key: cord-0948410-s7mcnbpq
authors: Liu, Hejun; Kaku, Chengzi I.; Song, Ge; Yuan, Meng; Andrabi, Raiees; Burton, Dennis R.; Walker, Laura M.; Wilson, Ian A.
title: A recurring YYDRxG pattern in broadly neutralizing antibodies to a conserved site on SARS-CoV-2, variants of concern, and related viruses
date: 2021-12-17
journal: bioRxiv
DOI: 10.1101/2021.12.15.472864
sha: d3106a68570545d78c577297b060478b122c071b
doc_id: 948410
cord_uid: s7mcnbpq

Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally and functionally characterized a potent human antibody ADI-62113 that also neutralizes SARS-CoV- 2 variants of concern and cross-reacts with many other sarbecoviruses. A YYDRxG motif encoded by IGHD3-22 in CDR H3 facilitates targeting to a highly conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences identified many antibodies with broad neutralization activity against SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to counteract sarbecoviruses. These findings also suggest an epitope targeting strategy to identify potent and broadly neutralizing antibodies that can aid in the design of pan-sarbecovirus vaccines and antibody therapeutics. Short Summary Decryption of a recurrent sequence feature in anti-SARS-CoV-2 antibodies identifies how potent pan-sarbecovirus antibodies target a conserved epitope on the receptor binding domain.

somatic mutations adjacent to the serine codon ( Figure 4A-B) , which may be a lesion site created 169 during antibody affinity maturation and serve as a prerequisite of converting S100b to R100b in 170 germinal center as somatic hypermutation of A:T pairs requiring additional mutagenic process at 171 neighboring sites (Di Noia & Neuberger, 2007; Franklin & Blanden, 2006) . In addition to the S100b 172 to R100b mutation in ADI-62113, mutation in a neighboring codon leads to somatically mutated no interaction with RBD indicated by the paucity of side-chain electron density ( Figure S2C ). Thus, 175 VH R100c is not absolutely required since a serine at the same position does not impact binding, 176 as observed in COVA1-16 ( Figure S1B ). N additions (N1 and N2) at both ends of IGHD3-22 during 177 V(D)J recombination seems important in determining the length of CDR H3 and the RF of IGHD3-and CDR H3 length might impact neutralization potency. Overall, our data suggest YYDRxG 219 antibodies are broadly neutralizing antibodies for counteracting SARS-CoV-2 VOCs. Meanwhile, 220 they are strongly associated with cross-species neutralization as eight of 10 tested antibodies 221 exhibit cross-neutralization activity ( Figure 5A and Table S2 ).

Of the YYDRxG antibodies against SARS-CoV-2, more than two thirds have only sequence 224 information available and have not been extensively evaluated or characterized ( Figure 3A and 225 Table S3 ). The strong correlation between the YYDRxG motif with experimentally characterized 226 neutralizing antibodies suggested that these antibodies may broadly neutralize SARS-CoV-2 227 variants and potentially other sarbecoviruses, as observed in the antibodies that have been tested 228 in the neutralization assay ( Figure 5A and Table S2) Overall, we report here on structural characterization of a cross-neutralizing antibody, ADI-62113, 247 that revealed a highly similar binding mode to the SARS-CoV-2 RBD that was first observed in 248 COVA1-16 (Liu et al., 2020). We found that antibody binding to a very highly conserved site on 249 the RBD appears to be determined primarily by the YYDRxG hexapeptide encoded by 250 in CDR H3. The extensive interaction with the conserved CR3022 site on the RBD and 251 stabilization of the CDR H3 local structure by a β-bulge make the YYDRxG pattern a desirable 252 feature for specific RBD recognition (Figure 2 and Figure S2A ), which appears to be even more (Figure 3C and Table S2 -3). The strong preference for one of the three possible reading frames 276 of IGHD3-22, the apparent requirement for somatic hypermutation at a specific position in this 277 region, local structural constraints, and the requirement for an extended length of CDR H3, make 278 these antibodies less abundant compared to some other neutralizing antibodies targeting SARS-

CoV-2 RBD. Our data and analysis show that antibodies with a YYDRxG pattern in their CDR H3 280 are more likely to target the highly conserved surface in sarbecovirus RBDs and to neutralize 281 SARS-CoV-2 VOCs, emerging variants, and SARS-CoV, indicating a common convergent 282 solution used by the human humoral immune system to counteract sarbecoviruses.

Finally, the high correlation between the presence of a YYDRxG pattern and broad 284 neutralization activity support its use as a sequence signature of broadly and cross-neutralizing 285 antibodies targeting this highly conserved site on the SARS-CoV-2 RBD as well as other related 286 coronaviruses. Since antibodies containing a YYDRxG feature can be elicited by both natural 287 infection and vaccination, interrogation of these signature sequences in serum can also serve as 288 biomarkers to evaluate vaccine breadth and guide rational design of next-generation vaccines. 

The dashed box indicates potential space constraints for the glycine in the YYDRxG motif in CDR

H3 as shown in Figure 2D . following the glycine residue (i+3) in the β-turn and comparison with a standard β-hairpin also 352 with a type 1 β-turn at its tip (PDB ID: 4H5U). Amino-acid side chains are simplified as gold

spheres. Arrows indicate the register change between the two motifs due to an additional residue 354 in the β-hairpin in ADI-62113. D. Limited space between residue VH G100d and RBD favors a 355 glycine residue at this position in the β-bulge. A hydrogen bond is formed between the VH G100d 356 carbonyl oxygen and S383 hydroxyl in the RBD. A π-π interaction is formed between VH Y100 and 357 the peptide backbone of 382VS383 of SARS-CoV-2 RBD. Table S2 . Table S4 . Table   622 S2 (tested against SARS-CoV-2) and YYDRxG antibodies against SARS-CoV-2 with no available antigen binding or neutralization 

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Prospective mapping of viral mutations that escape 1019 antibodies used to treat COVID-19

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Antibody resistance of 1059 SARS-CoV-2 variants B.1.351 and B.1.1.7

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IgBLAST: an immunoglobulin variable 1120 domain sequence analysis tool

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