Paramyxo- and coronavirus diversity and host associations in non-volant small mammals: evidence of viral sharing

Rodents and other non-volant small mammals (like shrews) maintain major ecological and epidemiological roles as reservoirs of zoonotic pathogens. Their presence within human-modified landscapes and interfaces with people, wildlife, and livestock create frequent opportunities for viral spillover. Despite this, the pathogen diversity and true risk of viral transmission are poorly understood by these hosts in Africa. Here, we explored the diversity and host association of paramyxoviruses and coronaviruses in non-volant small mammals from South Africa through longitudinal and opportunistic sample collection and molecular detection of viral RNA and host genetic barcoding. A high diversity of viruses was identified, with prevalences of 11.9% and 1.79% for paramyxoviruses and coronaviruses, respectively. Five instances of coinfections involving multiple paramyxoviruses and a coronavirus were detected, as well as nine Bayesian-supported paramyxovirus host genus, subfamily, and family switching, signifying frequent unrestrained viral sharing. Though the zoonotic potential of these identified viruses is unknown, the frequency of host switching suggests that these viruses may be more prone to adaptation to new host species or utilize highly conserved entry mechanisms. This highlights the risks for potential cross-species transmission events to livestock, domestic animals, and people, warranting continued surveillance.