Literature detail

Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam.

A Berto¹ P H Anh¹ J J Carrique-Mas^1,2 P Simmonds³ N Van Cuong¹ N T Tue¹ N Van Dung³ M E Woolhouse⁴ I Smith⁵ G A Marsh⁵ J E Bryant^1,2 G E Thwaites^1,2 S Baker^1,2,6 M A Rabaa^1,2 VIZIONS consortium

Affiliations 6 institutions

Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam.
Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK.
Health and Biosecurity, CSIRO, Australian Animal Health Laboratory, Geelong, Vic., Australia.
The London School of Hygiene and Tropical Medicine, London, UK.

PMID 28418192 2018 Zoonoses Public Health eng ppublish

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Article

Publication summary

Bats and rodents are being increasingly recognized as reservoirs of emerging zoonotic viruses. Various studies have investigated bat viruses in tropical regions, but to date there are no data regarding viruses with zoonotic potential that circulate in bat and rat populations in Viet Nam. To address this paucity of data, we sampled three bat farms and three wet markets trading in rat meat in the Mekong Delta region of southern Viet Nam. Faecal and urine samples were screened for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1%) and 11 of 222 (4.9%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22%) of bat faecal samples; filovirus RNA was not detected in any of the bat samples. Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus. Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam. Our study shows that potentially novel variants of paramyxoviruses and coronaviruses commonly circulate in bat and rat populations in Viet Nam. Further characterization of the viruses and additional human and animal surveillance is required to evaluate the likelihood of viral spillover and to assess whether these viruses pose a risk to human health.

bats coronavirus paramyxovirus rats Viet Nam zoonotic viruses Animals Chiroptera Coronavirus Feces Filoviridae Humans Paramyxoviridae Phylogeny Rats RNA, Viral Urine Vietnam

Structured evidence records

Evidence records

7 total

Genomic Evolution 3 records

Genomic Evolution Extraction confidence 0.80

Key finding

Phylogenetic analysis showed that bat and rat coronaviruses in Viet Nam were related to globally circulating viruses but displayed no evidence of cross-species viral exchange between bats and rats.

Virus

Host

Location

Supporting text

Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam.

Analysis methods: phylogenetic analysis

Genomic Evolution Extraction confidence 0.80

Key finding

Phylogenetic analysis showed that bat paramyxoviruses from Viet Nam were related to globally circulating bat paramyxoviruses without evidence of cross-species exchange with rats.

Virus

Host

Location

Supporting text

Analysis methods: phylogenetic analysis

Genomic Evolution Extraction confidence 0.80

Key finding

Phylogenetic analysis demonstrated that rat coronaviruses in Viet Nam cluster with globally circulating rodent coronaviruses and show no phylogenetic evidence of cross-species mixing with bat viruses.

Virus

Host

Location

Supporting text

Analysis methods: phylogenetic analysis

Reservoir Ecology 2 records

Reservoir Ecology Extraction confidence 0.90

Key finding

Bats from the Mekong Delta region of Viet Nam were found to harbor paramyxovirus and coronavirus RNA, suggesting they act as natural reservoirs for these viruses.

Virus

Host

Location

Supporting text

Faecal and urine samples were screened for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1%) and 11 of 222 (4.9%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22%) of bat faecal samples; filovirus RNA was not detected in any of the bat samples.

Method: field sampling; RNA screening
Sample type: faecal samples; urine samples
Geographic raw: Mekong Delta region of southern Viet Nam
Country inferred: Viet Nam

Reservoir Ecology Extraction confidence 0.90

Key finding

Rat populations in Viet Nam’s Mekong Delta carried coronavirus RNA, supporting their role as local reservoirs.

Virus

Host

Location

Supporting text

Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus.

Method: field sampling; RNA screening
Sample type: faecal samples
Geographic raw: Mekong Delta region of southern Viet Nam
Country inferred: Viet Nam

Zoonotic Surveillance 2 records

Zoonotic Surveillance Extraction confidence 0.95

Key finding

Paramyxovirus and coronavirus RNA were detected during surveillance of bat fecal and urine samples in southern Viet Nam.

Virus

Host

Location

Supporting text

Method: screening for viral RNA; phylogenetic analysis
Sample type: feces; urine
Geographic raw: Mekong Delta region of southern Viet Nam
Country inferred: Vietnam

Zoonotic Surveillance Extraction confidence 0.95

Key finding

Coronavirus RNA was detected through faecal sample surveillance in rats from southern Viet Nam.

Virus

Host

Location

Supporting text

Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus.

Method: screening for viral RNA; phylogenetic analysis
Sample type: feces
Geographic raw: Mekong Delta region of southern Viet Nam
Country inferred: Vietnam

Citation context

References

39 references

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Evidence overview

Evidence 7

Types 3

Virus 2

Host 2

Evidence types

Genomic Evolution 3 Reservoir Ecology 2 Zoonotic Surveillance 2

Linked entities

Viruses

Hosts

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Publication metadata

Journal: Zoonoses and public health
Volume / Issue / Pages: 65 / 1 / 30-42
ISSN: 1863-2378
Journal country: Germany
DOI: 10.1111/zph.12362