Decoding the RNA viromes of rodent lungs provides new visions into the origin and evolution pattern of rodent-borne diseases in Mainland Southeast Asia

Abstract

Abstract BACKGROUND As the largest group of mammalian species widely distributed all over the world, rodents are the natural reservoirs of diverse zoonotic viruses. Comprehensive understanding of the core virome in diverse rodent species could therefore assist efforts to predict and reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens. RESULTS This study aimed to describe the viral range detected in rodent lungs in Mainland Southeast Asia. Lung samples were collected from 3,284 rodents and insectivores of the orders Rodentia , Soricomorpha , Scandentia , and Erinaceomorpha in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006-2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of mammalian viruses within lungs and the ecological and genetic imprints of novel viruses. Further analysis revealed that the viral circulation in lungs is vastly different from those of throat and anal swabs reported previously. Many mammal or arthropod related viruses with distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genetic characters, host species, and locations. CONCLUSIONS These results expand our understanding of the core viromes of rodents and insectivores in Mainland Southeast Asia and suggest that a high diversity of viruses remain undiscovered in this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia.