No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity
Open accessAbstract
Hospital-based and community-based ‘high-risk cohort’ studies investigating humans at risk of zoonotic infection due to occupational or residential exposure to animals were conducted in Vietnam, with diverse viruses identified from faecal samples collected from humans, domestic and wild animals. In this study, we focus on the positive-sense RNA virus family Picornaviridae, investigating the prevalence, diversity, and potential for cross-species transmission. Through metagenomic sequencing, we found picornavirus contigs in 23% of samples, belonging to 15 picornavirus genera. Prevalence was highest in bats (67%) while diversity was highest in rats (nine genera). In addition, 22% of the contigs were derived from novel viruses: Twelve phylogenetically distinct clusters were observed in rats of which seven belong to novel species or types in the genera Hunnivirus, Parechovirus, Cardiovirus, Mosavirus and Mupivirus; four distinct clusters were found in bats, belonging to one novel parechovirus species and one related to an unclassified picornavirus. There was no evidence for zoonotic transmission in our data. Our study provides an improved knowledge of the diversity and prevalence of picornaviruses, including a variety of novel picornaviruses in rats and bats. We highlight the importance of monitoring the human–animal interface for possible spill-over events.
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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 [45]
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- Authors
- Lu, L., Ashworth, J., Nguyen, D., Li, K., Smith, D. B., Woolhouse, M., & on behalf of the VIZIONS Consortium
- Affiliations
- University of Edinburgh (GB)
- University of Oxford (GB)
- Corresponding author
- Lu, Lu
- Venue
- Viruses
- Publisher
- MDPI AG
- Published
- 2021-08-27
- Volume
- 13
- Issue
- 9
- Pages
- 1709
- ISSN
- 1999-4915 (ISSN-L)
- PMC
- PMC8473303
- OpenAlex
- W3198689075
- Cited by
- 11
- References
- 47
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 3 · 2023: 1 · 2022: 1
- FWCI
- 1.08
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Viruses (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- the Wellcome Trust (ref. WT/093724)
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Zoonotic diseases and public health
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Outbreaks Research
- Keywords
- picornavirus, zoonotic transmission, human-animal interface, bats, rats, parechovirus, cardiovirus, viral diversity, viral prevalence, close contacts, fecal samples
- MeSH terms
- Animals, Chiroptera, Feces, Humans, Phylogeny, Picornaviridae, Picornaviridae Infections, RNA, Viral, Genetic Variation, Vietnam, Cohort Studies, Prevalence, Genome, Viral, Rats, Metagenomics
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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