Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants

Abstract

SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading antibodies isolated earlier in the pandemic. Investigation of memory B cells from patients primarily with breakthrough infections with the Delta variant enables isolation of a number of neutralizing antibodies cross-reactive to heterologous variants of concern (VOCs) including Omicron variants (BA.1-BA.4). Structural studies identify altered complementarity determining region (CDR) amino acids and highly unusual heavy chain CDR2 insertions respectively in two representative cross-neutralizing antibodies—YB9-258 and YB13-292. These features are putatively introduced by somatic hypermutation and they are heavily involved in epitope recognition to broaden neutralization breadth. Previously, insertions/deletions were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. These data provide molecular mechanisms for cross-neutralization of heterologous SARS-CoV-2 variants by antibodies isolated from Delta variant infected patients with implications for future vaccination strategy.

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein driving the genesis of Omicron variants

“…5e ). Similar S-trimer disintegration has been observed previously in the presence of mAb R1-32 (He et al, 2022; Yu et al, 2023).…”

“…Indeed, we find that binding of R1-26, H18 and possibly other VL6-57 mAbs to the convergent cryptic epitope not only blocks ACE2 binding (Piccoli et al, 2020), but also prematurely triggers spike conformational change resulting in spike destruction. When paired with other RBD-specific antibodies, binding of antibodies to cryptic epitopes may also promote spike disintegration (He et al, 2022; Yu et al, 2023). The increased immune pressure may promote the introduction of S371L/F-S373P-S375F in Omicron variants.…”

“…S-protein or RBD expression vector was transiently transfected into Expi293F using polyethylenimine. Proteins were purified using IMAC (immobilized metal affinity chromatography) following previously described protocols (He et al, 2022; Xiong et al, 2020; Yu et al, 2023). All proteins were aliquoted, flash-frozen in liquid nitrogen and stored at -80 ℃.…”

“…Antibody sequence analyses in panels c-i used published bulk sequencing datasets (Niu et al, 2020; Yan et al, 2021; Zhang et al, 2022). j , The occurrence of VL6-57 mAbs with paired heavy chains containing the HCDR3 “WLRG” motif in the single-B V(D)J repertoires of COVID-19 patients, vaccinees and healthy donors (Barmada et al, 2023; Dugan et al, 2021; Ferreira-Gomes et al, 2021; Ren et al, 2021; Yu et al, 2023; Zhang et al, 2020). The two-sided chi-square test was performed in panels ( c ) and ( g ).…”

“…To further determine the abundance of B cells expressing mAbs of VL6-57 light chains paired with the HCDR3 “WLRG” motif, we analyzed published single-B V(D)J sequences from SARS-CoV-2-exposed and -naïve individuals (Barmada et al, 2023; Dugan et al, 2021; Ferreira-Gomes et al, 2021; Ren et al, 2021; Zhang et al, 2020) and our previously reported FACS-sorted RBD-reactive single-B memory cell sequences from COVID-19 convalescents (Yu et al, 2023) ( Fig. 4a, see method ).…”