 10 of 19 patients and resolution of lung opacities in 19 of 20 patients on chest CT; 19 of 20 patients were discharged.

T524

90902-91008

Sentence

denotes

All patients experienced an improvement in symptoms, and no subsequent pulmonary infections were reported.

T525

91009-91144

Sentence

denotes

A second report described an association between use of tocilizumab and reduced likelihood of ICU admission and mechanical ventilation.

T526

91145-91330

Sentence

denotes

Still, in 30 declining patients with severe COVID-19 pneumonia, this retrospective study did not report significant improvement in mortality on weighted analysis (Roumier et al., 2020).

T527

91331-91436

Sentence

denotes

Nevertheless, these studies are encouraging, but like other treatment approaches, larger RCTs are needed.

T528

91437-91515

Sentence

denotes

Table 2 Clinical Trials Evaluating the Efficacy of IL-6/IL-6R Blockade Therapy

T529

91516-91543

Sentence

denotes

Clinical Trial Intervention

T530

91544-91692

Sentence

denotes

NCT04331795 (COVIDOSE)NCT04320615 (COVACTA)NCT04332913 (TOSCA)NCT04317092 (TOCOVID-19)NCT04335071 (CORON-ACT)NCT04315480ChiCTR2000029765 tocilizumab

T531

91693-91714

Sentence

denotes

NCT04315298 sarilumab

T532

91715-91749

Sentence

denotes

NCT04310228 tocilizumabfavipiravir

T533

91750-91833

Sentence

denotes

NCT04306705 (TACOS) tocilizumabcontinuous renal replacement therapystandard of care

T534

91834-91897

Sentence

denotes

NCT04332094 (TOCOVID) tocilizumabazithromycinhydroxychloroquine

T535

91898-91965

Sentence

denotes

NCT04341870 (CORIMUNO-VIRO) sarilumabazithromycinhydroxychloroquine

T536

91966-92033

Sentence

denotes

NCT0433z638 (COV-AID) tocilizumabsiltuximabanakinrastandard of care

T537

92034-92274

Sentence

denotes

In addition to the IL-6 signaling pathway, other cytokine- and chemokine-associated elements, including IL-1R, GM-CSF, and the chemokine receptor CCR5, have been proposed as potential targets for blockade to manage COVID-19 CRS (Figure 6C).

T538

92275-92366

Sentence

denotes

Finally, complement activation was shown to be overactivated in lungs of COVID-19 patients.

T539

92367-92546

Sentence

denotes

Although results from the randomized trial are not yet published, anti-C5a monoclonal antibody therapy showed benefits in two critically ill COVID-19 patients (Gao et al., 2020d).

T540

92548-92616

Sentence

denotes

Neutralizing Antibodies and Convalescent Plasma Therapy for COVID-19

T541

92617-92822

Sentence

denotes

While vaccines are being developed to educate a person’s immune system to make their own nAbs against SARS-CoV-2, there is interest in using adoptive transfer of nAbs as a therapeutic approach (Figure 6D).

T542

92823-93078

Sentence

denotes

This strategy has already proven to be effective against SARS-CoV-1 (Cao et al., 2010, Ho et al., 2005, ter Meulen et al., 2004, Park et al., 2020, Sui et al., 2004, Zhu et al., 2007) and MERS-CoV (Forni et al., 2015, Jia et al., 2019, Ying et al., 2015).

T543

93079-93251

Sentence

denotes

In the case of SARS-CoV-2, these efforts are primarily centered on identifying nAbs made during natural infections or generating nAbs through animal vaccination approaches.

T544

93253-93288

Sentence

denotes

nAbs Derived from COVID-19 Patients

T545

93289-93474

Sentence

denotes

Patients who have recovered from SARS-CoV-2 infection are one potential source of nAbs (Chen et al., 2020a, Ju et al., 2020, Walls et al., 2020, Wölfel et al., 2020, Yuan et al., 2020).

T546

93475-93705

Sentence

denotes

In an effort to obtain these nAbs, scientists sorted RBD-specific memory B cells and cloned their heavy and light variable regions to express recombinant forms of the corresponding antibodies (Chen et al., 2020a, Ju et al., 2020).

T547

93706-93867

Sentence

denotes

Four of the antibodies produced in these studies (31B5, 32D4, P2C-2F6, P2C-1F11) showed high neutralizing potential in vitro, and all inhibited ACE2-RBD binding.

T548

93868-93987

Sentence

denotes

Successful antibody-mediated neutralization of SARS-CoV-2 seemed to be dependent on the inhibition of ACE2/RBD binding.

T549

93988-94182

Sentence

denotes

However, Chen et al. showed that nearly all antibodies derived from serum of 26 recovered patients bound to S1 and RBD, with only three actually inhibiting ACE2/RBD binding (Chen et al., 2020a).

T550

94183-94420

Sentence

denotes

Of note, a SARS-CoV-1-derived neutralizing antibody (47D11) (Wang et al., 2020a) and a single-chain antibody against SARS-CoV-2 (n3130) (Wu et al., 2020c) have also been shown to neutralize SARS-CoV-2 without inhibiting ACE2/RBD binding.

T551

94421-94511

Sentence

denotes

Thus, blocking this interaction may not be a prerequisite for an effective SARS-CoV-2 nAb.

T552

94512-94756

Sentence

denotes

The generation of a hybridoma producing a monoclonal nAb against SARS-CoV-2 provides the potential for a therapeutic Ab that can be directly administered to patients to block ongoing infection and potentially even as a prophylactic (Figure 6D).

T553

94758-94800

Sentence

denotes

SARS-CoV-1 nAbs Also Neutralize SARS-CoV-2

T554

94801-94891

Sentence

denotes

SARS-CoV-1 and SARS-CoV-2 consensus sequences share about 80% identity (Tai et al., 2020).

T555

94892-95061

Sentence

denotes

Thus, a wide range of SARS-CoV-1 nAbs have been tested for crossreactivity with SARS-CoV-2, as they could help speed up the development of potential COVID-19 treatments.

T556

95062-95187

Sentence

denotes

In a recent study, antibodies were isolated from the memory B cells of an individual who recovered from SARS-CoV-1 infection.

T557

95188-95341

Sentence

denotes

While 8 out of 25 isolated antibodies could bind SARS-CoV-2 S protein, one of them (s309; see Table 3 ) also neutralizes SARS-CoV-2 (Pinto et al., 2020).

T558

95342-95477

Sentence

denotes

The combination of s309 with a weakly neutralizing antibody that could bind another RBD epitope led to enhanced neutralization potency.

T559

95478-95631

Sentence

denotes

In addition, CR3022 (Table 3) was found to bind SARS-CoV-2 RBD (Tian et al., 2020b), but this antibody did not neutralize SARS-CoV-2 (Yuan et al., 2020).

T560

95632-95846

Sentence

denotes

Computational simulations identified three amino acids that could be modified on CR3022 to enhance its binding affinity with SARS-CoV-2 RBD (Giron et al., 2020), potentially augmenting its neutralization potential.

T561

95847-95911

Sentence

denotes

Table 3 Strategies to Isolate SARS-CoV-2 Neutralizing Antibodies

T562

95912-96007

Sentence

denotes

Ab Source Clone Target Type of Antibody Neutralization Inhibition of ACE2/RBD Binding Reference

T563

96008-96095

Sentence

denotes

Derived from COVID-19 patients 31B532D4 RBD human monoclonal yes yes Chen et al., 2020a

T564

96096-96156

Sentence

denotes

P2C-2F6P2C-1F11 RBD human monoclonal yes yes Ju et al., 2020

T565

96157-96281

Sentence

denotes

Derived from SARS-CoV-1 patients CR3022 RBD human monoclonal no no Tian et al., 2020b, Yuan et al., 2020, Giron et al., 2020

T566

96282-96333

Sentence

denotes

S309 RBD human monoclonal yes no Pinto et al., 2020

T567

96334-96443

Sentence

denotes

Derived from SARS-CoV-1 or MERS-CoV-1 animal models R325R302R007 S1 rabbit monoclonal yes no Sun et al., 2020

T568

96444-96567

Sentence

denotes

47D11 S1 recombinant human monoclonal (derived from hybridomas of immunized transgenic H2L2 mice) yes no Wang et al., 2020a

T569

96568-96642

Sentence

denotes

VHH-72-Fc S Fc-fusion derived from camelids VHH yes yes Wrapp et al., 2020

T570

96643-96718

Sentence

denotes

S polyclonal mouse antibodies yes N/A Walls et al., 2020, Yuan et al., 2020

T571

96719-96795

Sentence

denotes

Other ACE2-Fc RBD ACE2-Fc fusion yes N/A Lei et al., 2020a, Li et al., 2020d

T572

96796-96846

Sentence

denotes

RBD-Fc ACE2 RBD-Fc fusion yes N/A Li et al., 2020d

T573

96847-96945

Sentence

denotes

N3130 S1 human monoclonal single domain antibody isolated by phage display yes no Wu et al., 2020c

T574

96946-97021

Sentence

denotes

IVIg N/A polyclonal human IVIg N/A N/A Díez et al., 2020, Shao et al., 2020

T575

97022-97075

Sentence

denotes

F(ab′)2 RBD horse polyclonal yes N/A Pan et al., 2020

T576

97076-97094

Sentence

denotes

N/A, not assessed.

T577

97096-97121

Sentence

denotes

nAbs Derived from Animals

T578

97122-97205

Sentence

denotes

Animal models represent another tool to generate nAbs against SARS-CoV-2 (Table 3).

T579

97206-97412

Sentence

denotes

In one study, the authors developed a protocol to synthetize human nanobodies, smaller antibodies that only contain a variable heavy (VH) chain as first described in camelids (Wu et al., 2020c) (Figure 6D).

T580

97413-97621

Sentence

denotes

Another antibody isolated from camelids immunized with SARS-CoV-1 and MERS-CoV S proteins then fused to a human Fc fragment showed neutralization potential against SARS-CoV-2 (VHH-72-Fc) (Wrapp et al., 2020).

T581

97622-97806

Sentence

denotes

Genetically modified mice with humanized antibody genes can also be used to generate therapeutic monoclonal antibodies, as successfully experimented against Ebola virus (Levine, 2019).

T582

97807-98115

Sentence

denotes

Similar studies are now focused on the use of SARS-CoV-2 or derivatives to generate highly effective nAb in animal models, which can be directly given to infected patients, and efforts are already underway with estimates of clinical trials of pooled antibody cocktails beginning in early summer by Regeneron.

T583

98116-98301

Sentence

denotes

Finally, another approach to nAb development is to fuse ACE2 protein and the Fc part of antibodies, as they would bind RBD and potentially be crossreactive among other CoVs (Figure 6D).

T584

98302-98444

Sentence

denotes

Indeed, an ACE2-Fc (Lei et al., 2020a) and an RBD-Fc (Li et al., 2020d) have been shown to neutralize both SARS-CoV-1 and SARS-CoV-2 in vitro.

T585

98446-98473

Sentence

denotes

Convalescent Plasma Therapy

T586

98474-98679

Sentence

denotes

Although recombinant nAbs could provide an effective treatment, they will require a significant time investment to develop, test, and bring production to scale before becoming widely available to patients.

T587

98680-98856

Sentence

denotes

A faster strategy consists of transferring convalescent plasma (CP) from previously infected individuals that have developed high titer nAbs that target SARS-CoV-2 (Figure 6D).

T588

98857-99142

Sentence

denotes

Despite the current lack of appropriately controlled trials, CP therapy has been previously used and shown to be beneficial in several infectious diseases, such as the 1918 influenza pandemic (Luke et al., 2006), H1N1 influenza (Hung et al., 2011), and SARS-CoV-1 (Arabi et al., 2016).

T589

99143-99360

Sentence

denotes

Thanks to the development of serological tests (Amanat et al., 2020, Cai et al., 2020, Xiang et al., 2020b, Zhang et al., 2020d), recovered COVID-19 patients can be screened to select plasma with high antibody titers.

T590

99361-99629

Sentence

denotes

Some studies and case reports on CP therapy for COVID-19 have evaluated the safety and the potential effectiveness of CP therapy in patients with severe disease (Ahn et al., 2020, Duan et al., 2020, Pei et al., 2020, Shen et al., 2020, Zhang et al., 2020b) (Table 4 ).

T591

99630-99792

Sentence

denotes

These studies were neither controlled nor randomized, but they suggest that CP therapy is safe and can have a beneficial effect on the clinical course of disease.

T592

99793-99892

Sentence

denotes

Further controlled trials are needed to determine the optimal timing and indication for CP therapy.

T593

99893-100072

Sentence

denotes

CP therapy has also been proposed for prophylactic use in at-risk individuals, such as those with underlying health conditions or health care workers exposed to COVID-19 patients.

T594

100073-100155

Sentence

denotes

The FDA has approved the use of CP to treat critically ill patients (Tanne, 2020).

T595

100156-100424

Sentence

denotes

Determining when to administer the CP is also of great importance, as a study in SARS-CoV-1 patients showed that CP was much more efficient when given to patients before day 14 day of illness (Cheng et al., 2005b), as previously shown in influenza (Luke et al., 2006).

T596

100425-100522

Sentence

denotes

This study also showed that CP therapy was more efficient in PCR-positive, seronegative patients.

T597

100523-100619

Sentence

denotes

The amount of plasma and number of transfusions needed requires further investigation (Table 4).

T598

100620-100696

Sentence

denotes

Table 4 Clinical Studies of Convalescent Plasma Therapy in COVID-19 Patients

T599

100697-100758

Sentence

denotes

Patient Characteristics Start of CP Therapy Results Reference

T600

100759-100914

Sentence

denotes

5 severe patients (30–70 yo) between 10 and 22 days after hospital admission body temperature normalized within 3 days in 4 of 5 patients Shen et al., 2020

T601

100915-100935

Sentence

denotes

clinical improvement

T602

100936-100997

Sentence

denotes

viral loads became negative within 12 days of the transfusion

T603

100998-101018

Sentence

denotes

nAb titers increased

T604

101019-101126

Sentence

denotes

10 severe patients (34–78 yo) median 16.5 dpo disappearance of clinical symptoms after 3d Duan et al., 2020

T605

101127-101144

Sentence

denotes

chest CT improved

T606

101145-101209

Sentence

denotes

elevation of lymphocyte counts in patients with lymphocytopenia.

T607

101210-101242

Sentence

denotes

increase in SaO2 in all patients

T608

101243-101289

Sentence

denotes

resolution of SARS-CoV-2 viremia in 7 patients

T609

101290-101344

Sentence

denotes

increase in neutralizing antibody titers in 5 patients

T610

101345-101491

Sentence

denotes

4 critical patients (31–73 yo) at degradation of symptoms,between 11 and 19 days after hospital admission clinical improvement Zhang et al., 2020b

T611

101492-101510

Sentence

denotes

reduced viral load

T612

101511-101528

Sentence

denotes

chest CT improved

T613

101529-101641

Sentence

denotes

1 moderate patient, 2 critical patients 12 dpo, 27 dpo viral detection negative 4 days after CP Pei et al., 2020

T614

101642-101676

Sentence

denotes

clinical improvement of 2 patients

T615

101677-101763

Sentence

denotes

2 severe patients (67 and 71 yo) 7 dpo or 22 dpo clinical improvement Ahn et al., 2020

T616

101764-101782

Sentence

denotes

reduced viral load

T617

101783-101800

Sentence

denotes

chest CT improved

T618

101801-101849

Sentence

denotes

yo, years old; dpo, days post onset of symptoms.

T619

101850-101976

Sentence

denotes

Overall, CP therapy seems to be associated with improved outcomes and appears to be safe, but RCTs are needed to confirm this.

T620

101977-102060

Sentence

denotes

Several clinical trials are currently in progress worldwide (Belhadi et al., 2020).

T621

102062-102081

Sentence

denotes

Vaccine Development

T622

102082-102343

Sentence

denotes

The devastating effects of the pandemic spread of SARS-CoV-2 in a globally naive population has resulted in unprecedented efforts to rapidly develop, test, and disseminate a vaccine to protect against COVID-19 or to mitigate the effects of SARS-CoV-2 infection.

T623

102344-102525

Sentence

denotes

Although vaccination has a long and successful history as an effective global health strategy, there are currently no approved vaccines to protect humans against CoVs (André, 2003).

T624

102526-102734

Sentence

denotes

Previous work after the SARS-CoV-1 and MERS-CoV epidemics has provided a foundation on which many current efforts are currently building upon, including the importance of the S protein as a potential vaccine.

T625

102735-102923

Sentence

denotes

Diverse vaccine platforms and preclinical animal models have been adapted to SARS-CoV-2, facilitating fast-moving and robust progress in creating and testing SARS-CoV-2 vaccine candidates.

T626

102924-103060

Sentence

denotes

A number of vaccine candidates are already being tested in clinical trials, and more are continuing to progress toward clinical testing.

T627

103062-103095

Sentence

denotes

The S Protein as a Vaccine Target

T628

103096-103245

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Since SARS-CoV-1 first emerged, the S protein has been favored as the most promising target for vaccine development to protect against CoV infection.

T629

103246-103557

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This particular viral protein has important roles in viral entry and in stimulating the immune response during natural infection and in vaccination studies of both SARS-CoV-1 and MERS-CoV (Du et al., 2009, Song et al., 2019, Zhou et al., 2018), which has also been confirmed for SARS-CoV-2 (Walls et al., 2020).

T630

103558-103731

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The S protein has been found to induce robust and protective humoral and cellular immunity, including the development of nAbs and T cell-mediated immunity (Du et al., 2009).

T631

103732-104205

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In animal models, correlates of protection against SARS-CoV-1 infection appear to be induction of nAbs against the S protein, although antibodies to other proteins have been detected, such as those against nucleoprotein (N) and ORF3a (Qiu et al., 2005, Sui et al., 2005). nAbs are also believed to protect against infection by blocking receptor binding and viral entry, which has been shown with pseudovirus-based neutralization assays (Ni et al., 2020, Nie et al., 2020a).

T632

104206-104673

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Studies of SARS-CoV-1 indicate that T cell response against the S protein correlates with nAb titers and dominated the T cell response after natural infection, which also induced T cells active against the membrane (M) and N proteins, that memory T cell responses can persist even 11 years after infection, and that memory CD8+ T cells can protect mice from lethal challenge in the absence of memory CD4+ T cells and memory B cells (Li et al., 2008, Ng et al., 2016).

T633

104674-104871

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RBD-specific antiviral T cell responses have also been detected in people who have recovered from COVID-19, further validating its promise as a vaccine target (Braun et al., 2020, Ni et al., 2020).

T634

104873-104888

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Epitope Mapping

T635

104889-105141

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Although the antibodies targeting the RBD of the S protein have greater potential for providing cross-protective immunity, other fragments of the S protein and additional viral proteins have been investigated as target epitopes, especially for T cells.

T636

105142-105670

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Researchers have taken advantage of the genetic similarity between SARS-CoV-2 and SARS-CoV-1 and MERS-CoV and bioinformatics approaches to rapidly identify potential B and T cell epitopes in the S and other proteins, with many studies providing data regarding antigen presentation and antibody-binding properties and one study looking into the predicted evolution of epitopes (Ahmed et al., 2020, Baruah and Bose, 2020, Bhattacharya et al., 2020, Fast et al., 2020, Grifoni et al., 2020, Lon et al., 2020, Zheng and Song, 2020).

T637

105671-105902

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While the S protein has been found to be the most immunodominant protein in SARS-CoV-2, the M and N proteins also contain B and T cell epitopes, including some with high conservation with SARS-CoV-1 epitopes (Grifoni et al., 2020).

T638

105904-105920

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Vaccine Pipeline

T639

105921-106194

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For SARS-CoV-1 and MERS-CoV, animal studies and phase I clinical trials of potential vaccines targeting the S protein had encouraging results, with evidence of nAb induction and induction of cellular immunity (Lin et al., 2007, Martin et al., 2008, Modjarrad et al., 2019).

T640

106195-106311

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These findings are being translated into SARS-CoV-2 vaccine development efforts, hastening the progress drastically.

T641

106312-106471

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The WHO provided a report in April that reported 63 vaccine candidates in preclinical testing and three in clinical testing (World Health Organization, 2020b).

T642

106472-106578

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A recent search on May 1, 2020 on ClinicalTrials.gov revealed 10 registered vaccine candidates (Table 5 ).

T643

106579-106762

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The University of Pittsburgh is also looking to move their microneedle array vaccine candidate containing a codon-optimized S1 subunit protein into clinical trials (Kim et al., 2020).

T644

106763-107027

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Sanofi and GlaxoSmithKline (GSK) have recently reported their intent to collaborate and bring together Sanofi’s baculovirus expression system, which is used to produce the influenza virus vaccine, Flublok, to create an S protein vaccine adjuvanted with GSK’s AS03.

T645

107028-107228

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Sinovac Biotech will also enter testing in a clinical trial in China after it was found to protect rhesus macaques from viral challenge without signs of detectable immunopathology (Gao et al., 2020c).

T646

107229-107499

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Although some of these vaccine candidates are based on platforms that have been used or tested for other purposes, there remain questions regarding their safety and immunogenicity, including the longevity of any induced responses, that will require continual evaluation.

T647

107500-107567

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Table 5 Vaccine Candidates Currently Registered for Clinical Trials

T648

107568-107641

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Candidate Design Developer Similar Strategy ClinicalTrials.gov Identifier

T649

107642-107771

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mRNA-1273 LNP-encapsulated mRNA for full-length S protein ModernaTX CMV (John et al., 2018), ZKV (Pardi et al., 2017) NCT04283461

T650

107772-107953

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BNT162a1, b1, b2, c2 LNP-encapsulated mRNA vaccines with different formats of RNA and targets, two for larger S sequence and two for optimized RBD BioNTech SE and Pfizer NCT04368728

T651

107954-108097

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INO-4800 DNA vaccine for full-length S protein Inovio Pharmaceuticals MERS-CoV (Modjarrad et al., 2019), HPV (Trimble et al., 2015) NCT04336410

T652

108098-108258

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Ad5-nCoV adenovirus type 5 encoding full-length S protein CanSino Biologics EBV (Zhu et al., 2015, Zhu et al., 2017) NCT04313127 (phase I)NCT04341389 (phase II)

T653

108259-108410

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ChAdOx1 nCoV-19 adenovirus encoding full-length S protein University of Oxford MERS-CoV (Alharbi et al., 2017), IAV (Antrobus et al., 2014) NCT04324606

T654

108411-108609

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COVID-19 LV-SMENP-DC dendritic cells infected with lentivirus expressing SMENP minigenes to express COVID-19 antigens, together with activated CTLs Shenzhen Geno-Immune Medical Institute NCT04276896

T655

108610-108756

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COVID-19 aAPCs aAPCs infected with lentivirus expressing minigenes to express COVID-19 antigens Shenzhen Geno-Immune Medical Institute NCT04299724

T656

108757-108904

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bacTRL-Spike-1 live bacteria delivering plasmid encoding S protein Symvivo Corporation therapeutics reviewed (Charbonneau et al., 2020) NCT04334980

T657

108905-109012

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PiCoVacc inactivated SARS-CoV-2 vaccine Sinovac Biotech HAV, IAV, IBV, poliovirus, rabies virus NCT04352608

T658

109013-109115

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SARS-CoV-2 rS spike protein nanoparticle vaccine with or without Matrix-M adjuvant Novavax NCT04368988

T659

109116-109340

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aAPCs, artificial antigen-presenting cells; CMV, cytomegalovirus; EBV, Ebola virus; HAV, hepatitis A virus; HPV, human papillomavirus; IAV, influenza A virus; IBV, influenza B virus; LPN, lipid nanoparticle; ZKV, Zika virus.

T660

109342-109352

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Challenges

T661

109353-109558

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Although the development of a vaccine to protect against SARS-CoV-2 infection has progressed at an unprecedented rate and produced an impressive volume of candidates for testing, many challenges lie ahead.

T662

109559-109864

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The prior knowledge gained after SARS-CoV-1 was first discovered in 2003, and the subsequent emergence of MERS-CoV in 2012 provided a significant jumpstart, but the progress of SARS-CoV-2 vaccine development has already far outstripped the point of the blueprint created before COVID-19 became a pandemic.

T663

109865-110062

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While a variety of platforms are simultaneously being innovated or adapted, they each have strengths and limitations, many of which relate to the delicate balance between safety and immunogenicity.

T664

110063-110223

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Many shortcuts have been taken and will continue to be taken due to the urgency of the ongoing COVID-19 pandemic, but significant concerns need to be addressed.

T665

110224-110365

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One such concern involves the accumulating data supporting the initial assessment that COVID-19 is disproportionately severe in older adults.

T666

110366-110578

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In conjunction with the large body of work related to immune senescence, these findings indicate that vaccine design should take into consideration the impact of aging on vaccine efficacy (Nikolich-Žugich, 2018).

T667

110579-110856

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Furthermore, questions remain regarding the possibility of antibody-dependent enhancement of COVID-19, with in vitro experiments, animal studies, and two studies of COVID-19 patients supporting this possibility (Cao, 2020, Tetro, 2020, Zhang et al., 2020a, Zhao et al., 2020a).

T668

110857-111031

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Assuming vaccine candidates that can safely induce protective immune responses are identified, additional major hurdles will be the production and dissemination of a vaccine.

T669

111032-111330

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For some types of vaccines, large-scale production will not be as much of an issue, and infrastructure already in place to produce current Good Manufacturing Practice (cGMP)-quality biologics can be repurposed, but this will only be applicable to a subset of the candidates (Thanh Le et al., 2020).

T670

111331-111753

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In order to address the urgent need and stem the COVID-19 pandemic, regulatory agencies need to continue to support rapid testing and progression of vaccine candidates, companies need to disseminate important findings directly and openly, and researchers need to investigate correlates of protection using in-depth immune monitoring of patients with a broad range of clinical presentations and clinical trial participants.

T671

111754-111943

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The newly announced Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) is designed to bring together numerous governmental and industry entities to help address this need.

T672

111945-111963

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Concluding Remarks

T673

111964-112181

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The rapid spread of SARS-CoV-2 and the unprecedented nature of COVID-19 has demanded an urgency in both basic science and clinical research, and the scientific community has met that call with remarkable productivity.

T674

112182-112329

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Within months, there has been a significant generation of scientific knowledge that has shed some light on the immunology of SARS-CoV-2 infections.

T675

112330-112451

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Studies of past coronavirus outbreaks involving SARS-CoV-1 and MERS-CoV have provided a foundation for our understanding.

T676

112452-112594

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The pathology of severe cases of COVID-19 does indeed resemble certain immunopathologies seen in SARS-CoV-1 and MERS-CoV infections, like CRS.

T677

112595-112718

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However, in many other ways, immune responses to SARS-CoV-2 are distinct from those seen with other coronavirus infections.

T678

112719-113059

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The emerging epidemiological observation that significant proportions of individuals are asymptomatic despite infection not only reflects our current understanding that SARS-CoV-2 has a longer incubation period and higher rate of transmission than other coronaviruses, but also speaks to significant differences in the host immune response.

T679

113060-113258

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Therefore, it is imperative that immune responses against SARS-CoV-2 and mechanisms of hyperinflammation-driven pathology are further elucidated to better define therapeutic strategies for COVID-19.

T680

113259-113599

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Here, we reviewed the recent literature and highlighted hypotheses that interrogate mechanisms for viral escape from innate sensing, for hyperinflammation associated with CRS and inflammatory myeloid subpopulations, for lymphopenia marked by T cell and NK cell dysfunction, and for correlates of protection and their duration, among others.

T681

113600-113807

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Still, additional studies are needed to address how these immune differences across patients or between different types of coronavirus infections dictate who succumbs to disease and who remains asymptomatic.

T682

113808-113952

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Existing studies of SARS-CoV-1 and MERS-CoV and ongoing studies of SARS-CoV-2 will likely provide a robust framework to fulfill that unmet need.

T683

113954-113963

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Consortia

T684

113964-114187

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The members of the Sinai Immunology Review Project are Manasi Agrawal, Mark Aleynick, Meriem Belabed, Graham Britton, Matthew Brown, Maria Casanova-Acebes, Jovani Catalan, Monica Centa, Andrew Charap, Andrew Chan, Steven T.

T685

114188-114707

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Chen, Jonathan Chung, Cansu Cimen Bozkus, Evan Cody, Francesca Cossarini, Erica Dalla, Nicolas Fernandez, John Grout, Conor Gruber, Dan Fu Ruan, Pauline Hamon, Samarth Hegde, Etienne Humblin, Divya Jha, Maria Kuksin, Julia Kodysh, Andrew Leader, Rachel Levantovsky, Matthew Lin, Katherine Lindblad, Daniel Lozano-Ojalvo, Gabrielle Lubitz, Assaf Magen, Zafar Mahmood, Louise Malle, Gustavo Martinez-Delgado, Jaime Mateus-Tique, Elliot Meritt, Chang Moon, Alvaro Moreira, Justine Noel, Tim O’Donnell, Miyo Ota, Matthew D.

T686

114708-114824

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Park, Luisanna Pia, Tamar Plitt, Venu Pothula, Jamie Redes, Ivan Reyes Torres, Emma Risson, Mark Roberto, Alfonso R.

T687

114825-115039

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Sanchez-Paulete, Miriam Saffern, Bérengère Salomé, Myvizhi Esai Selvan, Joan Shang, Matthew Spindler, Alessandra Soares Schanoski, Maria Suprun, Jessica Tan, Michelle Tran, Verena van der Heide, Natalie Vaninov, C.

T688

115040-115201

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Matthias Wilk, Julio Aguirre-Ghiso, Konstantina Alexandropoulos, Nina Bhardwaj, Dusan Bogunovic, Brian Brown, Judy Cho, Jeremiah Faith, Emilie Grasset, Zeynep H.

T689

115202-115279

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Gümüş, Peter Heeger, Dirk Homann, Amir Horowitz, Ephraim Kenigsberg, Alice O.

T690

115280-115316

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Kamphorst, Florian Krammer, Maria A.

T691

115317-115420

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Curotto de Lafaille, Uri Laserson, Saurabh Mehandru, Miriam Merad, Robert Samstein, and Nicolas Vabret.

PMC:7200337 / 1427-116847 JSON TXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE Lectin_function IAV-Glycan

PMC:7200337 / 1427-116847 JSONTXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE Lectin_function IAV-Glycan

PMC:7200337 / 1427-116847 JSON TXT 12 Projects