Date of Award

Summer 8-15-2021

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Immunology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Chikungunya virus (CHIKV) is an arthritogenic alphavirus that acutely causes fever as well as severe joint and muscle pain. Chronic musculoskeletal pain persists in a substantial fraction of patients for months to years after the initial infection, yet we still have a poor understanding of the mechanisms responsible for chronic disease. While replicating virus has not been detected in joint-associated tissues of patients with persistent arthritis nor in various animal models at convalescent time points, viral RNA is detected months after acute infection. However, there has been a lack of tools to study the mechanisms of chronic CHIKV disease. To identify the cells that might contribute to pathogenesis during this chronic phase, we developed a recombinant CHIKV clone that expresses Cre recombinase (CHIKV-3ʹ-Cre). When Rosa26 tdTomato reporter mice are infected with CHIKV-3ʹ-Cre, cells that survive CHIKV are permanently marked with tdTomato. Using this system we demonstrated that cells do survive CHIKV infection in vivo and persist for at least three months post infection. Immunofluorescence microscopy and flow cytometric profiling revealed that these tdTomato+ cells are predominantly myofibers and dermal and muscle fibroblasts. Finally, flow cytometry-based sorting of the tdTomato+ fibroblasts from the skin and ankle revealed that the tdTomato+ cells harbor most of the persistent CHIKV RNA at chronic time points. Therefore, this CHIKV-3ʹ-Cre and tdTomato reporter mouse system identifies the cells that survive CHIKV infection in vivo and are enriched for persistent CHIKV RNA. This model represents a useful tool for studying CHIKV pathogenesis in the acute and chronic stages of disease. To address the lack of knowledge on type I IFNs during chronic CHIKV, we evaluated chronic CHIKV pathogenesis in mice lacking IFNβ or IFNα. We found that the IFNαs were the dominant subtype that controlled chronic disease. Despite detecting a varying type I IFN response throughout the course of disease, IFNα acted within the first few days of infection to limit the levels of persistent CHIKV RNA. In addition, using the CHIKV-3-Cre tdTomato reporter system, we showed that IFNα limited the number of dermal fibroblasts and immune cells that survive CHIKV at sites of dissemination. Though myofibers play a significant role in CHIKV disease, their survival was not impacted by the loss of IFNα. IFNβ only played a small role in controlling persistent RNA levels in the contralateral foot but had no impact on surviving cells. The type I IFN regulation on various cell types has been explored for some viruses, but most work has focused on the hematopoietic compartment. Our findings have indicated that myofibers and fibroblasts are key players during acute and chronic CHIKV infection. Cell type specific type I IFN responses have not been explored in the context of CHIKV infection. Therefore, to define key cell types that require type I IFN signaling to protect against CHIKV infection in vivo, we infected mice with conditional deletions of the type I IFN receptor. Conditional deletion of Ifnar1 in mesenchymal stromal cells (Pdgfra-CreERT2) but not myofibers (Acta1-Cre) resulted in uncontrolled CHIKV replication, tissue damage, and mortality. These data suggest a critical role for mesenchymal stromal cells in type I IFN regulation of CHIKV infection. Future studies will be focused on identifying the specific cell type responsible for these phenotypes in vivo and exploring the effects of Ifnar1 in mesenchymal stromal cell deletion on the immune response. Collectively, these findings begin to elucidate mechanisms of chronic CHIKV pathogenesis and reveal unique roles for the type I IFN subtypes and their cell type specific activities. Our studies highlight that IFNα and IFNβ play divergent roles during chronic CHIKV infection, mediate cell type specific responses, and that early events during infection can dictate chronic phenotypes. Continued pursuit of defining interactions between CHIKV and the host immune responses will be paramount in developing effective therapeutics and vaccines to combat CHIKV and other emerging tropical diseases, which remain a global health and economic burden.


English (en)

Chair and Committee

Deborah J. Lenschow

Committee Members

Megan Baldridge

Included in

Virology Commons