Bat coronavirus surveillance across different habitats in Yucatán, México

Bats, which play a vital role in maintaining ecosystems, are also known as natural reservoirs of coronaviruses (CoVs), thus have raised concerns about their potential transmission to humans, particularly in light of the emergence of MERS-CoV, SARS-CoV, and SARS-CoV-2. The increasing impact of human activities and ecosystem modifications is reshaping bat community structure and ecology, heightening the risk of the emergence of potential epidemics. Therefore, continuous monitoring of these viruses in bats is necessary. Despite the rich diversity of bats species in México, few studies have been conducted to search for CoVs in these group of mammals. In the present study we conducted CoV surveillance across previously unexplored sites in the state of Yucatán, a state located within the ecologically diverse Yucatán Peninsula, a tropical region undergoing pronounced anthropogenic changes, including deforestation, agricultural expansion and urbanization. We captured 191 bats between 2021 and 2022 in three different habitats: diversified rural (Tzucacab), rural (Tizimín) and urban (Mérida). Molecular analyses had revealed a 5.4% CoV prevalence, with the diversified rural site exhibiting a notably elevated rate (26.3%). Subsequent sequencing and phylogenetic assessment revealed four distinct Alphacoronavirus genotypes, indicating host-specific clustering among Phyllostomidae bats. Notably, one was detected for the first time in a Sturnira species. Our findings suggest a reduced likelihood of transmission of these viruses to humans or other species, evidenced by clustering patterns and sequence dissimilarity with known CoVs. We emphasize that maintaining sustained virus surveillance in bats is crucial to understanding viral diversity and identifying potential risks to human and animal health.