Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini

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Julie Teresa Shapiro
Sarah Mollerup
Randi Holm Jensen
Olofsson, Jill Katharina
Nam-phuong D. Nguyen
Thomas Arn Hansen
Vinner, Lasse
Ara Monadjem
Robert A. McCleery
Hansen, Anders Johannes

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.

Originalsprog	Engelsk
Tidsskrift	EcoHealth
Vol/bind	18
Udgave nummer	4
Sider (fra-til)	421-428
ISSN	1612-9202
DOI	https://doi.org/10.1007/s10393-021-01567-3
Status	Udgivet - 2021

Bibliografisk note

Funding Information:
We would like to thank Hervé Echecolonea, Phumlile Simelane, Mduduzi Ngwenya, and Zanele Dlamini for assistance in the field and Mandla Motsa, Smart Shabangu, Tal Fineberg the staff at Mbuluzi Game Reserve, Thea Litschka-Koen, Clifton Koen, Nick Jackson, and Kim Roques and All-Out Africa, for help with logistics. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1315138 (J.T.S), a National Science Foundation Graduate Research Opportunities Worldwide grant (J.T.S.), Innovation Fund Denmark (The Genome Denmark platform, grant no. 019-2011-2), a Student Research Grant from Bat Conservation International (J.T.S), a University of Florida Biodiversity Institute Fellowship (J.T.S), the Zuckerman STEM Leadership Program (J.T.S), and an NIH Grant (1R01GM114362) (N.D.N). Initial phylogenetic analyses used the Extreme Science and Engineering Discovery Environment (XSEDE) resources, which is supported by National Science Foundation grant number ACI-1053575. XSEDE resources were provided by project allocation TG-ASC160034.

Publisher Copyright:
© 2021, The Author(s).

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