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

Viruses. 2022 Dec 17;14(12):2820. doi: 10.3390/v14122820.

Abstract

Background and methods: 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.

Results: Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae 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 Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum 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.

Conclusions: Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.

Keywords: Africa; Kenya; astrovirus; bat; coronavirus; metagenome; retrovirus.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alphacoronavirus*
  • Animals
  • Astroviridae* / genetics
  • COVID-19*
  • Chiroptera*
  • Herpesviridae*
  • Kenya / epidemiology
  • Phylogeny
  • RNA Viruses* / genetics
  • Retroviridae
  • SARS-CoV-2

Grants and funding

Metagenomic sequencing and downstream analyzes were funded by the Armed Forces Health Surveillance Division—Global Emerging Infections Surveillance (AFHSD-GEIS) project P0124_20_WR to Y.-M.L. (EAST: A Pan-Regional Vector Biosurveillance Network to Detect, Characterize, and Predict Endemic and Emergent Zoonosis in East and Central Africa) and WRBU core laboratory support awards P0030_21_WR and P0065_22_WR to Y.-M.L., P.W.W. was supported in part through Partnerships for Enhanced Engagement in Research (PEER) funding (Award no. 2000011037), under the United States Agency for International Development (USAID) and the U.S. National Academies of Sciences, Engineering, and Medicine (NASEM). Funders had no influence on results presented.