Coronavirus Detection in Bats Captured on the Deforestation Arc of Mato Grosso, Brazil

Coronaviruses (CoV) are RNA viruses associated with enteric and respiratory diseases and known for their emergence potential in humans and other mammals. CoVs originate from zoonotic transmission, in which bats are natural reservoirs. Previous studies suggest that CoV diversity is positively correlated with bat diversity, whereas anthropogenic influence can increase prevalence in bat hosts. The present study investigates the presence of CoVs in bats in the Amazon-Cerrado transition region in the state of Mato Grosso, Brazil. In total, 57 individuals were captured, belonging to 17 species in 7 subfamilies and 4 families. Among the captured bats in the region, the most abundant species were Carollia perspicillata (24.6%; 14/57), C. brevicauda (17.5%; 10/57), and Phyllostomus hastatus (10.5%; 6/57). Bat sampling richness evidenced a diversity pattern consistent with fragmented forests. A total of 16 faecal samples were collected and tested for CoV infection, with 2 positive samples sequenced (12.5%; 95% CI 3.49-36.02). Phylogenetic analyses characterised the CoVs found as divergent sequences within distinct branches of American Alphacoronavirus lineages previously reported. The RdRp phylogenetic tree exhibited biome-associated structuring as well as multiple bat host species within the clades, indicating a wide distribution within hosts and biomes. Nevertheless, further studies are necessary to ascertain the relationship between CoV spatial dynamics and the role of the Brazilian Amazon-Cerrado transition zone, where deforestation increases human-bat contact and access its spillover potential risk.