Immunologic Studies Associated with COVID-19

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications, trials & patents

Abstract

In 2025, we focused our efforts on longitudinal analyses of antibody and B-cell responses following multiple exposures to SARS-CoV-2 through infection and/or vaccination; we contributed to studies on the mucosal response to the virus; and we contributed to another large longitudinal study that aimed to understand mechanisms associated with long COVID. Our efforts addressed: 1) humoral immunity to SARS-CoV-2 mRNA vaccines and the effects of SARS-CoV-2 infection on B-cell and antibody responses to the virus; 2) how these responses differ between peripheral blood and mucosal tissues; and 3) how B-cell and antibody responses to SARS-CoV-2 are modulated by long COVID. In 2025, we completed and published one large multi-year longitudinal study on humoral immunity to repeated SARS-CoV-2 exposures from infection and/or vaccination. From December of 2020 through August 2023, we collected serial blood samples from people who received three to five doses of the SARS-CoV-2 mRNA vaccine. Our first organized cohort was established in late 2020 using an existing blood draw protocol, ClinicalTrials.gov identifier NCT00001281, where we enrolled participants who were eligible to receive their two-dose mRNA vaccine and designed a study with serial blood draws to characterize the primary immune response to the vaccine. As it became clear that booster vaccines would be needed, we wrote a broad-purpose protocol, ClinicalTrials.gov identifier NCT05078905, that would allow us to rapidly study vaccine responses to SARS-CoV-2 and other emerging pathogens. We eventually modified the protocol to include the ability to compare responses to vaccination and breakthrough infections. From October 2021 through March of 2022, we enrolled 100 participants, including 25 individuals from the first cohort, to evaluate antibody and B-cell responses to the first SARS-CoV-2 mRNA booster vaccine (third dose) and to determine whether these responses were affected by prior or post-boost SARS-CoV-2 infection. A first interim analysis was performed through day 60 post-vaccination on 66 participants, 11 of whom had been infected prior to and another 11 after vaccination. We found that recent SARS-CoV-2 infection abrogated antibody and B-cell responses to the booster vaccine. These findings were published in Cell late 2022. The protocol was written in a way that reset study visits each time a participant received a booster vaccine, which by early 2023 had ranged from 3-5 doses. Additional protocol visits were added after breakthrough infections, at timepoints which matched those post-vaccination. By August 2023, we had collected longitudinal samples following 3-6 exposures to SARS-CoV-2 vaccine/infection and addressed the effect of these multiple and varied exposures on the temporal dynamics of B-cell and antibody responses to the virus. To this end, we focused on 450 samples collected on 33 participants over 18 timepoints, from the beginning of dose 2 through to 6 months after the bivalent dose, which was either the fourth or fifth vaccine dose. By the last timepoint, 11 of 33 study participants remained uninfected and among those who became infected, 16 had provided 1-2 additional blood samples post-infection. We assessed B-cell responses to SARS-CoV-2 spike proteins by spectral flow cytometry, as well as antibody responses by measuring binding antibodies against a panel of wild-type (WT) and eight variant receptor binding domain (RBD) proteins and antibody neutralizing titers against WT, BA.5 (to match the bivalent vaccine) and XBB.1.5 (to match the major variant in circulation at time of sample evaluation) with a pseudovirus-based assay. Using high-dimensional clustering and trajectory analyses of the flow cytometry data, we identified five clusters with distinct B-cell phenotypes that were the main drivers of RBD reactivity, peaking at day 14 after the first booster vaccine (dose 3) in the absence of infection, and with overall frequencies that were similar to responses at 14-28 days after a breakthrough infection. While there were differences in the distribution of RBD-reactive clusters at peak of response post-vaccination versus post-infection, the overall outcomes at the end of study were similar between the two groups. RBD reactivity in a subset of B-cell clusters also correlated with neutralizing antibody titers, suggesting a role for these B cells in the generation and durability of humoral immunity, which is critical for preventing and curtailing symptomatic SARS-CoV-2 infection. A manuscript describing these findings was published in Cell Reports in June 2025. In 2025, we have continued to collaborate with NIAID researchers, mainly by providing expertise that we have gained studying B cells in our various studies on SARS-CoV-2. We helped other teams design immunophenotyping panels to interrogate the response of B cells to SARS-CoV-2. One such study headed by our collaborators Kalpana Manthiram and Pamela Schwartzberg in the Laboratory of Immune System Biology has addressed the immune response to SARS-CoV-2 in pharyngeal lymphoid tissues of children following exposure to the virus through vaccination and infection. The contribution of our group was to help develop multiparameter B-cell panels for evaluating the antigen-specific responses to the virus in tonsil and adenoid lymphoid tissues. These results lay the groundwork for new studies on the persistence of tissue-specific immunity to SARS-CoV-2, and other respiratory viral pathogens and address effects of imprinting and multiple exposures on these responses. These findings have led to a manuscript that has been submitted to a high-tier journal. Finally, we continue to offer our B-cell and antibody expertise to studies on long-term sequelae of COVID-19 in a large cohort of participants enrolled in the clinical research protocol, ClinicalTrials.gov identifier NCT04411147, led by Dr. Michael Sneller in the LIR. Samples collected from our studies on the humoral response to vaccination with the SARS-CoV-2 mRNA vaccine helped demonstrate that the presence of the viral spike protein in serum is short-lived, observed only within 48 hours of vaccination but not during post-infection sequelae.