SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma

Abstract

To investigate the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the immune population, we coincupi bated the authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for seven passages, but, after 45 d, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed, at day 80, by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom, South Africa, Brazil, and Japan of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed.

Scientific rationale for developing potent RBD-based vaccines targeting COVID-19

“…In support of this theory, co-evolution of separate virus lineages around the globe (Alpha: lineage B.1.1.7 or 501Y.V1 in the UK; Beta: lineage B.1.351 or 501Y.V2 in the Republic of South Africa; and Gamma: lineage P.1 or 501Y.V3 in Brazil) appear to carry one or more of the same mutations in RBD: K417N/T, E484K, and N501Y (Table 3). Similar mutations were observed to occur in forced viral evolution experiments using convalescent or vaccinee serum; passage of prototype virus with high-titer neutralizing antisera yielded a mutant virus carrying similar NTD deletions and the RBD-specific E484K mutation 45 . Mutation at the E484 site was shown to impact virus neutralization of the ancestral B.1 virus, which has been noted as a concern for emerging variants 44,[46][47][48] (Table 3), although recent epidemiological trends show prevalence for the Delta (B.1.617.2) variant that lacks this mutation (https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/).…”

Mechanisms of SARS-CoV-2 entry into cells

“…The aforementioned Alpha, Beta, Gamma and Delta variants and the Epsilon variant (B.1.429, California lineage) exhibit decreased sensitivity to neutralization by immune plasma derived from convalescent patients with COVID-19 or vaccinated individuals [40][41][42][43][44][45]185,[189][190][191][192][193][194] . The possibility that these recent variants emerged from the infection of previously infected or vaccinated individuals is supported by studies in which escape variants were experimentally generated in the presence of neutrali zing antibodies, convalescent sera or sera derived from vaccinated individuals [195][196][197][198] . In these studies, the same mutations, including K417N, E484K and N501Y in the RBD, which are the hallmarks of the Alpha, Beta, and Gamma variants, were identified.…”

Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape

“…The 484 site mutation also reduced the neutralizing activity of a variety of monoclonal antibodies in clinical stage, including REGN10933 and LY-CoV-555 (2). Some studies have confirmed that the mutation of E484K could eliminate the key interaction between epitope antibodies against 484 and Arg50 or Arg96, resulting in decreased antibody neutralization efficiency (71,72). In contrast, Brii-196, COV2-2130, P2C-1F11, and H014 still preserved high neutralization ability, which may be due to their broad-spectrum antigen-binding epitopes (33,53,73).…”

“…E484 position, the targeting site of antibodies such as heavy chain germline IGHV3-53 and IGHV3-66, has the greatest influence on antibody binding and neutralization in RBD region (54,62,69,(74)(75)(76). E484K can escape not only the neutralization of monoclonal antibodies C121, C144 (77) and the serum from convalescent patients (72), but also the neutralization of the combination of REGN10989 and REGN10934 monoclonal antibody cocktail (78).…”