A wide diversity of viruses detected in African mammals involved in the wild meat supply chain

Abstract
The processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome of many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. Here, we present the findings of a metagenomic viral screening of 101 mammalian specimens belonging to 28 wild African species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected in various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of sixteen virus strains were detected, belonging to the families Arteriviridae, Retroviridae and Sedoreoviridae (primates), Picobirnaviridae (primates and rodents), Picornaviridae (rodents), Hepadnaviridae (hyrax), Orthoherpesviridae (artiodactylid and carnivore) and Spinareoviridae (carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during close interactions with wildlife in the wild meat supply chain.

Author summary
The wild meat supply chain represents a critical interface between humans and wildlife, posing significant risks for zoonotic disease emergence. Despite previous links between viral outbreaks and the wild meat supply chain, our understanding of the virome of many traded mammalian species remains incomplete. In this study, we conducted a metagenomic viral screening of 101 mammals from 28 wild African species and one domesticated species, all traded for their meat in the Democratic Republic of the Congo or Brussels, Belgium. We identified sixteen virus strains across multiple viral families, some of which were detected in these particular mammalian species for the first time. Notably, we found viruses closely related to known zoonotic pathogens, including human picobirnavirus, simian foamy viruses, and rotavirus A—with primates, a taxonomic group closely related to humans, serving as hosts. These findings highlight the vast viral diversity present in species involved in the wild meat trade and reinforce the potential for cross-species transmission during handling, trade, and consumption. Our study contributes to the growing understanding of wildlife viromes and provides crucial insights into the risks associated with the wild meat supply chain, emphasising the need for enhanced surveillance and mitigation strategies to prevent future zoonotic spillovers.