Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers

Abstract

A fraction of COVID-19 convalescent individuals mount a potent antibody response to SARS-CoV-2 with cross-reactivity to SARS-CoV-1. To uncover their humoral response in detail, we performed single B-cell analysis from 10 SARS-CoV-2 elite neutralizers. We isolated and analyzed 126 monoclonal antibodies, many of which were sarbecovirus cross-reactive, with some displaying merbecovirus- and embecovirus-reactivity. Several isolated broadly neutralizing antibodies were effective against B.1.1.7, B1.351, B.1.429, B.1.617, B.1.617.2 variants and 19 prominent potential escape sites. Furthermore, assembly of 716,806 SARS-CoV-2 sequences predicted emerging escape variants, which were also effectively neutralized. One of these broadly neutralizing potent antibodies, R40-1G8, is a IGHV3-53 RBD-Class-1 antibody. Remarkably, Cryo-EM analysis revealed that R40-1G8 has a flexible binding mode, targeting both ‘up’ and ‘down’ conformations of the RBD. Given the threat of emerging SARS-CoV-2 variants, we demonstrate that elite neutralizers are a valuable source for isolating ultrapotent antibody candidates to prevent and treat SARS-CoV-2 infection.

Potent Human Broadly SARS-CoV-2 Neutralizing IgA and IgG Antibodies Effective Against Omicron BA.1 and BA.2

“…Comparison of immunoglobulin gene features with IgG + memory B cells from healthy controls (Prigent et al, 2016) revealed an increased usage in the SARS-CoV-2 spike-specific B-cell repertoire of rearranged V H 3V λ 3 (p=0.0047) and V λ 3/J λ 2 (p=0.0019), J H 4 (p=0.0312), and J κ 4 (p=0.0387) genes, as well as IgG1 subclass (p=0.0001) ( Figures 2H and S2 ; Table S1 ). Anti-spike antibodies were also enriched in V H 1-24/-69 and V H 3-30/-33 genes ( Figure S2J ) as previously observed (Brouwer et al, 2020; Kreer et al, 2020; Vanshylla et al, 2022), and had reduced CDR H 3 positive charges (p=0.0001) and somatic mutations in IgH (9.5 vs 19.2, p<0.0001) and Igλ (6.8 vs 12.4, p<0.0001) ( Figures 2H, 2I , and S2H ; Table S1 ). Certain antibody clones were shared among several of the COVID-19 convalescents ( Figure 2J ), demonstrating further the inter-individual convergence of antibody responses to SARS-CoV-2 as observed by others (Brouwer et al, 2020; Chen et al, 2021; Galson et al, 2020; Kreye et al, 2020; Nielsen et al, 2020; Robbiani et al, 2020; Vanshylla et al, 2022).…”

“…Anti-spike antibodies were also enriched in V H 1-24/-69 and V H 3-30/-33 genes ( Figure S2J ) as previously observed (Brouwer et al, 2020; Kreer et al, 2020; Vanshylla et al, 2022), and had reduced CDR H 3 positive charges (p=0.0001) and somatic mutations in IgH (9.5 vs 19.2, p<0.0001) and Igλ (6.8 vs 12.4, p<0.0001) ( Figures 2H, 2I , and S2H ; Table S1 ). Certain antibody clones were shared among several of the COVID-19 convalescents ( Figure 2J ), demonstrating further the inter-individual convergence of antibody responses to SARS-CoV-2 as observed by others (Brouwer et al, 2020; Chen et al, 2021; Galson et al, 2020; Kreye et al, 2020; Nielsen et al, 2020; Robbiani et al, 2020; Vanshylla et al, 2022).…”

Delineating antibody escape from Omicron sublineages

“…To decode Omicron escape from neutralizing antibodies, we produced and tested 158 monoclonal antibodies isolated from SARS-CoV-2-convalescent individuals against all Omicron sublineages. These included 67 randomly selected antibodies from the CoV-AbDab (Raybould et al, 2021), 79 antibodies isolated in our previous work (Kreer et al, 2020; Vanshylla et al, 2022), as well as 12 clinically evaluated antibodies. In total, this antibody panel originated from at least 43 different individuals out of 19 independent studies ( Figure 3A, Table S2 ).…”

Rapid hypermutation B cell trajectory recruits previously primed B cells upon third SARS-CoV-2 mRNA vaccination

“…Interestingly, the strong mutational activity was essentially restricted to few lineages that were present and mutated already before the third vaccination and therefore likely involved in previously induced memory B cells that were once again recruited to the lymph node's germinal center for further refinement. Notably, we observed high mutational rates especially in IGHV3-21, IGHV3-23, IGHV3-53 and IGHV3-30-3 genes that were linked to antibodies isolated from elite neutralizers that have previously shown neutralizing potency against variants of concern after infection with the ancestral strain (12,(30)(31)(32)(33)(34). Interestingly, we did not observe any age-restriction for this maturation process indication that also older people benefit from a third vaccination although this needs further validation due to the limited size of the analyzed cohort.…”

“…Although the somatic hypermutation load per SARS-CoV-2 specific sequence numerically increased in primed participants, it was dramatically boosted by the third vaccination (Figure 4D). This was especially observed for BCR sequences encoded by the IGHV3-21, IGHV3-23, IGHV3-53 and IGHV3-30-3 genes (Figure 4E) which have been already linked to S-reactive antibodies with exceptional neutralizing potency (12,(30)(31)(32)(33)(34). The amount of hypermutation did not correlate with age (Figure 4F).…”