Decoding the RNA Viromes in Rodent Lungs Provides New Insight Into the Origin and Evolutionary Patterns of Rodent-borne Pathogens in Mainland Southeast Asia

Abstract

BACKGROUND: As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens. RESULTS: This study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3,284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006-2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations. CONCLUSIONS: These results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of 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.

Hidden viral sequences in public sequencing data and warning for future emerging diseases

“…Among the 59 samples, the pegiviral infections were detected in four samples collected from a research colony in the United Kingdom (Dataset S13). A recent report partially identified a pegiviral sequence (MT085214) in tree shrews collected in Southeast Asia (35), which showed 84.9% nucleotide sequence identity to the pegivirus identified in this study (Fig. 4E).…”

Rats in the city: implications for zoonotic disease risk in an urbanizing world

“…), that may have revealed the presence of other important drivers in this system (Lau et al 2020). However, a metagenomics-based study of all microbes carried by these same rodents and their ectoparasites is currently underway and is expected to reveal a greater diversity of potential zoonoses across the urban-rural gradient (Harvey et al 2019, Wu et al 2021).…”