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

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.

Discovery of Flaviviridae-derived endogenous viral elements in shrew genomes provide novel insights into Pestivirus ancient history

“…Viruses belonging to this genus were initially detected in a variety of artiodactylous hosts, such as ruminants and swine, in which they cause subclinical or clinical infections including hemorrhagic syndrome, abortion, acute fatal mucosal disease. Recent metagenomic studies extended the host range towards rodents (Wu et al, 2020(Wu et al, , 2018, bats (Wu et al, 2018), fish (Shi et al, 2018), and ticks (Sameroff et al, 2019), but to some extent, the restricted sampling beyond agriculturally important animals limits our understanding of the real host range. Shrews, for example, have been recently identified as host of hepaciviruses, another genus in the Flaviviridae family (Guo et al, 2019;Wu et al, 2020), but to date not of pestiviruses.…”

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

“…Over the past decade, virome studies exploring the roles of wild species as reservoirs of infectious diseases have become more common thanks to the technological breakthrough of high-throughput sequencing. Considering that some species are reservoirs of numerous viruses, some of which have large impacts on human health, studies on viral diversity in rodents have recently increased [ 3 , 9 , 84 , 85 , 86 ]. Hence, 173 viral species belonging to more than 65 genera have been described in rodents to date, among which 53 are zoonotic, such as mammarenaviruses and hantaviruses [ 30 , 87 ].…”

“…The latter viruses could indeed be from environment plants, insects, or fungi, and only incidentally found in rodents. Together, the use of organs should give a good representation of vertebrate viruses hosted by rodents [ 84 ].…”

Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses

“…Furthermore, there are several more recently discovered arteriviruses that have not yet been classified but for which a (near) complete genome sequence is available. While most of these yet unclassified viruses were found in rodents and cluster within the currently recognized subfamily Variarterivirinae , some others were found in reptiles and likely represent novel subfamilies within the family Arteriviridae , or even separate families [ 18 , 19 , 20 ].…”