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.