Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil

•We describe the circulation of CoV lineages, 13 α-CoV and two β-CoV in AFB bats.•Coronaviruses were detected in 15 bat samples from eight bat species (50% positivity).•A cluster of α-CoVs were detected in Sturnira bat that grouped with α-CoVs lineage-1.•We identified two distinct β-CoV that clustered within MERS-CoV containing lineage C.•Results highlight the virus richness of bats and their possible roles in the public health.

Bats are notorious reservoirs of genetically-diverse and high-profile pathogens, and are playing crucial roles in the emergence and re-emergence of viruses, both in human and in animals. In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. These results highlight the virus richness of bats and their possible roles in the public health.