Functional Adaptive Immune Response
The functional but well-regulated adaptive immune response is necessary to overcome the viral infection. Specifically, T cells when recruited to the site of infection engage in eliminating the infected cells and act in concordance with virus-specific neutralization antibodies to provide sustained immunity (Hor et al., 2015; De Biasi et al., 2020). Considering the recent extensive work in understanding the functional early immune response during COVID-19, it appears that a complex interplay between T and B cell immune response along with patient-specific underlying health condition and genetic factors determines the recovery, as will be discussed in following sections.

T Cell Response
Generation of early adaptive immune response is critical for the selective elimination of virus-infected cells and neutralization of viral antigens, thereby preventing the damage to the underlying lung parenchyma. Cytokines, chemokines, PAMPs, and DAMPs released by infected ATII and activated AMs in the lung are adequate to mount a well-coordinated and regulated adaptive immune response by priming lung resident DCs. After encountering the antigen-presenting DCs, naive CD4+ T cells differentiate into effector and memory CD4+ T cells. At least five different CD4+ T cell lineages are known (TH1, TH2, TH17, TFH, and TREG cells) with prominent roles of TH1 and TFH cells in mounting antiviral response during SARS-CoV infection (Channappanavar et al., 2014). Additionally, some studies have also shown a functional TH2 response in PBMCs derived from COVID-19 patients. Release of TH2 specific cytokines like IL-4 and IL-5 was observed in vitro after these cells were stimulated (Weiskopf et al., 2020). Similarly, these patients show enhanced production of IL-17 along with other TH17 cell-specific cytokines (Liu J. et al., 2020; Wu and Yang, 2020). These findings suggest that the TH cell response in COVID-19 patients is complex concerning other infections, and this complexity may partly depend upon the prevailing pathophysiological state of a patient.
During viral infections like SARS-CoV, TH1 differentiation is influenced by IL-12 and IFN-γ secreted by DCs along with co-stimulatory signaling via B7-1/2 and CD28. Whereas IL-6 secreted by DCs influence TFH differentiation to aid in antibody secretion by B cells (Tang et al., 2008; Lau et al., 2012). Under the influence of chemokines (CCL3, CCL4, CCL5, CCL8), TH1 cells are recruited to the site of infection and are distinguished by the secretion of IL-2, IFN-γ, IL-12, and TNF-α as the main effector cytokines during SARS-CoV infections (Li et al., 2008). Similarly, naive CD8+ T cells are activated by DCs by engaging MHC-I and TCR receptors, along with CD28-B7 co-stimulatory signaling and cytokines released by CD4+ T cells. IL-2 secreted chiefly by CD4+ T cells is also implicated in their long-term maintenance and proliferation (Eickhoff et al., 2015; Hor et al., 2015). Notably, CD8+ T cells could also be activated independently of help from CD4+ T cells under conditions where a robust IFN Type I response is present (Wiesel and Oxenius, 2012). These activated CD8+ T cells [also referred to as cytotoxic T lymphocytes (CTLs)] get subsequently recruited to the effector organ under the influence of chemokines (CCL3, CCL4, CCL5, CXCL9, and CXCL10) (Nolz, 2015). At the infected site, CTLs mount an antiviral response by directly killing the infected cells via secretion of cytotoxic molecules like granzymes, perforins, granulysin, and other cytotoxic granules. Very recently, a study shows that CTLs secrete the granzymes and perforins as supramolecular attack particles (SMAPs) in a glycoprotein complex along with over 283 other proteins (including cytokines such as IFN-γ and TNF-α) (Bálint et al., 2020). It will be interesting to know whether infection by CoVs also influences the release of SMAP by CTLs.
Animal studies have revealed the critical molecular insights of CD4+ cells in SARS-CoV clearance and attenuation of a pathological condition. The depletion of CD4+ cells was associated with reduced virus clearance and interstitial pneumonitis (Jin et al., 2005; Wang et al., 2006). In comparison, the adoptive transfer of virus-specific CD4+ and CD8+ T cells resulted in viral clearance (Zhao et al., 2010). Similarly, clinical data has consistently shown the presence of antigen-specific CD4+ and CD8+ T cells in the recovered patients, akin to what was found in immunized animals, reviewed in Channappanavar et al. (2014). On the other hand, severe cases of SARS-CoV infection were associated with a decline in T cells, as will be discussed in later sections. Thus, based on these animal and clinical data, CD4+ T and CD8+ T cells were central to the antiviral response during SARS-CoV infection (Peng et al., 2006; Oh et al., 2012).
A subset of primed CD4+ and CD8+ T cells differentiates into long-acting memory cells after the infection subsides. TCR-p: MHCII signaling helps in CD4+ T memory cell formation along with presence of cytokines like IL-2, IL-21 and interaction via CD40R-CD40L (Jaigirdar and MacLeod, 2015). Similarly, This CD8+ T cell transition to memory cells take place under the influence of CD8+ TREG cells via secreted IL-10 (Laidlaw et al., 2015). Long lasting CD4+ and CD8+ T memory cells were detected in the recovered SARS-CoV infected patients (Peng et al., 2006; Li et al., 2008).
Besides, other T cells subsets which are involved in antiviral response include unconventional NKT cells (CD56+) and MAIT (mucosa-associated invariant T) cells. NKT cells act at the interface between innate and adaptive immune response and traffic to the site of infection under the influence of cytokines (Tsay and Zouali, 2018). MAIT cells reside in the mucosal lining, such as in the lungs where they serve an immunoregulatory function. Both these cell types play an essential role in the early clearance of the SARS-CoV-2, along with other T cell subsets (Grifoni et al., 2020). Strategies to enhance their function are proposed to enhance the virial clearance during COVID-19 (Cao, 2020). Role of these cells will be further discussed under the dysfunctional immune response in section “T and B Cell Response in Mild/Moderate and Recovered COVID-19 Patients.”

B Cell Response
B cells, along with T cells, form the central adaptive response during viral infections. B cell response is highly specific, mounted by the virus-specific antibodies and other effector cytokines secreted by these cells. B cell activation can be follicular helper T (TFH) cell-dependent, or in some instances, independent of helper cells; both instances are prevalent in COVID-19 (Mathew et al., 2020). Under the influence of antigen-presenting dendritic cells, naïve CD4+ T cells differentiate into TFH cells, which are marked by high expressions of CXCR5 and IL-21, and low expressions of CCR7, IFN-γ, IL-4, and IL-17 (Rasheed et al., 2006; Nurieva et al., 2008; Morita et al., 2011). The activated TFH cells interact with B cells via CD40R-CD40L and other associated receptors to induce the production of antigen-specific antibodies in a well-coordinated and regulated process. This CD40R-CD40L interaction along with the secretion of IL-21 also allows the formation of long-lived memory B cells, while B cell-derived IL-6 and IL-27 help in reciprocal maintenance of TFH cells (Nurieva et al., 2008, 2009). A previous animal study has shown the essential role of these helper cells in mounting an adequate antibody response against SARS-CoV infection (Chen et al., 2010). The depletion of these cells was associated with a decline in antibody response and reduced viral clearance. Thus, virus-specific antibodies produced by B cells are critical for an effective immune response mounted by the host. These antibodies facilitate the clearance of the virus by either directly activating phagocytosis, opsonization, or activation of the antibody-dependent cellular cytotoxicity (ADCC) via effector NK cells. Cytokines released by the activation of innate and adaptive immune systems also activate the complement system. Viruses coated with the secreted antibodies from plasma cells eventually get eliminated by the complement system, reviewed by Risitano et al. (2020).

T and B Cell Response in Mild/Moderate and Recovered COVID-19 Patients
T cell response is an emerging critical determinant in keeping the SARS-CoV-2 infection under check (Huang C. et al., 2020; Liu J. et al., 2020). Across studies, a decline in the number of these cells positively correlates with poor clinical outcome and immuno-pathogenesis, whereas adequate T cell number and proper effector function are prevalent in patients who develop mild disease symptoms or those who successfully recovered (Chen G. et al., 2020; Li H. et al., 2020; Sekine et al., 2020; Tan L. et al., 2020b). Following a single patient (47-year-old woman) throughout the disease, Thevarajan et al. (2020) showed a concomitant increase in CD4+, CD8+, TFH cells, and antibody-secreting B cells from day seven after infection, which persisted for a week as the symptoms resolved. Other studies revealed a similar trend of revival in T cell response in patients who have successfully cleared the virus (Anft et al., 2020; Braun et al., 2020; Chen X. et al., 2020; Chen N. et al., 2020).
SARS-CoV-2 specific reactive CD4+ and CD8+ T cells were found in 100 and 80% patients who needed mechanical ventilation (n = 10). PBMCs derived from these patients showed reactivity against the S protein of SARS-CoV-2. Further, in vitro stimulation of CD4+ T cells led to their differentiation into TH1, TH2, and TH17 subsets, as revealed by the expression of their corresponding cytokines (Weiskopf et al., 2020). Interestingly, 20% of non-infected healthy controls also displayed reactive T cells. The main limitation with this study was that the T response was studied only in critically ill patients and the small sample size was small to provide.
By studying a cohort of 18 COVID-19 patients and 64 healthy donors, Braun et al. (2020) found reactive CD4+ (83%) cells in blood-derived from the convalescing COVID-19 patients. These reactive T cells were found specifically against the S protein. Interestingly about 35% of SARS-CoV-2 seronegative healthy donors also showed the presence of S protein reactive CD4+ T cells indicating previous exposure to the related coronavirus infections. Simultaneously, another study has found SARS-CoV-2 specific CD4+ T (100%) and CD8+ T (70%) cells in convalescent patients (n = 20) (Grifoni et al., 2020). In addition to being majorly reactive against S protein, the study found additional targets of these T cells in the form of M, N, and ORF8 proteins and other non-structural proteins like NSP3, NSP4, ORF3a. Further, in line with the study by Braun et al. (2020), T cells were found reactive against 40–60% of the SARS-CoV-2 uninfected patients, suggesting the presence of these reactive cells in response to previous viral infections.
In a yet to be a peer-reviewed article, Schulien et al. (2020) has extensively studied the SARS-CoV-2 epitope-specific role of CD8+ T cells in COVID-19 (Schulien et al., 2020). The study found the presence of newly generated and pre-existing SARS-CoV-2 specific cells with the positive response seen in 88.4% of patients who had mild disease symptoms (n = 26). The most substantial response was found against N protein and ORF3a. Further, CD8+ T cells response was shown persistent even in the individuals who became seronegative. In a patient studied longitudinally (70 days), CD8+ T cell response prolonged but antibody did not persist. All these three studies taken together point toward the presence of functional and long-lasting reactive T cells in convalescent individuals, while others also suggest the presence of reactive T cells in critically ill patients (Weiskopf et al., 2020). Thus, based on these studies, it appears that COVID-19 patients who exhibit mild disease symptoms and successfully recover, display functional and long-lasting T cell response. However, these findings may not be definitive to provide a coherent functional view of these cells during recovery, as none of these studies compared the T cell response to disease severity. A further difference in the time of sample collection may also complicate the findings. In the study by Grifoni et al. (2020) samples were collected throughout 20–35 days after symptom onset, whereas Weiskopf et al. (2020), used samples collected after 14 days of ICU admission. Thus, more studies under controlled clinical settings and large cohort size are warranted.
While addressing some of these concerns, a recent study explored T cell response in convalescent COVID-19 patients concerning disease severity (Peng et al., 2020). The study found robust CD4+ and CD8+ memory T cell response in severe cases (n = 14) than mild (n = 28), suggesting long-lasting memory of these cells to keep the infection in check. The limitation again here is the small sample size. Therefore, more such studies with large sample size are needed to fully understand the impact of T cell response and its long-term sustainability.
B cell response has a temporal dynamic to human infecting CoVs, with a median time of detection for SARS-CoV as 14 days, reviewed by Huang A.T. et al. (2020). The peak antibody titer for IgG and IgM, and detection time of neutralizing antibody varied across studies with a lower time point of seroconversion for IgG, IgM, and IgA as 15 days (Hsueh et al., 2004; Mo et al., 2006; Cao et al., 2007; Yang et al., 2009). A more dynamic range of seroconversion was observed in sera from the COVID-19 patients. A study by Liu X. et al. (2020) on 32 patients with varying disease severity has shown detectable IgM antibodies from day four and peaked at day 20, since the onset of the symptoms. At the same time, IgG antibodies appeared after day 7 with a peak on day 25. When compared to the disease severity, mild cases had peak IgM response earlier than in severe cases (day 17 vs day 21). Further, severe cases exhibited more robust IgG antibody response than mild cases, as will be discussed in the subsequent section C. In terms of the antibody response seen after symptom onset, a similar trend was shown by Liu X. et al. (2020) who detected IgM antibodies in SARS-CoV-2 infected patients between 3 and 6 days and IgG antibodies after day 8 of symptom onset, irrespective of the disease severity.
A study by Zhou P. et al. (2020) also found mean times of IgM, IgG, and neutralizing antibodies at 12, 14, and 11 days, respectively. These reports were consistent with the reports from Wu et al. (2020) in which neutralizing antibodies were detected starting from day 10. An elaborate antibody profile of 285 COVID-19 patients revealed 100% IgG and 94.1% IgM antibody response with a peak around the 3rd and 4th week after symptom onset, respectively (Long et al., 2020a). Thus, for a successful viral clearance, an adequate adaptive immune response is generated around 2nd week after symptom onset and peaks around the 3rd week for IgM and at the beginning of 4th week for IgG (Ni et al., 2020; Thevarajan et al., 2020; Wu et al., 2020; Zhao et al., 2020). Based on these and several other studies, it is evident that the antibody response is very dynamic in COVID-19 which may be dependent on the age, sex, genetic factors, underlying disease condition and most importantly, the type of assay used for serological testing (Guan et al., 2020; Hou et al., 2020). Overall, these initial reports unequivocally suggest an integral role of the regulated adaptive immune response in the early clearance of virus and thereby attenuation of the disease condition in almost 80% of the patients who show mild/moderate symptoms. On the other hand, in the rest, 20% severe and critically ill patients, disease symptoms positively correlate with the degree of lymphocytopenia, as will be discussed later in section C. A schematic representation of the functional immune response during COVID-19 is depicted in Figure 3.
FIGURE 3  Clearance of virus infected cells by engaging adaptive immune cells. Virus infected ATII cells activate the neighboring lung resident AMs by minimizing the CD200-200L interaction. Additional requisite activation signals are provided by DAMPs, viral derived PAMPs, and cytokines like IFN-γ. Activated AMs along with infected ATII derived molecules activate and recruit other innate immune cells, like circulating monocytes, dendritic cells, NK cells, and neutrophils which act in a coordinated manner to eventually recruit the adaptive effector immune cells like CTLs and CD4+T cells. These adaptive immune cells then specifically eliminate virus infected cells while minimizing the damage to the nearby uninfected cells. Thus, a well-coordinated and regulated adaptive immune response with help from innate immune cells is critical for initial antiviral response to limit the further spread of the virus. Green arrows indicate the cytokines released by the respective activated immune cells which activate other immune cells as well as mount an antiviral response by acting on lung epithelial cells. An immunological enigma still eluding researchers worldwide is how the majority of COVID-19 patients remain asymptomatic, and even some with high viral load (Lee S. et al., 2020). This dilemma can be partly explained based on the effective functional early immune response generated by the T and B cells. Mathew et al. (2020) used a multidimensional immunoprobing study and functionally characterized clinical features with immunological features. This study defined three immunotypes based on 50 clinical and 200 immune parameters. The immunotype 1 was positively associated with disease severity and had hyperactivated CD4+ and CD8+ T cells, with concomitant expression of exhaustion markers, indicating robust activation followed by the exhaustion of these cells. This immunotype may thus be vulnerable to cytokine storm, as discussed later in section “Cytokine Storm in COVID-19 Patients.” Immunotype 2 was associated with the presence of proliferating memory B cells with the optimal activation status of CD4+ and CD8+ T cells. This immunotype did not associate with disease severity. The immunotype 3 had no activation status of CD4+ and CD8+ T cells, and thus exhibited an inverse correlation with the disease severity. Overall, this study addressed some of the above questions that suggested that the presence of a regulated and functional adaptive immune response is key to preventing immunopathology. In a similar study, the activation status of T cells associated with disease severity (acute, moderate, and severe) (Sekine et al., 2020). The activation status of these T cells correlated with the presence of SARS-CoV-2 specific IgG antibodies in these patients.
Interestingly, T cells derived from convalescent mild and asymptomatic patients exhibited functional status when stimulated in vitro with SARS-CoV-2 specific antigens, suggesting the presence of well-regulated and functional T cell response in mild and asymptomatic convalescent patients. Thus, in patients with high viral load, an immunopathological state can be prevented if the adequate and regulated adaptive immune response is present in association with the proper interferon response. While in patients with compromised immune response, like in comorbid conditions, even a low viral load is sufficient to induce immunopathological changes, due to either ineffective immune response or uncontrolled hyper-activated response, as will be discussed in the subsequent sections.