Bats are associated with some of the most significant and virulent emerging zoonoses globally, yet research and surveillance of bat pathogens remain limited across parts of the world. We surveyed the prevalence and genetic diversity of coronaviruses from bats in Taita Hills, southeastern Kenya, as part of ongoing surveillance efforts in this remote part of eastern Africa. We collected fecal and intestinal samples in May 2018 and March 2019 from 16 bat species. We detected one genus of coronavirus (alphacoronavirus), with an overall RNA prevalence of 6.5% (30/463). Bat species-specific RNA prevalence was 3.8% (9/235) and 11.6% (21/181) for the two most commonly captured free-tailed bat species, Mops condylurus and M. pumilus respectively, with no detections from other bat species (0/90). Phylogenetic analyses based on partial RNA- dependent RNA polymerase gene and whole genome sequences revealed that the sequences clustered together and were closely related to alphacoronavirus detected in Eswatini, Nigeria and South Africa, and more distantly related to alphacoronavirus isolated from Chaerophon plicatus bat species in Yunnan province, China and Ozimops species from southwestern Australia. Incongruent clustering patterns based on distinct genomic regions indicate that this virus may have undergone recombination events during its evolution. These findings highlight coronavirus transmission among bats that share habitats with humans and livestock, posing a potential risk of exposure. Future research should investigate whether coronaviruses detected in these bats have the potential to spillover to other hosts.

The authors have declared no competing interest.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Bat trapping and sample collections were conducted under permits from the Kenyan National Commission for Science, Technology and Innovation (permit no. NACOSTI/P/18/76501/22243) and the Kenya Wildlife Service (permit no. KWS/BRM/500), and IACUC permits from the University of Nairobi (REF: FVM BAUEC/2018/180) and University of Arkansas (protocol #22012). Sample import to Finland was approved by the Finnish Food Safety Authority (EVIRA 4250/0460/2016 and 2809/0460/2018).

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The sequences data is currently being submitted to the NCBI gene bank and will be available when the manuscript is accepted