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 3284 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

“…A recent report partially identified a pegiviral sequence (GenBank accession no. MT085214.1) in tree shrews collected in Southeast Asia ( 36 ) which showed 84.9% nucleotide sequence identity to the pegivirus identified in this study ( Fig. 5E ).…”

A comprehensive survey of bat sarbecoviruses across China for the origin tracing of SARS-CoV and SARS-CoV-2

“…To develop the databases of the potential zoonotic viral pathogens and their reservoir hosts, we have conducted a series of viral surveys on rodents and bats across China and Southeast Asia (SEA) in the past ten years [24][25][26] , and established two online virome databases (DBatVir and DRodVir) 27,28 . In this study, we conducted retrospective CoV tests of environmental samples collected from Wuhan Huanan Market (WHM) and performed virome analysis of samples from over 13 thousand bats collected prior to and during Corona Virus Disease 2019 (COVID-19) pandemic from 14 provinces of China.…”

Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species

“…This new research area enables a systematic analysis of the existence of the vast majority pathogenic or non-pathogenic viruses, known or unknown viruses, and other endogenous or exogenous viruses that are carried by the wildlife, and enables the exploration of the roles of wild species as reservoirs of infectious diseases based on the results of Next Generation Sequencing (NGS) [58][59][60]. As rodents are the largest mammalian population with diverse and widespread groups that are important reservoirs of many zoonotic viruses that have large impacts on humans and other animals' health, interest in viral diversity in rodents has recently increased [13,17,37,[61][62][63]. Indeed, approximately 173 viral species belonging to more than 65 genera have been described in rodents to date, among which about 60 are zoonotic, such as hantaviruses (Bunyaviridae), mammarenaviruses (Arenaviridae), and picornaviruses (Picornaviridae) [13,[64][65][66].…”