- Authors: ViewAmarendra Pegu1,†, Sarah O’Connell1,† View ORCID ProfileStephen D. Schmidt1,†, Sijy O’Dell1,†, View ORCID ProfileChloe A. Talana1, Lilin Lai2, Jim Albert Science 12 Aug 2021: eabj4176m OI: 10.1126/science.abj4176
SARS-CoV-2 mutations may diminish vaccine-induced protective immune responses, particularly as antibody titers wane over time. Here, we assess the impact of SARS-CoV-2 variants B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.429 (Epsilon), B.1.526 (Iota), and B.1.617.2 (Delta) on binding, neutralizing, and ACE2-competing antibodies elicited by the vaccine mRNA-1273 over seven months. Cross-reactive neutralizing responses were rare after a single dose. At the peak of response to the second vaccine dose, all individuals had responses to all variants. Binding and functional antibodies against variants persisted in most subjects, albeit at low levels, for 6-months after the primary series of the mRNA-1273 vaccine. Across all assays, B.1.351 had the lowest antibody recognition. These data complement ongoing studies to inform the potential need for additional boost vaccinations.
SARS-CoV-2, the virus that causes COVID-19, has infected millions of people worldwide fueling the ongoing global pandemic (1). The combination of RNA virus mutation rates, replication and recombination, in a very large number of individuals is conducive to the emergence of viral variants with improved replication capacity and transmissibility, as well as immunological escape. Of particular interest are the Variants of Concern B.1.1.7 (20I/501Y.V1 or Alpha), B.1.351 (20H/501Y.V2 or Beta), P.1 (Gamma; first identified in Brazil), B.1.429 (Cal20 or Epsilon; first identified in California), and B.1.617.2 (Delta; first identified in India); and Variant of Interest B.1.526 (Iota; first identified in New York). In multiple studies, B.1.351 is the most resistant to neutralization by convalescent or vaccinee sera, with 6-15 fold less neutralization activity for sera from individuals immunized with vaccines based on the virus strain first described in January 2020 (Wuhan-Hu-1, spike also called WA1) (2–9). Most of these prior studies evaluated sera from vaccinated individuals at timepoints soon after the first or second dose, and had limited data on the durability of such responses. Likewise, clinical studies have reported somewhat reduced efficacy and effectiveness against the B.1.1.7, B.1.351, and B.1.617.2 variants (10–12). Although such data provide critical insights into the performance of the vaccines against viral variants, they have not fully addressed the durability of cross-reactive binding and functional antibodies.
Here we investigate the impact of SARS-CoV-2 variants on recognition by sera from individuals who received two 100 mcg doses of the SARS-CoV-2 vaccine mRNA-1273. mRNA-1273 encodes the full-length stabilized spike protein of the WA1 and was administered as a two-dose series 28-days apart. We previously described the binding and neutralization activity against the WA1 SARS-CoV-2 spike longitudinally over 7 months from the first vaccination in volunteers from the Phase 1 trial of the mRNA-1273 vaccine (13–16). In the current study, we demonstrate the utility of employing multiple methodologies to assess SARS-CoV-2 vaccine-elicited humoral immunity to variant viruses over time. We tested sera from a random sample of 8 volunteers in each of three age groups: 18-55, 55-70, and 71+ years of age, all of whom had samples available from four timepoints: 4 weeks after the first dose, and two weeks, 3 months, and 6 months after the second dose (Days 29, 43, 119, and 209 after the first dose, respectively).
Three functional assays and two binding assays were used to assess the humoral immune response to the SARS-CoV-2 spike protein. SARS-CoV-2 neutralization was measured using both a lentivirus-based pseudovirus assay, and a live-virus focus reduction neutralization test (FRNT) (17). The third functional assay was a MSD-ECLIA (Meso Scale Discovery-Electrochemiluminescence immunoassay)-based ACE2 competition assay. This method measured the ability of mRNA-1273 vaccine-elicited antibodies to compete with labeled soluble ACE2 for binding to the specific RBD (WA1 or variant) spotted onto the MSD plate. Antibody binding to cell-surface expressed full-length spike was analyzed by flow cytometry. Binding to soluble protein was measured by interferometry in the MSD-ECLIA platform. All samples were assessed against WA1 and the B.1.1.7 and B.1.351 variants in each of these orthogonal serology assays. In addition, all samples were tested against WA1 containing the D614G mutation in both neutralization assays, as well as binding in the cell-surface assay. Further variants were tested in binding assays as follows: S-2P and RBD binding, P.1 against all samples; cell-surface spike binding, P.1, B.1.429, B.1.526, and B.1.617.2 against all samples. A subset of samples – Day 43 to capture the peak response, and Day 209 to look at durability – were evaluated by pseudovirus neutralization against P.1, B.1.429, B.1.526, and B.1.617.2. The specific sequences used in each assay are defined in table S1.
We first assessed the patterns of antibody activity over time. Consistently across assays, low-level recognition of all variants was observed after a single dose (Day 29) (Fig. 1). Activity against all variants peaked two weeks after the second dose (Day 43) with moderate declines over time through Day 209 (Fig. 1). Notably, the values obtained for each assay on a per-sample basis correlated with each other (fig. S1). We next evaluated the relative impact of each variant, considering all timepoints together. Employing the pseudovirus assay, the neutralizing activity was highest against D614G and lowest against B.1.351, with values for all other variants tested falling in between those two variants (Fig. 1A and Fig. 2A). Similar to previous reports from our group (15) and others (18), pseudovirus neutralization ID50s to D614G were 3-fold higher than to WA1 (Fig. 2G). In contrast, using the live-virus FRNT neutralization assay (Fig. 1B and Fig. 2B), titers to WA1 were higher than to D614G, consistent with previous reports for that assay (19). For all other variants, the impact in the live-virus and pseudovirus neutralization assays were concordant: titers against B.1.1.7 were similar to D614G and lower against B.1.351. ACE2 competition was highest for WA1 RBD, intermediate for B.1.1.7, and lowest for B.1.351 (Fig. 1C and Fig. 2C). Spike-binding antibodies were measured using two different methodologies. In the cell-surface spike binding assay, serum antibodies were bound to full-length, membrane-embedded spike on the surface of transfected cells and measured by flow cytometry (20). In this assay (Fig. 1D and Fig. 2D), WA1 and D614G were nearly indistinguishable, with ~1.5-fold reduced binding to B.1.1.7, B.1.526, B.1.617.2, and 2.4 to 3.0-fold reduced binding to P.1, and B.1.429, and B.1.351. We also used the MSD-ECLIA multiplex binding assay to simultaneously measure IgG binding against both the stabilized soluble spike protein S-2P (21) and RBD proteins derived from WA1 and the B.1.1.7, B.1.351, and P.1 variants. The ECLIA assay showed slightly reduced binding to the variant S-2P (Fig. 1E and Fig. 2E) and RBD (Fig. 1F and Fig. 2F) proteins, with the rank order of highest to lowest binding as follows: WA1, B.1.1.7, P.1, and B.1.351. The overall effect of each variant in each assay is tabulated in Fig. 2G, which shows the geometric mean of the ratios between values for WA1 and variant or D614G and variant. In all assays, B.1.351 was the variant that caused the greatest reduction in titers compared to WA1 or D614G.
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