Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein

Abstract

Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike glycoprotein that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera , including the nine human coronaviruses, through recognition of a conserved motif that includes the S2´ site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice expressing human ACE2 against infection when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae , including SARS-CoV-2 variants.

Targetable elements in SARS-CoV-2 S2 subunit for the design of pan-coronavirus fusion inhibitors and vaccines

“…More recently, a FP-targeted nAb, fp.006, isolated from COVID-19 convalescents, binds to a core epitope (S 813 RRSFIEDLLFNK 825 ) containing the S2ʹ site and the helical FP segment. 54 Structural analysis further revealed that R815, E819 and F823 are the key residues recognized by fp.006, which is similar to FP-targeted nAbs (e.g., COV44-79 and COV44-79). The epitope peptide bound to fp.006 is folded as an amphipathic α-helix in the Fab groove.…”

“…4a, b ). 51 – 54 The representative broad-spectrum nAbs targeting fusion peptide are summarized in Table 1 .…”

“…The epitope peptide bound to fp.006 is folded as an amphipathic α-helix in the Fab groove. 54 In addition, fp.006 cross-reacts with a variety of α- and β-CoV spike proteins and cross-inhibits pseudovirus infection of SARS-CoV-2 ancestral virus and its VOCs in vitro, and prevents SARS-CoV-2 infection in vivo, suggesting that it may be a promising antiviral drug candidate to combat the ongoing COVID-19 pandemic. 54 …”

Longitudinal Variations in Antibody Responses against SARS-CoV-2 Spike Epitopes upon Serial Vaccinations

“…In this study, of the five peptides showing boosted responses, two overlapped the N- and C- termini of the receptor-binding domain (RBD), while the remaining three boosted epitopes were all located outside the RBD region, but their recognition strongly correlated with NT 50 . Consistent with the apparent importance of these non-canonical/non-RBD responses, a recent study described highly conserved coldspots across the S protein that are maintained in all SARS-CoV-2 variants that elicited neutralizing antibodies to five epitopes that overlap with the VirScan-defined vaccine-boosted epitopes (P1–P4) [ 48 ]. The exception was an epitope [aa 812–868] near the fusion peptide in the S2 subunit that did not show a stepwise increase in magnitude across post-vaccination timepoints.…”

Understanding the SARS-CoV-2 Virus Neutralizing Antibody Response: Lessons to Be Learned from HIV and Respiratory Syncytial Virus

“…Second, there is concern over pseudotype assays that, for the convenience of scale and automation, are used as surrogates for the neutralization of SARS-CoV-2, as the distributions of S trimers on VSV and authentic SARS-CoV-2 are very different, as mentioned above [ 14 , 15 ]. The S protein-VSV pseudotype was variously shown to give neutralization that was statistically close to the neutralization of an infectious SARS-CoV-2 laboratory-adapted virus of that time [ 34 ] or was 21-fold more sensitive [ 22 ].…”