biostudies-literatureKamau JWRBU core laboratoryArmed Forces Health Surveillance Division—Global Emerging Infections Surveillance (AFHSD-GEIS) projectUnited States Agency for International Development2820https://www.ebi.ac.uk/biostudies/studies/S-EPMC9785147biostudies-literatureUnknown14(12)<h4>Background and methods</h4>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.<h4>Results</h4>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 ferrumequiVirusesA Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats.PMC97851472000011037P0030_21_WRP0124_20_WRP0065_22_WRSimiyu COnyuok SLinton YMChege MNCaicedo-Quiroga LErgunay KHassell JMwaura DKBourke BPJusti SAKamau JKibiwot SLi TWebala PWZimmerman DMKamau MWfalseA Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats.<h4>Background and methods</h4>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.<h4>Results</h4>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 ferrumequi2022-01-01T00:00:00Z2022 Dec2026-04-08T18:29:00.582Z2025-04-06T11:11:29.21ZS-EPMC97851473656082410.3390/v14122820