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. 2021 Dec;18(4):421-428.
doi: 10.1007/s10393-021-01567-3. Epub 2021 Dec 30.

Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini

Julie Teresa Shapiro  1   2   3   4 , Sarah Mollerup  5 , Randi Holm Jensen  5 , Jill Katharina Olofsson  6 , Nam-Phuong D Nguyen  7 , Thomas Arn Hansen  5 , Lasse Vinner  6 , Ara Monadjem  8   9   10 , Robert A McCleery  11   8   10 , Anders J Hansen  6
Affiliations

Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini

Julie Teresa Shapiro et al. Ecohealth. 2021 Dec.

Abstract

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.

Keywords: Chiroptera; alphacoronavirus; betacoronavirus; emerging infectious diseases; human–wildlife interface; zoonotic disease.

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Figures

Figure 1
Figure 1
Map of study region. Site numbers indicate where bats were captured and are referenced in Table 2. Sites from which coronaviruses were detected in bats are marked in red, while coronaviruses were not detected in bats captured from sites marked in black. The area shaded in gray is Hlane National Park. Solid lines indicate national borders and dotted lines indicate roads.
Figure 2
Figure 2
Maximum likelihood phylogeny of coronaviruses (CoVs) based on full genomes, including reference genomes and the four full-length and partial genomes from this study, which are labelled in red and can be retrieved under accession numbers OL807608, OL807609, OL807610, OL807611. Stars indicate branches with 100% bootstrap support.
See this image and copyright information in PMC

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