Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality

Abstract

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.

Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein

“…We include the clinically-used REGN10933 (casirivimab) and REGN10987 (imdevimab) 33,34 , LY-CoV555 (bamlanivimab) 35 , and S309 (sotrovimab) 36,37 antibodies. We also tested four mAbs with quaternary RBD binding modes 27,31,38 (C002, C144, 2-43, and N3-1) and the pan-variant mAb S2H97 31,32,37,38 . Together, this panel provides a comprehensive overview of neutralizing antibody escape by variant spike proteins.…”

Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor

“…Previously reported antibodies with a quaternary epitope on the SARS-CoV-2 RBD generally bind to two down RBDs to trap the S trimer in its closed state ( 25 , 53 , 54 ). A notable exception is the antibody N3-1 from a synthetic SARS-CoV-2 convalescent repertoire, which has a down RBD epitope similar to E7 involving F486 and Q493 but with different residues forming the up RBD portion of its epitope similar to the S2X259 epitope ( 55 ).…”

Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

“…This procedure identified 6650 COVID-associated clonotypes when using only CDR3 aa identity for the definition of sharing (CDR3 sharing, S1 Table ), and 2502 if we impose V and J gene identity (full amino-acid sequence sharing, S2 Table ). To validate their COVID specificity, we cross-checked this list against a database of antibodies with reported specificity for SARS-CoV-2, which we built from the literature (compiled in S3 Table) [35][36][37][38][39][40][41][42][43][44][45][46][47][48][49]. Among the COVID-associated CDR3, 175 sequences (� 2.6% of the overshared sequences) had at least a 90% Levenshtein similarity (one or two mismatches or gaps) in amino acid content with the CDR3 of reported SARS-CoV-2 binding antibodies.…”