Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia
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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.
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In the capsid phylogeny, EMCV-2 rodent isolates from Germany and the United Kingdom grouped with three Asian viruses from Rattus and Bandicota rats and an agouti in the deepest lineage.
“In the capsid (VP4-VP2-VP3-VP1) phylogeny, EMCV-2 rodent isolates from Germany and the United Kingdom (JX257003 and OP381184) grouped with three Asian viruses (MZ544255, MT085334, MN547968) from Rattus and Bandicota rats and an agouti (Dasyprocta sp.) in the deepest lineage (Fig 3) [45,46].”
From Zoological transmission of encephalomyocarditis virus in the United States: Virus evolution, host ecology, and capsid antigenicity derived from an outbreak (2026) · cites this paper as [46]
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Nilubol, D., Tripipat, T., Hoonsuwan, T., et al. (2012) · Emerging infectious diseases · doi:10.3201/eid1811.111105 · Cited by 30 · see citing works
Genomic sequencing, evolution and molecular epidemiology of rabies virus
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Genetic diversity of coronaviruses in Miniopterus fuliginosus bats
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Comparison of two zoonotic viruses from the order Bunyavirales
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Self-citationA Novel Squirrel Respirovirus with Putative Zoonotic Potential
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Self-citation
Flagged first, then by citations
Research works printed but not linked: 1
- [91]Wu Z Du J Lu L Yang L Dong J Sun L Zhu Y Liu Q Jin Q Detection of Hantaviruses and Arenaviruzses in three-toed jerboas from the Inner Mongolia Autonomous Region, China Emerg Microbes Infect 2018 7 35 29559618 PMC5861045
Cited by
Sorted by citations
Adhikari, A., Feng, K. H., Shrestha, A., Rodriguez, C. E., Nolan, E. C., Pye, G. W., Gauger, P. C., Denagamage, T., Holmes, E. C., & Allison, A. B. (2026) · PLOS Pathogens · doi:10.1371/journal.ppat.1013861 · Cited by 1 · see citing works
“In the capsid (VP4-VP2-VP3-VP1) phylogeny, EMCV-2 rodent isolates from Germany and the United Kingdom (JX257003 and OP381184) grouped with three Asian viruses (MZ544255, MT085334, MN547968) from Rattus and Bandicota rats and an agouti ( Dasyprocta sp.) in the deepest lineage (Fig 3) [45,46].”
- Authors
- Wu, Z., Han, Y., Liu, B., Li, H., Zhu, G., Latinne, A., Dong, J., Sun, L., Su, H., Liu, L., Du, J., Zhou, S., Chen, M., Kritiyakan, A., Jittapalapong, S., Chaisiri, K., Buchy, P., Duong, V., Yang, J., Jiang, J., Xu, X., Zhou, H., Yang, F., Irwin, D. M., Morand, S., Daszak, P., Wang, J., & Jin, Q.
- Affiliations
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- EcoHealth Alliance (US)
- Wildlife Conservation Society (US)
- Kasetsart University (TH)
- Mahidol University (TH)
- Institut Pasteur du Cambodge (KH)
- Yunnan Institute of Parasitic Diseases (CN)
- University of Toronto (CA)
- Corresponding author
- Jin, Qi
- ORCID
- Venue
- Microbiome
- Published
- 2021-01-21
- Volume
- 9
- Issue
- 1
- Pages
- 18-18
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC7818139
- OpenAlex
- W3120632188
- Cited by
- 92
- References
- 99
- Citations by year
- 2026: 9 · 2025: 15 · 2024: 15 · 2023: 16 · 2022: 21 · 2021: 16
- FWCI
- 15.79
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbiome (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- TSpace (University of Toronto) (submittedVersion, cc-by)
- Funders
- National Natural Science Foundation of China (81772228)
- Mega-projects of Science Research for the thirteenth Five-Year Plan (2018ZX10101001)
- CAMS Innovation Fund for Medical Sciences (2016-I2M-1-014 and 2017-I2M-B&R-12)
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Zoonotic diseases and public health
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Vectors
- Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
- Keywords
- emerging infectious diseases, viral evolution, novel virus discovery, insectivores, arboviruses, Mainland Southeast Asia, Thailand, Laos, Cambodia
- MeSH terms
- Virome, Animals, Asia, Southeastern, Insecta, Lung, RNA, Viral, Rodentia
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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