Metagenomic analysis reveals previously undescribed bat coronavirus strains in Eswatini

We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii. All bats from which we detected coronaviruses were captured leaving buildings or near human settlements, demonstrating the importance of continued surveillance of coronaviruses in bats to better understand the prevalence, diversity, and potential risks for spillover.The National Science Foundation Graduate Research Fellowship; a National Science Foundation Graduate Research Opportunities Worldwide grant; Innovation Fund Denmark; a Student Research Grant from Bat Conservation International; a University of Florida Biodiversity Institute Fellowship; the Zuckerman STEM Leadership Program and an NIH Grant.http://link.springer.com/journal/10393hj2022Mammal Research InstituteZoology and Entomolog