SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera

Abstract

Toward eradicating the COVID-19 pandemic, vaccines that induce high humoral and cellular immune responses are essential. However, SARS-CoV-2 variants have begun to emerge and raise concerns, as they may potentially compromise vaccine efficiency. Here, we monitored neutralization potency of convalescent or Pfizer-BTN162b2 post-vaccination sera against pseudoviruses displaying spike proteins derived from wild-type SARS-CoV-2, or its UK-B.1.1.7 and SA-B.1.351 variants. Compared to convalescent sera, vaccination induces high titers of neutralizing antibodies, which exhibit efficient neutralization potential against pseudovirus carrying wild-type SARS-CoV-2. However, while wild-type and UK-N501Y pseudoviruses were similarly neutralized, those displaying SA-N501Y/K417N/E484K spike mutations moderately resist neutralization. Contribution of single or combined spike mutations to neutralization and infectivity were monitored, highlighting mechanisms by which viral infectivity and neutralization resistance are enhanced by N501Y or E484K/K417N mutations. Our study validates the importance of the Pfizer vaccine but raises concerns regarding its efficacy against specific SARS-CoV-2 circulating variants.

Keywords: COVID-19; Pfizer-BTN162b2 vaccine; SARS-CoV-2; Spike; UK and SA variants; United Kingdom and South African variants; neutralization antibodies.

Graphical abstract

Figure 1

Neutralization of wild-type SARS-CoV-2 pseudovirus by convalescent or post-vaccination sera (A) Schematic organization of SARS-CoV-2 spike indicating domains and studied RBD mutations. (B) Convalescent or post-vaccination sera neutralize pseudoviruses carrying wild-type SARS-CoV-2 spike. Neutralization assays were performed by transducing HEK293T-ACE2 cells with pseudovirus displaying wild-type SARS-CoV-2 spike in the presence of increasing dilutions of sera drawn from convalescent or post-vaccinated individuals. 48 h post-transduction, cells were harvested and their luciferase readings were monitored. Neutralizing potency was calculated at increased serial dilutions, relative to transduced cells with no sera added. Neutralization, NT₅₀ is defined as the inverse dilution that achieved 50% neutralization. Results are the average of two independent biological experiments. Triplicates were performed for each tested serum dilution. Black bars represent geometric mean of NT₅₀ values, indicated at the top. Statistical significance was determined using one-tailed t test ^∗∗∗p < 0.001.

Figure 2

Pseudoviruses carrying SARS-CoV-2 spike variants are neutralized to a different extent by convalescent or post-vaccination sera (A and B) Neutralization sensitivity of SARS-CoV-2 pseudoviruses displaying UK or SA spike variants by convalescent (A) or post-vaccination sera (B). Pseudoviruses displaying wild-type or mutant SARS-CoV-2 spike from UK-N50Y or SA-N501Y/K417N/E484K variants were used in neutralization assays. HEK293T-ACE2 cells were transduced with the indicated pseudoviruses in the presence of increasing dilutions of convalescent or vaccination sera. 48 h post-infection, cells were harvested and their luciferase readings were monitored. Serum neutralizing potency was calculated at serial dilutions, relative to transduced cells with no sera added. Results are the average of two independent experiments. Triplicates were performed for each tested sera and pseudovirus. Horizontal black bars represent geometric mean NT₅₀, indicated at the top. Statistical significance was determined using one-tailed t test ^∗∗∗p < 0.001. (C) SARS-CoV-2 pseudoviruses from UK and SA variants exhibit different infectivity levels. Pseudoviruses bearing wild-type or the indicated mutant SARS-CoV-2 spike were used to transduce HEK293T-ACE2 cells. Equal viral loads were normalized based on p24 protein levels. 48 h post-transduction, cells were harvested and their luciferase readouts were monitored. Bar graphs show mean values ± SD error bars of three independent experiments. Measured statistical significance was calculated between experiments by a two-tailed Student’s t test ^∗∗∗p ≤ 0.001. (D) Neutralization sensitivity of SARS-CoV-2 pseudoviruses variants displaying combined UK and SA spike mutants. Pseudoviruses displaying wild-type or the indicated SARS-CoV-2 mutant spike were used in neutralization assays. HEK-ACE2 cells were transduced with the indicated pseudoviruses in the presence of increasing dilutions of a mixed vaccination serum drawn from vaccinated individuals that received the second dose (n = 10). 48 h post-transduction, cells were harvested and their luciferase readouts were monitored. Percentage of neutralizing potential was calculated at serial dilutions, relative to transduced cells with no sera added. Arrows indicate NT₅₀ values obtained for each mutant. Results are the average of two independent experiments. Black arrows represent mean NT₅₀ values. Measured statistical significance was calculated between experiments by a two-tailed Student’s t test ^∗∗∗p ≤ 0.001.