T cell immunity induced by SARS-CoV-2 and flavivirus vaccination

Emerging viruses is a continued threat to global public health and vaccines is the most effective medical intervention to reduce viral infectious disease. This thesis contains clinical studies that were conducted to better understand T cell responses to vaccination against SARS-CoV-2 and flaviviruses. Multiple vaccine platforms have been studied, including mRNA-based vaccines against COVID-19 and live attenuated or inactivated whole flavivirus vaccines. This thesis presents studies in the chronological order they were conducted, with Papers I-III focusing on SARS-CoV-2 and Paper IV on flaviviruses.

In Paper I, we studied the T cell response in patients with CLL after primary vaccination with the mRNA BNT162b2 vaccine. Using an IFN-y ELISpot assay, we longitudinally assessed an increased T cell response after two doses of mRNA BNT162b2. Compared to healthy individuals the T cell response was lower, indicating that a booster dose may be important to reach higher protective levels. In Paper II, a cohort of patients with CLL with hybrid immunity was studied to measure the adaptive immune response. Spike- and nucleocapsid-specific antibodies were measured in serum and saliva, and T cell responses were evaluated using an IFN-y ELISpot assay and AIM assay. A robust antibody response in serum and saliva, as well as in the T-cell compartment, was observed after three doses of mRNA vaccination in a hybrid setting of CLL patients. In Paper III, we studied the relationship between SARS-CoV-2 and HCoV-OC43 T cells in unexposed individuals to better understand pre-existing immunity to SARS-CoV-2. We mapped and identified several T cell epitopes in spike, nucleocapsid and membrane regions of SARS-CoV-2 and OC43 using a FluroSpot assay.

In Paper IV, we longitudinally assessed the T cell response in a clinical cohort of healthy participants co-administrated with YFV vaccine and either TBEV or JEV vaccines. Using an AIM assay, we measured the frequency of activated CD4+ and CD8+ T cells specific for envelope (E), capsid (C) and non-structural (NS) 5 proteins. We detected robust T cell responses after flavivirus vaccination that was primarily directed against envelope. Comparing single vaccinated individuals with concomitant vaccinated participants revealed strikingly similar results. Across all vaccine cohorts, limited cross-reactivity between different flaviviruses, including Zika peptides, was observed. Detectable cross-reactive responses were more prominent for CD8+ T cells. In conclusion, this study demonstrates that co-vaccination elicits responses comparable to single administration and importantly, does not diminish the virus-specific T cell response.

The clinical studies in this thesis have expanded our understanding of T cells in the viral vaccine response. These findings offer valuable insights into the immune mechanisms induced by infection with and vaccination against emerging viruses.

List of scientific papers

I. Blixt, L *. , Wullimann, D *. , Aleman, S., Lundin, J., Chen, P., Gao, Y., Cuapio, A., Akber, M., Lange, J., Rivera-Ballesteros, O., Buggert, M., Ljunggren, H. G., Hansson, L., & Österborg, A. (2022). T-cell immune responses following vaccination with mRNA BNT162b2 against SARS-CoV-2 in patients with chronic lymphocytic leukemia: results from a prospective open-label clinical trial. Haematologica, 107(4), 1000-1003. *Joint first authors.
https://doi.org/10.3324/haematol.2021.280300

II. Blixt, L., Gao, Y *. , Wullimann, D *. , Murén Ingelman-Sundberg, H., Muschiol, S., Healy, K., Bogdanovic, G., Pin, E., Nilsson, P., Kjellander, C., Grifoni, A., Sette, A., Sällberg Chen, M., Ljunggren, H. G., Buggert, M., Hansson, L., & Österborg, A. (2022). Hybrid immunity in immunocompromised patients with CLL after SARS-CoV-2 infection followed by booster mRNA vaccination. Blood, 140(22), 2403-2407. * Authors contributed equally.
https://doi.org/10.1182/blood.2022016815

III. Humbert, M., Olofsson, A., Wullimann, D., Niessl, J., Hodcroft, E. B., Cai, C., Gao, Y., Sohlberg, E., Dyrdak, R., Mikaeloff, F., Neogi, U., Albert, J., Malmberg, K. J., Lund-Johansen, F., Aleman, S., Björkhem- Bergman, L., Jenmalm, M. C., Ljunggren, H. G., Buggert, M., & Karlsson, A. C. (2023). Functional SARS-CoV-2 cross-reactive CD4+ T cells established in early childhood decline with age. Proceedings of the National Academy of Sciences of the United States of America, 120(12), e2220320120.
https://doi.org/10.1073/pnas.2220320120

IV. Wullimann, D., Sandberg, J. T., Akber, M., Löfling, M., Gredmark-Russ, S., Michaëlsson, J., Buggert, M., Blom, K., & Ljunggren, H. G. (2025). Antigen-specific T cell responses following single and co- administration of tick-borne encephalitis, Japanese encephalitis, and yellow fever virus vaccines: Results from an open-label, non- randomized clinical trial-cohort. PLoS neglected tropical diseases, 19(2), e0012693.
https://doi.org/10.1371/journal.pntd.0012693