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Literature detail

Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini.

Julie Teresa Shapiro1,2,3,4 Sarah Mollerup5 Randi Holm Jensen5 Jill Katharina Olofsson6 Nam-Phuong D Nguyen7 Thomas Arn Hansen5 Lasse Vinner6 Ara Monadjem8,9,10 Robert A McCleery11,8,10 Anders J Hansen6
Affiliations 11 institutions
  1. School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA. [email protected].
  2. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA. [email protected].
  3. University of Lyon, CIRI INSERM U1111 - CNRS UMR5308 - ENS Lyon, 46 Allée d'Italie, 69364, Lyon, France. [email protected].
  4. Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel. [email protected].
  5. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  6. Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
  7. Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
  8. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA.
  9. Department of Biological Sciences, University of Eswatini, Private Bag 4, Kwaluseni, Eswatini.
  10. Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa.
  11. School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA.
PMID 34970712 2021 Ecohealth eng ppublish
PubMed DOI Browse context

Article

Publication summary

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.

alphacoronavirus betacoronavirus Chiroptera emerging infectious diseases human–wildlife interface zoonotic disease Chiroptera Coronavirus Coronavirus Infections Metagenomics Animals Eswatini Genetic Variation Genome, Viral Phylogeny

Structured evidence records

Evidence records

3 total
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.85
Key finding

Full or near-full-length coronavirus genomes were recovered from Chaerephon pumilus and Afronycteris nana, revealing previously undescribed bat coronavirus strains in Eswatini.

Location
Not specified
Supporting text

We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana. MeSH terms include 'Coronavirus / genetics', 'Genome, Viral', 'Metagenomics', and 'Phylogeny'.

Genes or proteins
whole genome
Analysis methods
metagenomic sequencing; phylogenetic analysis
Genomic Evolution Extraction confidence 0.85
Key finding

Genome fragments from bat coronaviruses were recovered from multiple bat species, indicating genetic diversity and multiple divergent strains present in Eswatini.

Location
Not specified
Supporting text

We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana. Additional genome fragments were recovered from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii.

Genes or proteins
whole genome
Analysis methods
metagenomic sequencing; phylogenetic analysis
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Metagenomic sequencing detected coronaviruses in bats sampled in northeastern Eswatini.

Host
Chiroptera
Location
Eswatini Eswatini
Supporting text

We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples.

Method
high-throughput sequencing; metagenomics
Sample type
fecal samples
Geographic raw
northeastern Eswatini
Country inferred
Eswatini