Virus-host associations of bat coronaviruses along a land-use gradient in the Yucatán Peninsula, México.

Coronavirus (CoV) spillover from wildlife to humans is increasing and has caused major global epidemics, facilitated by human-induced habitat alteration that promotes zoonotic emergence. This highlights the need for sustained surveillance and a better understanding of circulation patterns within wildlife reservoirs. Although Neotropical bats harbour a highly diverse CoV community, how host traits and ecological factors shape CoV circulation and virus-host associations remains poorly characterized. During 2021-3, we conducted extensive bat sampling across 12 localities along an anthropogenic land-use gradient in the Yucatan Peninsula, Mexico, to characterize bat community diversity. We then screened bats for CoVs and evaluated the association between CoV detection and host traits and ecological variables. Detected CoVs were subsequently sequenced and phylogenetically characterized. Using publicly available databases and host phylogenetic diversity metrics, we further analysed the putative host range of each identified CoV taxon and their distribution along the gradient. Bat diversity was significantly lower in urban sites. Although overall CoV positivity was low (3.2%), we identified eight divergent CoV taxa, including two novel Alphacoronavirus sequences, one of which represents the first CoV reported from Lophostoma brasiliense. Juvenile bats were more likely to be CoV-positive, a pattern particularly pronounced in Sturnira parvidens but absent in Artibeus jamaicensis. We found variation in putative host breadth among the identified CoV taxa, supported by differences in host phylogenetic distances. Notably, CoV taxa detected at sites with lower bat diversity were associated with a greater number of reported host species and higher host phylogenetic diversity. Our findings expand the known diversity of Neotropical bat CoVs and reveal distinct patterns in CoV detection and virus-host associations across viral taxa. Sustained viral surveillance, complemented by broader genomic studies and deeper investigation into variation within and among CoV taxa, is needed to clarify these patterns, guide research priorities in the Neotropical CoVs, and help mitigate the risk of future zoonotic emergence.