SARS-CoV-2 variant B.1.617 is resistant to bamlanivimab and evades antibodies induced by infection and vaccination

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants threatens efforts to contain the coronavirus disease 2019 (COVID-19) pandemic. The number of COVID-19 cases and deaths in India has risen steeply, and a SARS-CoV-2 variant, B.1.617, is believed to be responsible for many of these cases. The spike protein of B.1.617 harbors two mutations in the receptor binding domain, which interacts with the angiotensin converting enzyme 2 (ACE2) receptor and constitutes the main target of neutralizing antibodies. Therefore, we analyze whether B.1.617 is more adept in entering cells and/or evades antibody responses. B.1.617 enters two of eight cell lines tested with roughly 50% increased efficiency and is equally inhibited by two entry inhibitors. In contrast, B.1.617 is resistant against bamlanivimab, an antibody used for COVID-19 treatment. B.1.617 evades antibodies induced by infection or vaccination, although less so than the B.1.351 variant. Collectively, our study reveals that antibody evasion of B.1.617 may contribute to the rapid spread of this variant.

Keywords: B.1.617; SARS-CoV-2; antibodies; cell entry; convalescence; immune evasion; mutations; spike protein; vaccination.

Graphical abstract

Figure 1

Schematic overview of the S proteins from SARS-CoV-2 variants B.1.617 and B.1.351 The location of the mutations in the context of the B.1.617 or B.1.351 S protein domain organization is shown in the upper panel. RBD, receptor binding domain; TD, transmembrane domain. The location of the mutations in the context of the trimeric S protein is shown in the lower panels. Color code: light blue, S1 subunit with RBD in dark blue; gray, S2 subunit; orange, S1/S2 and S2′ cleavage sites; red, mutated amino acid residues.

Figure 2

The S protein of SARS-CoV-2 variant B.1.617 drives efficient entry into human cell lines (A) S protein of the SARS-CoV-2 variant B.1.617 mediates robust entry into cell lines. The indicated cell lines were inoculated with pseudotyped particles bearing the S proteins of the indicated SARS-CoV-2 variants or the wild-type (WT) SARS-CoV-2 S protein. Transduction efficiency was quantified by measuring virus-encoded luciferase activity in cell lysates 16–18 h after transduction. Presented are the average (mean) data from three biological replicates (each conducted with technical quadruplicates) for which transduction was normalized against SARS-CoV-2 WT S protein (= 100%). Error bars indicate the standard error of the mean (SEM). Statistical significance of differences between the WT and the variant S proteins was analyzed by one-way analysis of variance (ANOVA) with Dunnett’s posttest (p > 0.05, not significant [ns]; ^∗p ≤ 0.05; ^∗∗p ≤ 0.01; ^∗∗∗p ≤ 0.001). See also Figure S1. (B) BHK-21 cells transfected with empty plasmid or ACE2 plasmid were inoculated with pseudotyped particles bearing the indicated S proteins, VSV-G, or no viral glycoprotein (control; data not shown). Presented are the average (mean) data from three biological replicates (each conducted with technical quadruplicates) for which transduction was normalized against the background (signal obtained for particles without viral glycoprotein = 1, as indicated by the dashed line). Error bars indicate the SEM. Statistical significance of differences between empty vector and ACE2-transfected cells was analyzed by multiple t test with correction for multiple comparison (Holm-Sidak method; p > 0.05, ns; ^∗∗∗p ≤ 0.001).

Figure 3

Entry driven by the S protein of SARS-CoV-2 variant B.1.617 can be blocked with soluble ACE2 and camostat mesylate (A) S protein-bearing particles were incubated with different concentrations of soluble ACE2 (sol-ACE2) for 30 min at 37°C before the mixtures were inoculated onto Caco-2 cells. (B) Caco-2 target cells were preincubated with different concentrations of the serine protease inhibitor camostat mesylate for 1 h at 37°C before S protein-bearing particles were added. Transduction efficiency was quantified by measuring virus-encoded luciferase activity in cell lysates 16–18 h after transduction. For normalization, SARS-CoV-2 S protein-driven entry in the absence of sol-ACE2 or camostat was set as 0% inhibition. Presented are the average (mean) data from three biological replicates (each performed with technical quadruplicates. Error bars indicate the SEM. Statistical significance of differences between the WT and the variant S proteins or VSV-G was analyzed by two-way ANOVA with Dunnett’s posttest (p > 0.05, ns [not significant, not indicated in the graphs]; ^∗∗∗p ≤ 0.001).

Figure 4

The S protein of SARS-CoV-2 variant B.1.617 is resistant to neutralization by bamlanivimab S protein-bearing particles were incubated with different concentrations of monoclonal antibodies for 30 min at 37°C before the mixtures were inoculated onto Vero cells. Transduction efficiency was quantified by measuring virus-encoded luciferase activity in cell lysates 16–18 h after transduction. For normalization, SARS-CoV-2 S protein-driven entry in the absence of monoclonal antibody was set as 0% inhibition. Presented are the average (mean) data from three biological replicates (each performed with technical quadruplicates). Error bars indicate the SEM. Statistical significance of differences between the WT and the variant S proteins was analyzed by two-way ANOVA with Dunnett’s posttest (p > 0.05, ns [not significant, not indicated in the graphs]; ^∗p ≤ 0.05; ^∗∗p ≤ 0.01; ^∗∗∗p ≤ 0.001). See also Figure S2.

Figure 5

The S protein of SARS-CoV-2 variant B.1.617 evades neutralization by antibodies induced upon infection or vaccination with BNT162b2 The S protein of SARS-CoV-2 variant B.1.617 evades neutralization by convalescent plasma (A) or plasma from BNT162b2-vaccinated individuals (B). S protein-bearing particles were incubated with different plasma dilutions (derived from infected or vaccinated individuals) for 30 min at 37°C before the mixtures were inoculated onto Vero cells. Transduction efficiency was quantified by measuring virus-encoded luciferase activity in cell lysates 16–18 h after transduction and used to calculate the plasma/serum dilution factor that leads to 50% reduction in S protein-driven cell entry (neutralizing titer 50 [NT50]). Presented are the average (mean) data from a single biological replicate (performed with technical quadruplicates). Error bars indicate the standard deviation. Identical plasma samples are connected with lines, and the numbers in brackets indicate the average (mean) reduction in neutralization sensitivity for the S proteins of the respective SARS-CoV-2 variants. Statistical significance of differences between the WT and the variant S proteins was analyzed by paired two-tailed Student’s t test (p > 0.05, ns; ^∗∗p ≤ 0.01; ^∗∗∗p ≤ 0.001). See also Figure S3 and Tables S1 and S2.