A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats
2022
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
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 <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. Conclusions: Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.
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