B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies

Abstract

DNA sequence analysis recently identified the novel SARS-CoV-2 variant B.1.526 that is spreading at an alarming rate in the New York City area. Two versions of the variant were identified, both with the prevalent D614G mutation in the spike protein, together with four novel point mutations and with an E484K or S477N mutation in the receptor-binding domain, raising concerns of possible resistance to vaccine-elicited and therapeutic antibodies. We report that convalescent-phase sera and vaccine-elicited antibodies retain full neutralizing titer against the S477N B.1.526 variant and neutralize the E484K version with a modest 3.5-fold decrease in titer compared to D614G. The E484K version was neutralized with a 12-fold decrease in titer by the REGN10933 monoclonal antibody, but the combination cocktail with REGN10987 was fully active. The findings suggest that current vaccines and Regeneron therapeutic monoclonal antibodies will remain protective against the B.1.526 variants. The findings further support the value of widespread vaccination. IMPORTANCE A novel SARS-CoV-2 variant termed B.1.526 was recently identified in New York City and has been found to be spreading at an alarming rate. The variant has mutations in its spike protein that might allow it to escape neutralization by vaccine-elicited antibodies and might cause monoclonal antibody therapy for COVID-19 to be less successful. We report here that these fears are not substantiated; convalescent-phase sera and vaccine-elicited antibodies neutralized the B.1.526 variant. One of the Regeneron therapeutic monoclonal antibodies was less effective against the B.1.526 (E484K) variant but the two-antibody combination cocktail was fully active. The findings should assuage concerns that current vaccines will be ineffective against the B.1.526 (E484K) variant and suggest the importance of continued widespread vaccination.

Keywords: B.1.526; Moderna mRNA-1273; Pfizer BNT162b2; REGN10933; REGN10987; SARS-CoV-2; neutralization; spike protein.

FIG 1

Analysis of B.1.526 pseudotyped lentiviral virions. (A) The domain structure of the wild-type SARS-CoV-2 spike protein is shown above. NTD, N-terminal domain; RBD, receptor-binding domain; RBM, receptor-binding motif; SD1 subdomain 1; SD2, subdomain 2; FP, fusion peptide; HR1, heptad repeat 1; HR2, heptad repeat 2; TM, transmembrane region; IC, intracellular domain. The locations of the mutations in the two B.1.526 spike proteins are diagrammed below with the distinguishing E484K and S477N mutations in bold. (B) The locations of the B.1.526 variant spike protein mutations are shown on the 3D structure of the trimeric spike protein. One RBD region is shown for simplicity. The 484 (red) and 477 (blue) amino acid residues are indicated. (C) Immunoblot analysis of B.1.526 spike protein pseudotyped lentiviral virions and cell lysates of transfected producer cells. The blots were probed for the full-length S and processed S2 proteins and with anti-P24 antibody to detect the virions. GAPDH served as a loading control for the cell lysates. Arrows indicate the full-length spike (S), S2 subunit (S2). (D) Infectivity of B.1.526 pseudotyped virus in ACE2.293T cells. ACE2.293T cells were infected with pseudotyped viruses normalized for RT activity. Luciferase activity was measured 2 days postinfection as relative light units (RLU).

FIG 2

Convalescent serum, antibodies elicited by BNT162b2 vaccine, antibodies elicited by mRNA-1273 vaccine, antibody REGN10933, and antibody REGN10987 all neutralize B.1.526 variant spikes. (A) Neutralization of viruses with D614G, B.1.526 variant spikes by convalescent-phase sera (n = 6). The data are shown as the percentage infectivity in the absence of serum (left). IC₅₀ (serum dilution) of sera from convalescent individuals (n = 6) against virus with B.1.526 and E484K variant spikes (right). (B) Neutralizing titers of serum samples from BNT162b2-vaccinated individuals (n = 5) (left) and mRNA-1273-vaccinated donors (n = 3) (right) were measured. IC₅₀ values of neutralization of virus with D614G, B.1.1.7, B.1.351, and B.1.526 are shown. (C) A 1:1 mixture of the two antibodies was measured on viruses pseudotyped with B.1.526, D614G and E484K variant spike proteins. Neutralization curves of REGN10933, REGN10987, and a 1:1 mixture of REGN10933 and REGN10987 on viruses with the B.1.526, D614G and E484K variant spike proteins. (D). The effect of the MAb ratio on neutralization of variant B.1.526 (E484K) was tested by holding REGN10933 constant at its IC₅₀ and titrating in REGN10987 (left) or holding REGN10987 constant at its IC₅₀ and titrating in REGN10933.