Viruses (Dec 2022)

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

  • Joseph Kamau,
  • Koray Ergunay,
  • Paul W. Webala,
  • Silvia A. Justi,
  • Brian P. Bourke,
  • Maureen W. Kamau,
  • James Hassell,
  • Mary N. Chege,
  • David K. Mwaura,
  • Cynthia Simiyu,
  • Sospeter Kibiwot,
  • Samson Onyuok,
  • Laura Caicedo-Quiroga,
  • Tao Li,
  • Dawn M. Zimmerman,
  • Yvonne-Marie Linton

DOI
https://doi.org/10.3390/v14122820
Journal volume & issue
Vol. 14, no. 12
p. 2820

Abstract

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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.

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