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