key: cord-0922321-ssmw2jef
authors: Wang, Pengfei; Wang, Maple; Yu, Jian; Cerutti, Gabriele; Nair, Manoj S.; Huang, Yaoxing; Kwong, Peter D.; Shapiro, Lawrence; Ho, David D.
title: Increased Resistance of SARS-CoV-2 Variant P.1 to Antibody Neutralization
date: 2021-03-02
journal: bioRxiv
DOI: 10.1101/2021.03.01.433466
sha: 692b65b3ac03251730d310bf781437f54b70e0cd
doc_id: 922321
cord_uid: ssmw2jef

The relative resistance of SARS-CoV-2 variants B.1.1.7 and B.1.351 to antibody neutralization has been described recently. We now report that another emergent variant from Brazil, P.1, is not only refractory to multiple neutralizing monoclonal antibodies, but also more resistant to neutralization by convalescent plasma (6.5 fold) and vaccinee sera (2.2–2.8 fold). The P.1 variant threatens current antibody therapies but less so the protective efficacy of our vaccines.

(bamlanivimab) 9,10 , and CB6 (etesevimab) 10, 11 . As shown in Fig. 1a (left panel) and 55 Supplementary Fig. 2a , the neutralizing activities of three of the mAbs with EUA were 56 markedly or completely abolished against BZ∆10. The only mAb with EUA retaining its 57 activity was REGN10987. We next tested the neutralizing activity of eight additional RBD 58 mAbs, including ones from our own collection (2-15, 2-7, 1-57, & 2-36) 6 as well as S309 12 the specific mutations responsible for the observed pattern of neutralization, we then 72 tested these NTD mAbs against a panel of pseudoviruses, each containing only a single 73 NTD mutation found in P.1 (Supplementary Fig. 2b ). As expected, 5-24 ad 4-8 retained 74 activity against all single-mutation pseudoviruses. P26S only partially accounted for the 75 loss of activity of 4-18; L18F/T20N/D138Y contributed to the loss of activity of 2-17 and 76 4-19; and L18F/T20N/D138Y/R190S together resulted in the loss of activity of 5-7. 77 . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made

The copyright holder for this preprint this version posted March 2, 2021. ;

Overall, these neutralization results were consistent with the positions of the P.1 78 mutations on NTD in relation to the antibody epitopes (Supplemental Fig. 3a ). For 79 antibodies 5-24 and 4-8, the mutated residues on NTD were not part of their epitopes 80 (Supplemental Fig. 3b ). The drop in neutralization potency of 2-17 is explained by L18F 81 and T20N comprising a part of the epitope, while D138 is proximal to these two residues. 82 However, the loss or activity of 4-18 and 5-7 is not well explained structurally, because 83 their inactivity is likely due to the combined effect of different NTD mutations. was noted for every sample, but the magnitude of the loss was modest (2.8 fold, Moderna; 99 . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Overall, the SARS-CoV-2 P.1 variant is of concern because of its rapid rise to dominance 103 as well as its extensive spike mutations, which could lead to antigenic changes 104 detrimental to mAb therapies and vaccine protection. Here we report that P.1 is indeed 105 resistant to neutralization by several RBD-directed mAbs, including three with EUA. The 106 major culprit is the shared E484K mutation, which has emerged independently in over 50 107 lineages, including in B.1.526 that we 18 and others 19 have identified in New York recently. 108

As for the NTD-directed mAbs, the resistance profiles are markedly different for P. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made

The copyright holder for this preprint this version posted March 2, 2021. ; https://doi.org/10.1101/2021.03.01.433466 doi: bioRxiv preprint

Monoclonal antibodies, patients and vaccinees. Monoclonal antibodies, convalescent 185 plasma, and vaccinee sera were the same as previously reported 3

Plasmids encoding the single-mutation variants 187 found in P.1 and 10-mutation variant (BZ∆10) were generated by Quikchange II XL site-188 directed mutagenesis kit (Agilent)

SARS-CoV-2 spike variants were generated as previously described 3

Neutralization assays were performed by incubating pseudoviruses with serial dilutions 191 of mAbs or heat-inactivated plasma or sera, and scored by the reduction in luciferase 192 gene expression as previously described 3

Materials used in this study will be made available but may require 194 execution of a material transfer agreement

This study was supported by funding from Andrew & Peggy 197

Barbara Picower and the JPB Foundation

The study was conceptualized by D.D.H. The experiments were

The manuscript was 203 written by