Detection and genetic characterization of alphacoronaviruses in co-roosting bat species, southeastern Kenya

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. Author SummaryBats are known to carry several zoonotic pathogens with potential to cause serious illnesses and death in humans. Yet, surveillance on the pathogens they carry remains limited in much of the world. We studied the prevalence and diversity of coronaviruses from bats in Taita Hills, southeastern Kenya to better understand the circulation of these viruses and inform disease preparedness. We detected alphacoronaviruses in urban Mops condylurus and M. pumilus bat species. Our bat alphacoronaviruses detected were closely related to alphacoronaviruses that have been previously detected in bats elsewhere in Africa and distantly related to alphacoronavirus detected from Chaerophon plicatus bat species in Yunnan province, China and Ozimops species from southwestern Australia. We identified possible recombination events between the virus strains in the study area. This work demonstrates coronavirus circulation among bats that share habitats with people and livestock providing conditions that can lead to spillover. Identifying whether coronaviruses detected in these bats have the potential to infect other hosts is critical for developing countermeasures and mitigating potential outbreaks.