T Cell Responses Induced by Attenuated Flavivirus Vaccination Are Specific and Show Limited Cross-Reactivity with Other Flavivirus Species

Abstract

Members of the flavivirus genus share a high level of sequence similarity and often circulate in the same geographical regions. However, whether T cells induced by one viral species cross-react with other related flaviviruses has not been globally addressed. In this study, we tested pools of epitopes derived from dengue (DENV), Zika (ZIKV), Japanese encephalitis (JEV), West Nile (WNV), and yellow fever (YFV) viruses by intracellular cytokine staining (ICS) using peripheral blood mononuclear cells (PBMCs) of individuals naturally exposed to DENV or immunized with DENV (TV005) or YF17D vaccine. CD8 T cell responses recognized epitopes from multiple flaviviruses; however, the magnitude of cross-reactive responses was consistently severalfold lower than those to the autologous epitope pools and was associated with lower expression of activation markers such as CD40L, CD69, and CD137. Next, we characterized the antigen sensitivity of short-term T cell lines (TCL) representing 29 different individual epitope/donor combinations. TCL derived from DENV monovalent vaccinees induced CD8 and CD4 T cells that cross-reacted within the DENV serocomplex but were consistently associated with >100-fold-lower antigen sensitivity for most other flaviviruses, with no cross-recognition of YFV-derived peptides. CD8 and CD4 TCL from YF17D vaccinees were associated with very limited cross-reactivity with any other flaviviruses and in five out of eight cases >1,000-fold-lower antigen sensitivity. Overall, our data suggest limited cross-reactivity for both CD4 and CD8 T cell responses between flaviviruses and have implications for understanding immunity elicited by natural infection and strategies to develop live attenuated vaccines against flaviviral species. IMPORTANCE The envelope (E) protein is the dominant target of neutralizing antibodies for dengue virus (DENV) and yellow fever virus (YFV). Accordingly, several DENV vaccine constructs use the E protein in a live attenuated vaccine format, utilizing a backbone derived from a heterologous flavivirus (such as YF) as a delivery vector. This backbone comprises the nonstructural (NS) and capsid (C) antigens, which are dominant targets of T cell responses. Here, we demonstrate that cross-reactivity at the level of T cell responses among different flaviviruses is very limited, despite high levels of sequence homology. Thus, the use of heterologous flavivirus species as a live attenuated vaccine vector is not likely to generate optimal T cell responses and might thus impair vaccine performance.

Cross-reactive memory T cells and herd immunity to SARS-CoV-2

“…The difference in the abundance of CD4 + versus CD8 + cross-reactive memory T cells likely reflects the basic differences in antigen recognition between these T cell types. In a study examining T cell responses to different flavivirus species, it was found that cross-reactivity for CD8 + T cells was limited to peptides carrying one or two substitutions, whereas cross-reactivity for CD4 + T cells could be detected for peptides with far lower degrees of homology 19 . In sum, the cross-reactive immune memory to SARS-CoV-2 appears limited largely to one of the three major arms of adaptive immunity, the 'helper' or CD4 + T cells.…”

Differential T cell reactivity to seasonal coronaviruses and SARS-CoV-2 in community and health care workers

“…The CMV MP is a pool of previously reported Class I and Class II epitopes ( 43 ). To study T cell responses against SARS-CoV-2, we used the entire SARS-CoV-2 genome (GenBank: MN908947 ) and we generated a MP of 15-mer peptides (overlapping by 10 amino acids) spanning the entire sequence of the spike protein and a MP for the remainder genome consistent of dominant HLA Class II predicted CD4 + T cell epitopes as previously described ( 44 , 69 ). ( Supplementary Table 1 ).…”

Viral Emerging Diseases: Challenges in Developing Vaccination Strategies

“…Recently, the analysis of PBMCs isolated from individuals infected by DENV or vaccinated with DENV TV005 or YF17D vaccines, and pulsed with a pool of antigens from autologous and heterologous flaviviruses, indicated that both CD4 and CD8 T-cell responses were specific, with little or no cross-reactivity, despite the high level of homology ( 183 ). Individuals pre-exposed to DENV infection developed T-cell responses against non-structural ZIKA proteins rather than structural envelope protein, suggesting that previous flaviviral infections biased the T-cell response toward more cross-reactive non-structural epitopes ( 184 ).…”