Genomic characterization of novel orthohepeviruses in shrews and rats from Kenya

Rodents and shrews are two groups of small mammals living in proximity with humans and have been known to harbour a variety of zoonotic pathogens. Cross-species transmission of hepeviruses from animals, particularly the recent sporadic emergence of human infections by rat-borne hepeviruses, has posed a growing threat to human health. Here, we report the full-genome identification of two orthohepeviruses in African giant shrew (<i>Crocidura olivieri</i>) and black rat (<i>Rattus rattus</i>) from Kenya, named Co-KY2016 and Rr-KY2016, respectively, the partial polymerase gene sequences of which were previously described. Co-KY2016 is highly distinct from representative strains of all currently recognized orthohepevirus species, sharing less than 55% overall genome identity and possibly representing at least a novel virus species together with other recently reported shrew hepeviruses. Rr-KY2016 shared higher similarity with other hepeviruses of rat origin in the <i>Rocahepevirus</i> genus, including human-infecting strains. Our results provide more evidence that rats and shrews are reservoir hosts of hepeviruses and support previous findings that different hepeviruses have undergone co-speciation with their hosts during evolution. This study increases our understanding of the distribution and genetic diversity of hepeviruses in wildlife as well as their spillover risk in Africa. It also highlights the importance of identifying hepeviruses in rodents, shrews or other wildlife and investigating possible zoonotic transmission of hepeviruses to mitigate the emergence of future diseases that could threaten public health.