The emergence of the SARS-CoV-2 Omicron variant, with numerous mutations in the spike region, posed a significant challenge to vaccine efficacy. Omicron's ability to evade vaccine-induced neutralizing antibodies highlighted the need for booster doses to enhance immune response. While studies have examined immune responses after vaccination and infection, many were short-term, conducted on specific populations, or lacked correlation analysis of antibody and T cell responses within individuals. This is crucial as antibodies and T cells work synergistically to provide protection against severe disease and reinfection. Malaysia utilized multiple COVID-19 vaccines, including mRNA (BNT162b2), adenoviral vector (ChAdOx1-S), and inactivated virus vaccines. A significant portion of the population received a BNT162b2 booster regardless of the primary vaccination regime, creating a unique opportunity to study both homologous and heterologous boosting strategies. This study aimed to conduct a longitudinal analysis of neutralizing antibody and T cell responses in a Malaysian cohort receiving different vaccination regimens, including those experiencing breakthrough infections, to inform public health policy regarding vaccine administration strategies.

Existing literature highlights the waning of vaccine-induced immunity over time and the reduced efficacy of two vaccine doses against Omicron. Studies demonstrated that booster doses improve cross-neutralization against Omicron, though antibody levels remain lower than those against wild-type spikes. Conversely, T cell responses appeared more stable and able to cross-recognize Omicron. While numerous studies provided insights into immune responses, most were short-term, focused on specific populations (e.g., healthcare workers), or lacked longitudinal correlation analysis of antibody and T cell responses in the same individuals. Few studies from Asia have addressed these aspects. Previous research indicated that both antibodies and T cells play vital roles in immunity against SARS-CoV-2, acting at different infection/vaccination stages. This study builds on existing knowledge by examining the longitudinal correlation between antibody and T cell responses, particularly focusing on different vaccination approaches and breakthrough infections, to provide comprehensive data for improved public health decision-making.

This longitudinal study enrolled 100 individuals (73 after exclusions) from August 26, 2021, to March 8, 2022. Participants were divided into five groups: (1) 25 uninfected individuals with two BNT doses; (2) 8 post-COVID-19 individuals with two doses of any vaccine; (3) 14 uninfected individuals with BNT primary doses and BNT booster (homologous); (4) 15 uninfected individuals with ChAdOx1-S primary doses and BNT booster (heterologous); and (5) 11 individuals with BNT primary and booster doses who experienced breakthrough infections. Plasma samples were collected at various time points before and after vaccinations and breakthrough infection. Neutralizing antibody titers were measured using a SARS-CoV-2 pseudovirus neutralization test against WT and Omicron spikes. T cell responses were assessed using the QuantiFERON SARS-CoV-2 assay, measuring interferon-γ (IFN-γ) release. Statistical analysis included unpaired t-tests, Fisher's exact tests, Wilcoxon matched-pairs signed-rank tests, Mann-Whitney U-tests, and Spearman rank correlation coefficient to compare group differences and correlations between antibody and T cell responses. Elecsys Anti-SARS-CoV-2 S and Elecsys Anti-SARS-CoV-2 N assays were also used for antibody detection.

Post-COVID-19 individuals had significantly higher and more durable neutralizing antibodies against WT and Omicron compared to uninfected vaccinated individuals. Two doses of BNT162b2 induced stronger antibody and T cell responses than ChAdOx1-S. The BNT162b2 booster significantly improved humoral responses against WT but showed comparable cross-neutralization against Omicron and T cell responses in both homologous and heterologous groups, although the homologous group maintained higher WT neutralizing antibodies after three months. Breakthrough infections significantly boosted neutralizing antibodies but not T cell responses in the homologous booster group. There was a strong positive correlation between neutralizing antibodies and T cell responses in post-COVID-19 and homologous booster groups, while the uninfected group showed a weak negative correlation. Before the booster, the BNT-primed group demonstrated a stronger correlation than the ChAd-primed group. Following the booster, the correlation varied among groups; the homologous group showed moderate correlation, but the heterologous group showed weak correlation.

The findings underscore the importance of booster doses in enhancing immunity against Omicron, particularly the superior humoral response of the BNT162b2 booster. While heterologous boosting provides comparable T cell responses and Omicron cross-neutralization, the homologous regimen provides superior protection against WT. The significant increase in neutralizing antibodies after breakthrough infection, without a concurrent increase in T cell responses, suggests a dominant role for humoral immunity in recovery from mild breakthrough cases. The differences in correlation between antibody and T cell responses across groups point towards distinct immunological mechanisms in response to different vaccination strategies. These data support the continued use of BNT162b2 as a booster. The study highlights the value of considering both humoral and T cell responses in vaccine strategies.

This study demonstrated that both humoral and cellular immune responses were detectable up to three months after the second and booster doses. Homologous BNT162b2 boosting provided better protection against WT, while heterologous boosting offered similar protection against Omicron and T cell responses. The correlation between antibody and T cell responses varied across groups. Breakthrough infections significantly increased neutralizing antibodies but not T cell responses. These results provide insights to guide public health policies on vaccination strategies, suggesting flexibility in vaccine use should shortages occur.

The study had a relatively small sample size, which could limit the generalizability of the findings. The study duration of six months might not capture long-term immune response durability. The cohort primarily consisted of healthy, relatively young individuals, potentially limiting the applicability of the results to older populations or those with underlying health conditions. The QuantiFERON assay may have limitations in detecting T cell responses beyond six months. Finally, the study focused only on mRNA and adenoviral vector vaccines, not including other vaccine platforms.