Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Abstract

Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.

Multiple infections of zoonotic pathogens in wild Brandt's voles (Lasiopodomys brandtii)

“…As a result, it is necessary to monitor pathogenic microorganisms of wild rodents in Inner Mongolia for the prevention of zoonoses and the prevention and control of EIDs. In addition to identifying pathogens causing diseases that have already emerged, virome and zoonotic bacterial surveillance provide abundant data to help elucidate the distribution and richness of microorganisms carried by wildlife organisms (He et al., 2022 ).…”

“…In addition, rodents have close contact with arthropods (e.g. fleas, ticks and mites), wildlife and domestic animals and are a critical link in the transmission of various zoonotic pathogens between animals and humans (Cutler et al., 2010 ; ; He et al., 2022 ; Phan et al., 2011 ). Among the most important diseases in terms of public health, salmonellosis, plague, leptospirosis, bartonellosis, haemorrhagic fever with renal syndrome and tick‐borne relapsing fever are all caused by rodent‐borne pathogens (Bordes et al., 2015 ; Jin et al., 2018 ; Li et al., 2016 ; Milholland et al., 2018 ; Shimi et al., 1979 ; Wu et al., 2018 ).…”

VirID: Beyond Virus Discovery - An Integrated Platform for Comprehensive RNA Virus Characterization

“…To demonstrate VirID's visualization capabilities, we analyzed 20 SRA libraries from a large scale animal study conducted in China (76) that comprised 14 species across five provinces. In addition, we assessed the versatility of VirID through the analysis of 192 public libraries from seven studies, which included a wide range of samples from human swabs (77) and diverse animal tissues (78)(79)(80), as well as arthropod (81), plant (82), and soil samples (83). The public metagenomes utilized in this analysis were sourced from NCBI, with details provided in Supplementary Table S2, S3.…”

The Genetic Diversity and Interspecific Transmission of Circovirus in Rhizomys sinensis in Guangdong, Southern China

“…Over 200 rodent species from 12 families have been found in China [16]. Viral metagenome suggests that rodents can be infected by or carry numerous vertebrate-associated viruses, many of which can cause severe human diseases [10,[17][18][19]. Most virome studies have been focused on rodent species such as Mus musculus, Rattus norvegicus, Rhombomys opimus, and Urocitellus undulates.…”