Potent universal beta-coronavirus therapeutic activity mediated by direct respiratory administration of a Spike S2 domain-specific human neutralizing monoclonal antibody

Abstract

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) marks the third novel β-coronavirus to cause significant human mortality in the last two decades. Although vaccines are available, too few have been administered worldwide to keep the virus in check and to prevent mutations leading to immune escape. To determine if antibodies could be identified with universal coronavirus activity, plasma from convalescent subjects was screened for IgG against a stabilized pre-fusion SARS-CoV-2 spike S2 domain, which is highly conserved between human β-coronavirus. From these subjects, several S2-specific human monoclonal antibodies (hmAbs) were developed that neutralized SARS-CoV-2 with recognition of all variants of concern (VoC) tested (Beta, Gamma, Delta, Epsilon, and Omicron). The hmAb 1249A8 emerged as the most potent and broad hmAb, able to recognize all human β-coronavirus and neutralize SARS-CoV and MERS-CoV. 1249A8 demonstrated significant prophylactic activity in K18 hACE2 mice infected with SARS-CoV-2 lineage A and lineage B Beta, and Omicron VoC. 1249A8 delivered as a single 4 mg/kg intranasal (i.n.) dose to hamsters 12 hours following infection with SARS-CoV-2 Delta protected them from weight loss, with therapeutic activity further enhanced when combined with 1213H7, an S1-specific neutralizing hmAb. As little as 2 mg/kg of 1249A8 i.n. dose 12 hours following infection with SARS-CoV Urbani strain, protected hamsters from weight loss and significantly reduced upper and lower respiratory viral burden. These results indicate in vivo cooperativity between S1 and S2 specific neutralizing hmAbs and that potent universal coronavirus neutralizing mAbs with therapeutic potential can be induced in humans and can guide universal coronavirus vaccine development.

Structure and epitope of a neutralizing monoclonal antibody that targets the stem helix of β coronaviruses

“…(B) Binding constants for NMAbs binding to SARS‐CoV‐2 S (taken from Ref. [33]) and the SH‐FC fusion peptide.SH‐FC binding constants were derived from the sensorgrams in (A).…”

“…In both cases, the common aliphatic regions of MERS‐CoV Q1232 and SARS‐CoV‐2 K1149 sidechains bury significant amounts of surface area into the 1249A8 interface to maintain high affinity binding. In contrast to 1249A8 ( K D = 0.58 n m ), other C1 NMAbs tested exhibit reduced (S2P6, K D = 8.5 n m ) or essentially no affinity (CV3‐25 and CC40.8) for the MERS‐CoV S2 [33]. Analysis of modelled S2P6/MERS‐CoV SH and CC40.8/MERS‐CoV SH complexes show replacement of K1149 with Q induces steric clashes within the S2P6 and CC40.8 binding sites, consistent with their low or absent affinity for MERS‐CoV SH (Fig.…”

“…Binding studies were performed by capturing the NMAbs to CM-5 chip surfaces using a human antibody capture kit (Cytiva). Kinetic binding parameters were derived for the previously described stem helix FC fusion protein (SH-FC) consisting of SARS-CoV-2 SH residues 1131-1171 [33]. SH-FC was injected over NMAbs at four concentrations (32,8,4, and 1 nM) with a contact time of 240 s and a 300 s dissociation time.…”

“…To address this hypothesis, we previously reported a series of human S2-targeting MAbs, of which four derived from IGHV1-46/IGKV3-20 germline sequences, bound to OC43, SARS-CoV, SARS-CoV-2, SARS-CoV-2 VoC, as well as MERS-CoV [33]. One MAb, 1249A8, neutralized authentic SARS-CoV-2, VoC (delta and omicron), SARS-CoV, and MERS-CoV [33]. BNMAb 1249A8 targets the stem helix (SH) of β-CoV S proteins, as previously described for S2P6, which is also an IGHV1-46/ IGKV3-20 BNMAb [34].…”

Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that bind a conserved membrane proximal epitope of the spike

“…The S2 subunit is more conserved than S1 and, therefore, considered an attractive target for the development of neutralizing antibodies with broad anti-sarbecovirus potential. Several monoclonal antibodies that recognize conserved sites in the S2 subunit such as the stem helix or the fusion peptide of SARS coronaviruses have been described (6)(7)(8)(9)(10). In general, however, S2-specific monoclonal antibodies exhibit poor virus neutralizing activity.…”