COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants

The study addresses how well the BNT162b2 (Pfizer–BioNTech) mRNA COVID-19 vaccine induces antibody responses capable of neutralizing circulating SARS‑CoV‑2 variants, particularly D614G, B.1.1.7 (Alpha), and B.1.351 (Beta). The context is the global spread of SARS‑CoV‑2, the development and deployment of multiple vaccines, and concerns about variant-associated immune escape. SARS‑CoV‑2 infection elicits antibodies against spike (S) and nucleoprotein (N), with spike-specific antibodies being neutralizing and associated with protection. Vaccination and prior infection have been linked to reduced infection rates, and infection-induced neutralizing antibodies can persist for at least six months. Four vaccines authorized by EMA (two mRNA and two adenoviral vector vaccines) target the spike protein and induce neutralizing antibodies. However, variants of concern, especially B.1.1.7 and B.1.351 defined by multiple spike mutations, raise concerns regarding transmissibility and vaccine efficacy. This study aims to characterize the magnitude, kinetics, and breadth of antibody and neutralization responses induced by two doses of BNT162b2 in healthcare workers, compared with convalescent, non-hospitalized COVID-19 patient sera.

Background literature and surveillance data indicate that authorized COVID-19 vaccines induce neutralizing antibodies against early circulating strains (e.g., D614G). Variants of concern such as B.1.1.7 and B.1.351 harbor multiple spike mutations, including changes within or near the receptor-binding domain (e.g., N501Y, K417N, E484K) implicated in altered transmissibility and decreased neutralization by antibodies. Initial reports suggested retained neutralization against B.1.1.7 but reduced neutralization against B.1.351 by vaccine-elicited sera. Observational studies and trials have shown that prior SARS-CoV-2 infection enhances responses to a single vaccine dose and that vaccine effectiveness against severe disease remains high across variants, though neutralization titres can vary across lineages.

Design and participants: Prospective study of 180 Finnish healthcare workers (HCWs) receiving two BNT162b2 doses 3 weeks apart. Sequential serum samples were collected at baseline (0 day), 3 weeks after first dose, and 6 weeks after first dose (approximately 3 weeks after second dose). A convalescent cohort of 50 non-hospitalized, RT-PCR–confirmed COVID-19 patients provided sera collected 14 days to 6 weeks after positive test. Twenty pre-pandemic sera served as negative controls. Ethical approvals were obtained; written informed consent was collected. Serology (EIA/ELISA): Anti-S1 IgG, IgA, IgM, and total immunoglobulins were quantified using enzyme immunoassays. Optical densities were converted to EIA units using positive and negative controls to minimize inter-assay variation. Anti-N (nucleoprotein) antibodies (IgG, IgA, IgM, total Ig) were also measured to help identify recent/previous infection. Cut-off values were set based on negative controls (mean + 3 SD). Virus isolates and sequencing: Four live SARS-CoV-2 isolates circulating in Finland were used for neutralization testing: FIN-25 (B.1 lineage; D614G), SR121 (B.1.463; D614G), 85HEL (B.1.1.7/Alpha), and HEL12-102 (B.1.351/Beta). Viruses were propagated in VeroE6 or VeroE6-TMPRSS2 cells. Whole-genome/spike sequencing confirmed lineage-defining mutations and D614G in all isolates. Some passages introduced a minority deletion (aa 674–678) and R682W near the furin cleavage site in FIN-25; other isolates maintained an intact cleavage site or carried the deletion at low frequency. Structural mapping highlighted the locations of spike mutations (including K417N, E484K, N501Y in B.1.351) relative to the RBD–ACE2 interface. Microneutralization test (MNT): Neutralizing antibody titres against each isolate were determined by live-virus microneutralization assay. Titres <20 were plotted as 10. Geometric mean titres (GMTs) and proportions above threshold were reported for vaccinee and convalescent sera at each timepoint. Subgroup analyses: Responses were stratified by age groups (20–34, 35–44, 45–54, 55–65 years) and by gender to assess differences in anti-S1 IgG and neutralization titres. Statistics: Wilcoxon matched-pairs signed-rank test compared neutralization titres across isolates within subjects; Mann–Whitney U tested age/gender differences. Correlations between EIA measurements and MNT titres were assessed (Pearson and/or Spearman), with two-tailed p<0.05 considered significant.

- After two doses of BNT162b2, vaccinee sera effectively neutralized D614G (FIN-25, SR121) and B.1.1.7 (85HEL), while neutralization of B.1.351 (HEL12-102) was reduced approximately five-fold compared to D614G and B.1.1.7. - Despite reduced titres, 92% of initially seronegative vaccinees had neutralization titres >20 against B.1.351 after the second dose, indicating some level of protection. By contrast, 100% had neutralizing antibodies against D614G and B.1.1.7 after the second dose. - Three weeks after the first dose in initially seronegative HCWs, GMTs were modest and variant-dependent (e.g., FIN-25 ≈26; SR121 ≈32; B.1.1.7 ≈24; B.1.351 ≈12), demonstrating lower activity against B.1.351. After the second dose, GMTs rose substantially across variants, but titres for B.1.351 remained significantly lower (≈5-fold) than for D614G and B.1.1.7. - Vaccinees with prior SARS-CoV-2 infection showed higher baseline titres and robust boosting after the first and second doses (e.g., baseline GMTs against FIN-25, B.1.1.7, and B.1.351 of ~35, ~31, and ~16, increasing markedly post-vaccination). - Vaccine-induced neutralization GMTs exceeded those of convalescent-phase sera from non-hospitalized patients. - Correlations between neutralization titres against different isolates were high and significant: FIN-25 vs HEL12-102 (B.1.351) r=0.74; 85HEL (B.1.1.7) vs HEL12-102 (B.1.351) r=0.75; p<0.0001. - EIA measurements correlated strongly with neutralization titres (anti‑S1 IgG and total S1 Ig vs MNT against FIN-25; p<0.0001), supporting EIA as a practical proxy for neutralization capacity. - Age effects: older vaccinees (55–65 years) had significantly lower anti‑S1 IgG and neutralization titres after the first dose compared to younger groups, but after the second dose, titres were comparable across age groups (reported GMTs approximately 210–268). Gender effects were minimal; females had slightly higher titres than males after the second dose (non-significant).

Two doses of BNT162b2 elicited very high spike-specific antibody levels and strong neutralizing activity against D614G and B.1.1.7 in all vaccinees. Although neutralization of B.1.351 was reduced, most subjects (92%) still mounted detectable neutralizing titres, indicating partial cross-protection. Neutralization titres in vaccinees surpassed those in convalescent, non-hospitalized individuals, underscoring the potency of the vaccine-induced response. Early age-associated attenuation of responses was overcome by the second dose, supporting the importance of the complete vaccination series. Strong correlations between EIA anti‑S1 measurements and live-virus neutralization suggest that serological assays can serve as scalable surrogates for neutralization testing. These findings address concerns regarding variant escape by demonstrating substantial, albeit reduced, cross-neutralization of B.1.351 and reinforce the value of two-dose vaccination regimens for broad protection.

The BNT162b2 mRNA vaccine induces robust humoral immunity with high neutralizing antibody titres against D614G and B.1.1.7 variants and reduced but prevalent neutralizing activity against B.1.351 in most recipients after two doses. Vaccine-induced titres exceed those of convalescent, non-hospitalized COVID-19 patients. EIA-based anti‑S1 measurements correlate strongly with neutralization, offering practical immune monitoring. Future research should evaluate the durability of these responses, expand assessments to additional and emerging variants, and characterize vaccine-induced cell-mediated immunity and its role in cross-protection and longevity.

- Short follow-up: immune responses were assessed up to approximately 6 weeks after the first dose (about 3 weeks post-second dose), limiting conclusions on durability. - Cohort composition: healthcare workers aged 20–65 with female predominance (~83%) may limit generalizability to other populations, age groups, and sexes. - Variant scope: neutralization was tested against four isolates (D614G lineages, B.1.1.7, and B.1.351); findings may not generalize to other variants. - Virus passage effects: minor heterogeneity near the furin cleavage site was observed in one isolate (FIN-25) due to cell culture passage, though reported not to affect growth; potential effects on antigenicity cannot be completely excluded. - Cellular immunity was not measured; conclusions focus on humoral responses.