Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini

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

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


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.

Original languageEnglish
Pages (from-to)421-428
Number of pages8
Issue number4
StatePublished - 1 Dec 2021


  • Chiroptera
  • alphacoronavirus
  • betacoronavirus
  • emerging infectious diseases
  • human–wildlife interface
  • zoonotic disease

ASJC Scopus subject areas

  • Ecology
  • Health, Toxicology and Mutagenesis


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