Temporal transcriptomic and microbial changes in American bison during experimental SARS-CoV-2 challenge

SARS-CoV-2 continues to pose a threat to humans as well as domestic and wild animals. The variability in severity of clinical signs, the zoonotic potential, and the host-specific response to infection contribute to the persistence of circulation of disease. In wildlife species white-tailed deer have been shown to be more permissive to infection than bovids. However, amongst bovids, American bison have shown a greater susceptibility than cattle. In this study we investigate the transcriptomic response to experimental SARS-CoV-2 infection in bison over time. Substantial numbers of differentially expressed genes were identified between pre- and 2, 5, 7, 14, and 21 days post-infection. KEGG and GO term analysis identified associations with immune response, inflammatory response, and viral infection including COVID-19. IPA analysis of the SARS coronavirus pathway highlighted differences in signaling at days 2 versus 21 post-infection. We additionally examined changes in the nasal microbiome of bison over the course of experimental infection, which suggested an increase in opportunity for secondary infection causing pathogens such as Mannheimia. Collectively this study presents a profile of bison transcriptomic response to SARS-CoV-2 infection and continues to expand our understanding of variation in host response. SummarySARS-CoV-2 remains a threat to humans, domestic animals, and wildlife. Among bovids, American bison show greater susceptibility than cattle. We characterized the bison transcriptomic response to experimental infection across six timepoints, identifying extensive differential gene expression associated with immune, inflammatory, and antiviral pathways. KEGG, GO, and IPA analyses revealed activation of coronavirus-related signaling and shifts between days 2 and 21. We additionally examined changes in the nasal microbiome of bison over the course of experimental infection, which suggested an increase in opportunity for secondary infection causing pathogens such as Mannheimia. The results refine understanding of host responses to SARS-CoV-2 in bison.