Immune response to SARS-CoV-2 variants of concern in vaccinated individuals

Abstract

SARS-CoV-2 is evolving with mutations in the receptor binding domain (RBD) being of particular concern. It is important to know how much cross-protection is offered between strains following vaccination or infection. Here, we obtain serum and saliva samples from groups of vaccinated (Pfizer BNT-162b2), infected and uninfected individuals and characterize the antibody response to RBD mutant strains. Vaccinated individuals have a robust humoral response after the second dose and have high IgG antibody titers in the saliva. Antibody responses however show considerable differences in binding to RBD mutants of emerging variants of concern and substantial reduction in RBD binding and neutralization is observed against a patient-isolated South African variant. Taken together our data reinforce the importance of the second dose of Pfizer BNT-162b2 to acquire high levels of neutralizing antibodies and high antibody titers in saliva suggest that vaccinated individuals may have reduced transmission potential. Substantially reduced neutralization for the South African variant further highlights the importance of surveillance strategies to detect new variants and targeting these in future vaccines.

Fig. 1. IgG and IgA response in serum samples of vaccinated, infected, and negative individuals.

IgG (a, c) and IgA (b, d) response in sera from vaccinated (pre second vaccination (light blue, n = 25), post second vaccination (dark blue, n = 20)), infected (red) (n = 35), and negative (gray) (n = 20) individuals were measured with MULTICOV-AB. IgG (a) and IgA (b) response is shown as normalized RBD wild-type (wt) versus normalized nucleocapsid MFI values allowing for visualization of separation between the different groups. Increasing antibody titers in vaccinated individuals for IgG (c) and IgA (d) is shown with increasing days post vaccination, with samples colored based on whether they are before (light blue) or after (dark blue) the second dose. Lines indicate paired samples from the same donor. Source data are provided as a Source Data file.

Fig. 2. IgA and IgG response in saliva samples of vaccinated, infected, and negative individuals.

Box and whisker plots for the IgA (a) and IgG (b) response in the saliva of vaccinated (blue, n = 22), infected (red, n = 26), and negative (gray, n = 45) individuals. All samples were measured three times using MULTICOV-AB, normalized against QC values to remove confounding effects, and the mean calculated and displayed. Panel b is presented using a logarithmic scale for clarity. As additional controls, one infected and then vaccinated sample and two vaccinated samples from individuals not in contact with active COVID-19 infections are displayed as triangles. Boxes represent the median, 25th and 75th percentiles, whiskers show the largest and smallest non-outlier values. Outliers were determined by 1.5 times IQR. Statistical significance was calculated by Mann–Whitney U (two-sided) with significance determined as being < 0.01. **< 0.001; ***< 0.0001. Source data are provided as a Source Data file.

Fig. 3. South African RBD mutant has a reduced response compared to UK RBD mutant.

UK (a) and South African (SA) RBD mutants (b) have differing effects upon antibody binding. RBD mutant antigens were generated and added to MULTICOV-AB to measure the immune response towards them in sera from vaccinated pre-second dose (light blue, n = 25), post second dose (dark blue, n = 20), and infected (red, n = 35) individuals, compared to the wild-type (wt) RBD. A linear curve (y = x) is shown as a dashed gray line to indicate an identical response between wild-type and mutant. Kendall’s tau was calculated to measure the ordinal association between the mutant and wild-type. Source data are provided as a Source Data file.

Fig. 4. South African RBD variant has decreased neutralization compared to wild-type in vaccinated and infected samples.

Neutralization for the South African variant (SA) displayed as virus neutralizing titers (VNT₅₀) was measured in a virus neutralization assay compared to a wild-type variant (wt) (a) with sera from vaccinated (pre second vaccination (light blue, n = 9), post second vaccination (dark blue, n = 7)), infected (red, n = 6), and negative (pre-pandemic) (gray, n = 2) individuals. To confirm the reduction in neutralization seen, an ACE2 competition assay was developed and used to measure neutralization capacity for wild-type RBD (wt) and the South African RBD mutant (SA) (b) on sera from vaccinated (pre second vaccination (light blue, n = 25), post second vaccination (dark blue, n = 20)), infected (red, n = 35) and negative (pre-pandemic, gray, n = 20) individuals. 0 indicates that no neutralization is present while 1 indicates maximum neutralization. A linear regression (y = −0.044 + 0.408x) for all samples is shown in gray with the R² included. When examining vaccinated samples only, wild-type neutralization (c) is significantly increased following the second vaccine dose. For South African neutralization (d), while it is increased following the second dose, there is a significant reduction when compared to wild-type. Lines in (a), (c), and (d) indicate paired samples from the same donor. Source data are provided as a Source Data file.