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Literature detail

A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats.

Joseph Kamau1 Koray Ergunay2,3,4,5 Paul W Webala6 Silvia A Justi2,3,5 Brian P Bourke2,3,5 Maureen W Kamau7,8 James Hassell7,9,10 Mary N Chege1 David K Mwaura1 Cynthia Simiyu6 Sospeter Kibiwot6 Samson Onyuok11 Laura Caicedo-Quiroga2,3,5 Tao Li12 Dawn M Zimmerman2,5,11 Yvonne-Marie Linton2,3,5
Affiliations 12 institutions
  1. One Health Centre, Institute of Primate Research (IPR), Nairobi 00502, Kenya.
  2. Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA.
  3. One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA.
  4. Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey.
  5. Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC 20560, USA.
  6. Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya.
  7. Mpala Research Centre, Nanyuki 10400, Kenya.
  8. Global Health Program, Smithsonian Conservation Biology Institute (SCBI), Front Royal, VA 22630, USA.
  9. Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT 06520, USA.
  10. International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
  11. Zoology Department, National Museums of Kenya, Nairobi 00100, Kenya.
  12. Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
PMID 36560824 2022 Viruses eng epublish
PubMed DOI Browse context

Article

Publication summary

To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing. Viruses belonging to the <i>Astroviridae</i>, <i>Circoviridae</i>, <i>Coronaviridae</i>, <i>Dicistroviridae</i>, <i>Herpesviridae</i> and <i>Retroviridae</i> were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised <i>Myotis myotis</i>, <i>Myotis ricketti</i>, <i>Myotis daubentonii</i> and Galidia endogenous retroviruses, murine leukemia virus-related virus and <i>Rhinolophus ferrumequinum</i> retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified. Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.

Africa astrovirus bat coronavirus Kenya metagenome retrovirus Alphacoronavirus Astroviridae Chiroptera COVID-19 Herpesviridae RNA Viruses Animals Kenya Phylogeny Retroviridae SARS-CoV-2

Structured evidence records

Evidence records

5 total
Zoonotic Surveillance 3 records
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Metagenomic sequencing of bat samples from Kenyan caves identified a novel alphacoronavirus lineage with 24.1% prevalence among bats.

Host
Chiroptera
Location
Kenya Kenya
Supporting text

Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage.

Method
metagenome sequencing
Sample type
oral-fecal swabs
Geographic raw
Kenya
Country inferred
Kenya
Zoonotic Surveillance Extraction confidence 0.97
Key finding

Astrovirus sequences were frequently detected among Kenyan cave bat samples, showing substantial viral diversity.

Virus
Astroviridae
Host
Chiroptera
Location
Kenya Kenya
Supporting text

Astrovirus sequences were detected in 25.9% of all samples, with considerable diversity.

Method
metagenome sequencing
Sample type
oral-fecal swabs
Geographic raw
Kenya
Country inferred
Kenya
Zoonotic Surveillance Extraction confidence 0.96
Key finding

Metagenomic surveillance found retrovirus sequences in 74.1% of bat samples from Kenyan caves, varying by species and site.

Virus
Retroviridae
Host
Chiroptera
Location
Kenya Kenya
Supporting text

Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species.

Method
metagenome sequencing
Sample type
oral-fecal swabs
Geographic raw
Kenya
Country inferred
Kenya
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.85
Key finding

A near-complete Rhinolophus ferrumequinum retrovirus genome from Kenyan bats showed 2.8% nucleotide divergence from the prototype strain, indicating local genomic evolution.

Virus
Retroviridae
Host
Chiroptera
Location
Not specified
Supporting text

A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized.

Genes or proteins
whole genome
Analysis methods
metagenome sequencing; comparative genomic analysis
Genomic Evolution Extraction confidence 0.85
Key finding

ORF1ab sequence analysis identified a novel alphacoronavirus lineage in Kenyan cave bats.

Host
Chiroptera
Location
Not specified
Supporting text

Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage.

Genes or proteins
ORF1ab
Analysis methods
sequence analysis; phylogenetic analysis