Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes

The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following SARS-CoV-2 infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor-binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an N-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multi-donor class of “public” antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that “public” NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.

The SARS-CoV-2 spike ectodomain (S-ECD) folds into a multidomain architecture (1,2) and includes the RBD, which is essential for viral infectivity, and the structurally adjacent NTD, which plays an uncertain role. Humoral immunity to the spike (S) surface glycoprotein can correlate with protection, (3) and it is the primary antigenic target for most vaccines and monoclonal antibodies (mAbs). That the B cell repertoire can recognize multiple spike epitopes is supported by extensive single-cell cloning campaigns (4)(5)(6)(7)(8)(9). However, the identity, abundance, and clonality of the IgG plasma antibody repertoire and the epitopes it may target are not known (10)(11)(12). Divergence between the two repertoires is biologically plausible (13)(14)(15)(16)(17) and the evidence in COVID-19 includes a paradoxical disconnect between virus-neutralizing IgG titers and RBD-specific B cell immunity (6,11,18,19).
To analyze the IgG repertoire, blood was collected during early convalescence from four seroconverted study subjects (P1-P4) who experienced mild COVID-19 disease that manifested with plasma virus-neutralization titers in the lowest quartile (P1 and P3), the second highest quartile (P2), or the highest quartile (P4) compared to a larger cohort (table S1 and fig. S1). The lineage composition and relative abundance of constituent IgG antibodies comprising the plasma response to either intact stabilized S-ECD (S-2P (1)) or RBD was determined using the Ig-Seq pipeline (13,14,20) that integrates analytical proteomics of affinity purified IgG fractions with peripheral B cell antibody variable region repertoires (BCR-Seq).
IgG lineages detected by Ig-Seq in the S-ECD fraction but absent from the RBD fraction were deemed to be reactive with spike epitopes outside the RBD. In subject P3, we detected six IgG lineages that bound to S-ECD (Fig. 1A). Four of these (Lin.1 to Lin.4) accounted for 93.5% abundance of the total plasma IgG S-ECD response and exhibited extensive intralineage diversity ( fig. S2) indicative of clonal expansion and selection. Notably, the top three lineages (Lin.1 to Lin.3; Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following SARS-CoV-2 infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor-binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an N-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multi-donor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape. >85% abundance) all bound to non-RBD epitopes (S2 subunit or NTD). Bulk serology ELISAs recapitulated the Ig-Seq result and demonstrated similarly high levels of non-RBD-binding IgG (P>0.05) (Fig. 1B), confirming that RBD-binding plasma antibodies comprise only a minor proportion of all spikebinding IgG in naturally infected individuals (21). In all four subjects, the detected plasma IgG repertoire to S-ECD was oligoclonal, comprising only 6-22 lineages, with the top-ranked lineage comprising 15 to 50% total abundance. On average, 84% of the anti-S-ECD plasma IgG repertoire bound to epitopes outside the RBD (Fig. 1C), a finding consistent with data from single B cell analyses (22), and the most abundant plasma IgG lineage in all donors recognized a non-RBD epitope (Figs. 1A and 2A and fig. S3). Binding analysis of P3 mAbs CM29-CM32 representing the most expanded clones within each of lineages Lin.1 to Lin.4 showed that CM29 (Lin.1) recognizes the S2 subunit (KD = 6.6 nM), CM30 and CM31 (Lin.2 and Lin.3 with KD = 0.8 and 37.7 nM, respectively) were specific for the NTD, and CM32 (Lin.4) bound the RBD (KD = 6.0 nM), as expected from the Ig-Seq differential affinity purifications ( Fig. 1A and table S2). CM30 potently neutralized authentic SARS-CoV-2 in vitro (IC50 = 0.83 μg/ml), CM32 was slightly less potent (2.1 μg/ml), whereas CM29 and CM31 showed minimal neutralization activity (Fig. 1D).
We then determined the capacity of mAbs CM29-CM32, singly and in combination, to confer prophylactic protection in vivo to virus challenge using the MA10 mouse model of SARS-CoV-2 infection (23,24). Even though the RBD-directed mAb CM32 could neutralize authentic virus in vitro and had relatively high antibody-dependent cellular phagocytosis (ADCP) activity ( fig. S4), it did not protect in vivo (fig. S5), possibly due to amino acid changes in the MA10 virus. Similarly, no protection was observed for the non-neutralizing S2directed mAb CM29 or non-neutralizing NTD-directed mAb CM31. The neutralizing mAb CM30, derived from the topranking NTD-targeting IgG lineage (21% abundance), was the sole plasma antibody that conferred complete protection to MA10 viral challenge (Fig. 1, E and F, and fig. S5). Interestingly, administration of a cocktail comprising the top non-RBD plasma mAbs CM29-CM31 (>85% of the IgG plasma lineages to S-ECD; Fig. 1A) showed the most robust protection and lung viral titers below the limit of detection (LOD) in high viral load challenge (10 4 PFU).
To better understand the IGHV1-24 interactions with the spike NTD, we determined a cryo-EM structure of CM25 Fabs bound to trimeric S-ECD ( Fig. 4A and figs. S7 and S8). Focused refinement of the CM25-NTD interface resulted in a 3.5-Å reconstruction that revealed a heavy-chain-dominant mode of binding, with substantial contacts mediated by interactions between the three CDRs and the N3 and N5 loops of the NTD (Fig. 4B). The light chain contributes only 11% (86 Å 2 ) of the total CM25 binding interface, mainly through a stacked hydrophobic interaction between CDR-L2 Tyr55 and Pro251 within the N5 loop. Unique germline IGHV1-24 residues contribute 20% (149 Å 2 ) of the total binding interface. CDR-H1 interacts extensively through hydrogen bonds and contacts between hydrophobic residues, including a salt bridge formed between the conserved Glu36 residue and the N5 loop residue Arg246 (Fig. 4C). The common IGHV1-24 Phe56 residue in CDR-H2 forms a pi-cation interaction with Lys147 in the N3 loop (Fig. 4C). CM25 contains a 14-aminoacid CDR-H3 loop that contributes 35% (261 Å 2 ) of the total interface, including the AV aliphatic motif found in all but one of the convergent IGHV1-24 NTD-binding mAbs. Ala109 and Val110 are buried at the interface in a binding pocket framed by the N3 and N5 loops. A comparison of CM25 with an extant structure of an IGHV1-24 NTD-binding antibody isolated by B cell cloning, 4A8 (4), revealed that the AV dipeptide interaction is structurally conserved, and the 21 amino-acid CDR-H3 of 4A8 extends along the outside of the NTD, contributing three additional contacts and 46% (415 Å 2 ) of the total binding interface (Fig. 4D). Both structures show extensive contacts between the heavy chain of the Fabs and the NTD N3 and N5 loops. The Glu36-Arg246 salt bridge and an identical CDR-H2 contact between Phe56 and Lys147 are conserved in the 4A8-NTD interface. SARS-CoV-2 variants of concern contain mutations in the NTD N3 and N5 loops, including Y144/Y145Δ and K147E (UK lineage B.1.1.7), W152C (California B.1.429), and 242-244Δ or R246I (South Africa B.1.351). Alanine substitutions at several of these positions ablated binding or reduced affinity more than fivefold by public IGHV1-24 antibodies as exemplified by 4A8, CM17, and CM25 ( Fig. 4E and fig. S9), a result consistent with the CM25-NTD and 4A8-NTD structures. Additionally, we confirmed that an engineered N3-N5 doublemutant and native B.1.351 (28) both evade neutralization by mAbs CM25 and 4A8 (Fig. 4F). Thus, mutations in SARS-CoV-2 variants confer escape from public neutralizing anti-NTD antibodies.
In conclusion, we find that the convalescent plasma IgG response to SARS-CoV-2 is oligoclonal and directed overwhelmingly toward non-RBD epitopes in the S-ECD. This includes public, near-germline, and potently neutralizing antibodies against the NTD. The degree to which public anti-NTD antibodies contribute to protection is likely related to their relative levels in plasma, which can be dominant in some individuals. Our finding that mutations present in circulating SARS-CoV-2 variants can impair or ablate binding and neutralization by public anti-NTD antibodies may constitute a mechanism of viral escape in a subset of the population. Numerous other NTD mutations-which overlap with the structural epitope recognized by the public IGHV1-24 antibody class-have been described in additional circulating variants, in laboratory escape mutants, and in immunocompromised patients (12,(29)(30)(31)(32)(33). J.J.L., and G.C.I.). Data and materials availability: FASTQ VH and VH:VL sequence files have been deposited in the NCBI Sequence Read Archive with accession numbers PRJNA422864. The monoclonal antibodies have been deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank/) with accession numbers MZ049539 to MZ049552. Coordinates for the CM25 Fab in complex with trimeric spike ectodomain have been deposited to the Protein Data Bank as PDBID:7M8J. Cryo-EM maps have been deposited to the Electron Microscopy Data Bank under accession code EMD-23717. These structural data are presented in Fig. 4, table S4, and figs. S7-S8. All other data are available in the main text or the supplementary materials. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.