Bats from an area of the Colombian Caribbean reveal the circulation of Alphacoronavirus

Abstract

The evolutionary origin of coronaviruses is related to bats (order Chiroptera), and their association with pathologies in animals and humans is expected. Anthropic threats reduce bat diversity and expose humans to extraordinary transmission and spread of associated viruses, putting health and food security at risk owing to the multiple ecological roles that bats play. This study aimed to determine the presence of coronaviruses in bats in the Department of Córdoba, Colombia. Between 2022 and 2023, 11 municipalities were selected using non-probabilistic sampling methods. A total of 262 bats belonging to 16 species of five families were captured and identified. Serological tests were performed to detect SARS-CoV-2, and nested polymerase chain reaction (PCR) was performed to detect the coronavirus RdRp gene. RdRp-positive samples were sequenced using Sanger sequencing. Five specimens (2.7%) had antibodies against the coronavirus N protein, and the RdRp gene was detected in 55 specimens (21.0%), all belonging to the family Phyllostomidae. Phylogenetic analysis of the RdRp gene revealed that the newly generated sequences represented alphacoronaviruses. Bats tested in ecoregions with greater anthropogenic intervention were shown to be carriers of coronaviruses, unlike bats from conserved ecoregions. Coronavirus surveillance in bats has revealed previous infections through serology and circulating infections in natural populations of different ecoregions of the Department of Córdoba, where inter-species jumps could be generated by contact between bats and domestic/wild animals, or humans.