Longitudinal analysis of hybrid immunity in a Vietnamese COVID-19 cohort demonstrates vaccination-associated broadening of cross-variant neutralization across diverse HLA backgrounds

Abstract

Introduction Despite extensive research on SARS-CoV-2 immunity, longitudinal studies integrating functional neutralization, antigenic relationships, and host genetic variability remain limited, particularly in Southeast Asian populations with distinct HLA backgrounds. Here, we performed a longitudinal analysis of a Vietnamese COVID-19 cohort before and after vaccination to characterize determinants of cross-variant antibody responses. Our findings indicate that while HLA polymorphisms contribute to inter-individual variability following natural infection, vaccination substantially enhanced cross-variant neutralization and reduced the apparent contribution of HLA-associated variability of neutralizing responses across genetically diverse individuals. Methods We analyzed 189 Vietnamese COVID-19 convalescent individuals at approximately 7 months post-infection (unvaccinated) and 72 individuals at approximately 15 months (predominantly vaccinated). Anti-S1 and anti-RBD IgG were quantified by ELISA, and neutralizing antibody titers (PRNT50) were measured against Wuhan and major variants of concern. High-resolution HLA genotyping was performed using next-generation sequencing, and associations with antibody responses were evaluated using linear regression models with correction for multiple comparisons. Results Vaccination markedly increased antibody levels and neutralizing titers across all variants, with fold-increases ranging from approximately 10-fold (Omicron) to 132-fold (Wuhan). Neutralization breadth expanded substantially after vaccination, although reduced activity against Omicron persisted. Strong correlations between binding and neutralizing antibodies were observed, particularly post-vaccination. While several HLA alleles were associated with variation in neutralizing antibody magnitude at earlier time points, multivariable analyses demonstrated that vaccination was the strongest factor associated with neutralization breadth at 15 months. Conclusion Vaccination robustly enhances both the magnitude and breadth of humoral immunity in previously infected individuals, consistent with hybrid immunity. Although HLA polymorphisms contribute to inter-individual variability, their contribution appeared smaller than the effect associated with vaccination. These findings highlight how vaccination reshapes immune variability across genetically diverse populations and provide population-specific insight into long-term SARS-CoV-2 immunity.