A Novel Nobecovirus in an Epomophorus wahlbergi Bat from Nairobi, Kenya

Abstract

Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species-<i>Eidolon helvum</i> (<i>n</i> = 6) and <i>Epomophorus wahlbergi</i> (<i>n</i> = 43) (family Pteropodidae)-in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the <i>Coronaviridae</i> family <i>Betacoronavirus</i> genus and <i>Nobecovirus</i> subclade was characterized from <i>E. wahlbergi</i>. Phylogenetic analysis indicates this unique <i>Nobecovirus</i> clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa's most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.