6  SARS-CoV-2: from 2019 to present
The novel SARS-CoV-2 coronavirus, first appeared in Wuhan, China, in December 2019, is creating a pandemic over the world with the number of confirmed cases reached 3,529,408, of which 248,025 were dead up to the 4th May 2020 [1]. Phylogenetic analysis of SARS-CoV-2 demonstrated similarity with SARS-CoV and bat-derived SARS-like coronaviruses (SL-CoVs) with 79.6% and 88% sequence identity, respectively. They belong to lineage B of the beta coronavirus genus [73,74]. SARS-CoV-2 seems to be more contagious but less pathogenic than SARS-CoV [75]. COVID-19 is a self-limiting disease in >80% of patients. Same as Spanish influenza viruses, SARS-CoV and SARS-CoV-2 induce a “cytokine storm” but to different degrees. The difference of some conserved interferon antagonists and of inflammasome activators explains their abilities to modulate antiviral and proinflammatory responses.
Along with the race of finding therapeutic treatment, nAbs and vaccine development are also important to control the spread in the long run. SARS-CoV-2 entries the host via the binding of its spike S protein to the ACE2 receptor - sharing receptor, but with higher affinity than SARS-CoV S [76], suggesting a basis for the greater human-to-human transmission of SARS-CoV-2 [51,77].
S protein of SARS-CoV-2 composed of 1273 amino acids [76] uses its N-terminal S1 subunit to bind ACE2 receptor with a better affinity than SARS-CoV S glycoprotein for entry [78]. Effectively, S1 subunit divides into an N-terminal domain (NTD) and a receptor-binding domain (RBD). The latter is necessary for viral binding and a potential target for nAbs. During infection, SARS-CoV-2 first binds the host cell through interaction between its S1-RBD and ACE2, triggering conformational changes in the S2 subunit that is indispensable for virus fusion and entry into the target cell [79,80]. Some recent studies also confirmed that RBD is a conformational epitope [78]. Antibodies binding RBD may sterically hinder binding to the nearby peptide S14P5 of ACE2 receptor, thereby abolishing virus infection [34].
SARS-CoV-2 nAbs could be detected in patients from 10 to 15 days after symptoms onset and the positive rate for IgG reached close to 100% around 20 days [81,82] with the highest level during day 31–40 since onset. Some patients (5.7%) had neutralizing Abs titers under the detectable level (ID50: <40) [83]. The level of IgG antibodies was different between gender, age and clinical classification. The average IgG antibody level in female patients was higher than in male patients [84]. Patient over 40 years old developed higher levels of SARS-CoV-2 specific nAbs than the younger persons. Patients with a worse clinical classification had a higher antibody titer [83]. This remark is useful to select a research candidate and to save research time. The passive antibody therapy, such as plasma fusion containing polyclonal antibodies from COVID-19 neutralized patients has been tested. This method was tested as an option to treat other viruses such as influenza, Ebola or SARS-CoV [[85], [86], [87], [88], [89]]. The lack of human sera, and the possibility of contamination with other infectious agents limit this strategy. However, several groups have reported some positive results demonstrating the potential of this approach. After one dose of 200 mL of convalescent plasma derived from recently recovered donors with the neutralizing antibody titers above 1:640, the patients with SARS-CoV-2 positive revealed an improvement. Among ten patients, seven patients were virus-negative post transfusion [90]. Whereas in another study, among 5 patients received transfusion with convalescent plasma with a neutralization titer >40, 3 have been discharged from the hospital (length of stay: 53, 51, and 55 days), and 2 are in stable condition at 37 days after transfusion [91]. More studies might brighter this approach but evaluation in clinical trials are also still far from a bold conclusion.

6.1  Effect of cross-reactive antibodies on SARS-CoV-2 pandemic
Due to the high similarity of S proteins from SARS-CoV and MERS-CoV [73], their specific cross-nAbs were tested against SARS-CoV-2 infection in the COVID-19 outbreak. Serum Abs from recovered SARS-CoV patients could efficiently cross-neutralize SARS-CoV-2 but with lower efficiency as compared to SARS-CoV [92]. Cross-reactive Abs against SARS-CoV-2 S protein mostly target non-RBD regions [93]. Using simulation technique, the binding of five Abs against SARS-CoV, six Abs anti-MERS-CoV to RBD of SARS-CoV-2 was predicted with Rosetta antibody-antigen docking protocols. The amino acid position 445–449 (VGGNY) and 470–486 (TEIYQAGSTPCNGVEGF) were found to be conserved in SARS-CoV-2. Moreover, in addition to the amino acid positions 71–77 (GTNGTKR) in the NTD region of the S protein, aa 445–449 and 470–486 are potential for further development [94].
The difference between RBD of SARS-CoV and SARS-CoV-2 is located at the C-terminus residues. This change has an important impact on the cross-reactivity of nAbs. This difference was observed using bioinformatic approaches of epitope analysis. The antibody epitope score of SARS-CoV-2 is higher than SARS-CoV. Moreover, compared with the conserved regions, the non-conserved regions had a significantly higher antibody epitope score indicating that non-conserved regions of spike proteins are much more antigenic. The non-conserved regions also showed significantly higher surface epitope accessibility scores suggesting an easier accessibility for antibody recognition of non-conserved regions. The divergence of spike proteins is considered as a major change in the antibody epitopes. The search for SARS-CoV-2 requires more effort than simply screening SARS-CoV antibodies [95].
Antibody response to RBD is viral species-specific. Effectively, none of the found SARS-CoV-2 antibodies nor the infected plasma cross-reacted with RBDs from either SARS-CoV or MERS-CoV. In a study, 206 monoclonal antibodies specific to the RBD SARS-CoV-2 were identified in eight patients. These mAbs are different in: antibody heavy and light chains, antibody clones, CDR3 length… which lead to different binding and neutralizing capacities. ACE2 is out-competed with almost 100% efficacity by some mAbs such as P2B-2F6 and P2C-1F11. Interestingly the latter and a moderate antibody P2C-1C10 seems to target the different epitopes, and they could be combined for synergistic antiviral effect [96]. CR3022, a SARS-CoV RBD-specific antibody, can bind strongly with a kd of 6.3 nM to an epitope on RBD that does not overlap with the SARS-Cov-2 ACE-2 binding site [34]. Despite its strong binding, CR3022 could not neutralize SARS-CoV-2 [97].
S1 is a specific antigen for SARS-CoV-2 diagnostics [98]. The S1 subunit of SARS-CoV or SARS-CoV-2 has four core domains S1A through S1D. The human 47D11 antibody binds the S1B of both viruses, without competing with S1B binding to ACE2 receptor expressed at the cell surface, and showed cross-neutralizing activity by an unknown mechanism that is different from receptor binding interference [99]. An immunogenic domain in the S2 subunit of SARS-CoV S (aa 1029–1192) was highly conserved in several strains of SARS-CoV-2. Four murine monoclonal Abs, 1A9, 1G10, 2B2 and 4B12, against this S2 subunit of SARS-CoV can also cross-reactive with the S protein of SARS-CoV-2. Interestingly, 1A9 can strongly bind the S2 subunit of SARS-CoV-2 through a novel epitope (aa 1111–1130) and can detect S protein in SARS-CoV-2 during infection [100]. This epitope also overlaps with one of two cytotoxic T-lymphocyte epitopes (aa 884–891 and 1116–1123) of SARS-CoV S2 subunit [101]. 1A9 is therefore suggested to induce both humoral and cellular immune responses against SARS-CoV and SARS-CoV-2.
In a serologic cross-reactivity test, Khan et al. found out that 4 out of 5 showed high IgG seroreactivity across the 4 common human coronaviruses but all showed low IgG seroreactivity to SARS-CoV-2, SARS-CoV, and MERS-CoV [102]. The weak cross-immunity against SARS-CoV-2 from others betacoronaviruses, such as HCoV-OC43 and HCoV-HKU1, could restraint the transmission of SARS-CoV-2 but a resurgence is possible in the future [103]. Moreover, spike- and non-spike specific CD4+ T cell responses were detectable not only in SARS-CoV-2 infected patients but also in uninfected individuals. If there is an absence of antibody cross-reactivity, T lymphocyte cross-reactivity present in 50% of cases will be responsible for the epidemiological evolution of SARS-CoV-2 infection [104].

6.2  Anti-SARS-CoV-2 specific antibodies
Up to this moment, only few tests of specific Abs against SARS-CoV-2 have been reported. 311mab-31B5 and 311mab-32D4 human monoclonal Abs could strongly and specifically bind the RBD protein. These mAbs could efficiently block SARS-CoV-2-ACE2 interaction and neutralize pseudovirus entry into host cells ectopically expressing ACE2 [105].
Peptides S14P5 and S21P2 in the two distinct peptide pools S14 and S21 from SARS-CoV-2 S library were strongly detected in COVID-19 patients but not in SARS-CoV patients by using pools of overlapping linear peptides and functional assays [78]. With the data from antibodies depletion assays, researchers indicated that S14P5 and S21P2 were necessary for SARS-CoV-2 neutralization. Moreover, pool S51 contains very conserved fusion peptide in coronavirus [106,107] and is partially overlapped in the sera of SARS-CoV and SARS-CoV-2 patients. These results suggested that S51 may be a potential pan-coronavirus epitope. Sera from recalled SARS-CoV patients could neutralize SARS-CoV, but not the SARS-CoV-2 pseudotyped lentiviruses [78].
In an effort to screen a set of B cell and T cell epitopes of SARS-CoV toward to the spike S and nucleocapsid (N) proteins of SARS-CoV-2, 27 epitope-sequences were identical within SARS-CoV-2 proteins among 115 T cell epitopes. However, 19 out of 27 epitopes are associated with five distinct MHC alleles (at 4-digit resolution): HLA-A*02:01, HLA-B*40:01, HLA-DRA*01:01, HLA-DRB1*07:01, and HLA-DRB1*04:01. For B cell epitopes, they found 49 identical match epitope-sequences that have potential for developing effective vaccines to combat the SARS-CoV-2 [108]. Based on the sequence of the spike glycoprotein, seven epitope residue/regions (491–505, 558–562, 703–704, 793–794, 810, 914, and 1140–1146) in the surface glycoprotein were predicted to be associated with a robust immune response to SARS-CoV-2 [30]. Other candidate epitopes need to be confirmed [95,108].
Using the memory B cells from a survivor who was SARS-CoV infected in 2003, one nAb anti-RBD named S309 was found to bind to SARS-CoV-2 without interfering ACE2 binding. Besides, S309 could recognize a N343-glycan epitope that is distant from the RBM of SARS-CoV-2. Interestingly, N343-glycan of SARS-CoV-2 corresponds to SARS-CoV N330 and they are highly conserved. S309 potently neutralized both pseudotyped SARS-CoV and SARS-CoV-2 and also the authentic SARS-CoV-2 [109].
Using machine learning approaches with the data from other virus outbreaks, some synthetic nAbs named C3, C7, C14, C17, C18, Co1, Co2 and Co4 showed a potential to against SARS-CoV-2. The authors also confirmed that the mutations of Methionine and Tyrosine could increase the affinity of antibody-target binding [110].
19 potential immunogenicity B-cell epitopes, including 2 epitopes located within the RBD region were reported using in silico analysis. 17 of them have >14 amino acids. The B-cell epitopes which had highest score in this study is the 1052-FPQSAPH-1058 located at position 1052aa of S protein. 499 T-cell epitopes bound 34 most popular HLA alleles in the Chinese population were also found. Around 30 candidate vaccine peptides in which 5 peptides located within the RBD region and 17 of them contained both B- and T-cell epitopes, were designed [111]. These vaccine candidates are theoretically able to induce either specific humoral or cellular immune against SARS-CoV-2.
A panel of five humanized single domain antibodies (sdAbs) or nanobodies, 1E2, 2F2, 3F11, 4D8 and 5F8, was recently discovered. These sdAbs bound SARS-CoV-2 tightly but not SARS-CoV, except for 5F8 could bind both viruses but with weaker affinity to SARS-CoV. They also showed neutralization activity against both pseudotyped and authentic SARS-CoV-2. 1E2, 3F11 and 4D8 completely prevented SARS-CoV-2 RBD-ACE2 binding but this effect of 2F2 and 5F8 was only partial. Interestingly, the fusion of the human IgG1 Fc to these sdAbs improved their neutralization activity by 10- to 80-fold [112].
Due to the lack of repairing mechanism of RNA virus replicase complex, SARS-CoV-2 mutations frequently occur during viral replication [111]. The genetic drifts of SARS-CoV-2 are a selective evolution toward less immunogenicity for host immune surveillance by T- or B-cells. The latter appearing strains are less immunogenic than earlier ones [113]. Antigenic drift is also reported in the COVID-19 pandemic. The highly prevalent 23403A > G (p.D614G) variant in the European population may result in vaccine mismatches with little protection to that group of patients [114,115].
Though SARS-COV-2 genome has a much lower mutation rate and genetic diversity than SARS, some of its mutations attract the special attention of scientists. Single amino acid mutation R408I in RBD can reduce the affinity of ACE2 receptor binding [115] that leads to a low or ineffective vaccine for the future epidemic. Effectively, sequence alignment showed that this 408R is strictly conserved in SARS-CoV-2, SARS-CoV. 408R located at the interface between RBD and ACE2, but positioned relatively far away from ACE2, does not have direct interaction with ACE2. 408R can form a hydrogen bond with the 90 N of ACE2. This hydrogen bond is suggested to contribute to the high binding affinity of ACE2 binding [115].