Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014.

Nguyen Quynh Huong¹ Nguyen Thi Thanh Nga¹ Nguyen Van Long² Bach Duc Luu² Alice Latinne^1,3,4 Mathieu Pruvot³ Nguyen Thanh Phuong⁵ Le Tin Vinh Quang⁵ Vo Van Hung⁵ Nguyen Thi Lan⁶ Nguyen Thi Hoa⁶ Phan Quang Minh² Nguyen Thi Diep² Nguyen Tung² Van Dang Ky² Scott I Roberton¹ Hoang Bich Thuy¹ Nguyen Van Long¹ Martin Gilbert³ Leanne Wicker¹ Jonna A K Mazet⁷ Christine Kreuder Johnson⁷ Tracey Goldstein⁷ Alex Tremeau-Bravard⁷ Victoria Ontiveros⁷ Damien O Joly³ Chris Walzer^3,8 Amanda E Fine^1,3 Sarah H Olson³

Affiliations 8 institutions

Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam.
Department of Animal Health, Ministry of Agricultural and Rural Development of Viet Nam, Ha Noi, Viet Nam.
Wildlife Conservation Society, Health Program, Bronx, New York, United States of America.
EcoHealth Alliance, New York, New York, United States of America.
Regional Animal Health Office No. 6, Ho Chi Minh City, Viet Nam.
Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Ha Noi, Viet Nam.
One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America.
Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria.

PMID32776964 DOI10.1371/journal.pone.0237129 Year2020 Journal PloS one PLoS One Languageeng Statusepublish

Abstract

Outbreaks of emerging coronaviruses in the past two decades and the current pandemic of a novel coronavirus (SARS-CoV-2) that emerged in China highlight the importance of this viral family as a zoonotic public health threat. To gain a better understanding of coronavirus presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet Nam 2013-2014, we used consensus Polymerase Chain Reactions to detect coronavirus sequences. In comparison to previous studies, we observed high proportions of positive samples among field rats (34.0%, 239/702) destined for human consumption and insectivorous bats in guano farms (74.8%, 234/313) adjacent to human dwellings. Most notably among field rats, the odds of coronavirus RNA detection significantly increased along the supply chain from field rats sold by traders (reference group; 20.7% positivity, 39/188) by a factor of 2.2 for field rats sold in large markets (32.0%, 116/363) and 10.0 for field rats sold and served in restaurants (55.6%, 84/151). Coronaviruses were also detected in rodents on the majority of wildlife farms sampled (60.7%, 17/28). These coronaviruses were found in the Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are raised on wildlife farms for human consumption as food. We identified six known coronaviruses in bats and rodents, clustered in three Coronaviridae genera, including the Alpha-, Beta-, and Gammacoronaviruses. Our analysis also suggested either mixing of animal excreta in the environment or interspecies transmission of coronaviruses, as both bat and avian coronaviruses were detected in rodent feces on wildlife farms. The mixing of multiple coronaviruses, and their apparent amplification along the wildlife supply chain into restaurants, suggests maximal risk for end consumers and likely underpins the mechanisms of zoonotic spillover to people.

Supporting text Virus Host Location

Animals 1948 Animals, Wild 187 Chiroptera 371 Coronavirus 92 Coronavirus Infections 171 Disease Reservoirs 149 Feces 113 Food Supply 3 Humans 1440 Meat 6 Phylogeny 805 Polymerase Chain Reaction 38 Porcupines 1 Rats 73 Risk 9 RNA, Viral 193 Vietnam 14 Zoonoses 397

Evidence records

6 total

Zoonotic Surveillance

5 records · 2 evidence types

Evidence type Viral Detection

4 records

OVE4029 Viral Detection

Key finding

Coronavirus RNA was detected in field rats and insectivorous bats sampled in Viet Nam between 2013 and 2014.

Virus

Host

Location

Supporting text

To gain a better understanding of coronavirus presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet Nam 2013-2014, we used consensus Polymerase Chain Reactions to detect coronavirus sequences. In comparison to previous studies, we observed high proportions of positive samples among field rats (34.0%, 239/702) destined for human consumption and insectivorous bats in guano farms (74.8%, 234/313) adjacent to human dwellings.

Method: consensus Polymerase Chain Reactions
Sample type: guano samples | wildlife farm specimens
Geographic raw: Viet Nam
Country inferred: VNM

OVE4030 Viral Detection

Key finding

Coronaviruses were detected in Malayan porcupines and bamboo rats raised on wildlife farms in Viet Nam.

Virus

Host

Location

Supporting text

Coronaviruses were also detected in rodents on the majority of wildlife farms sampled (60.7%, 17/28) in Viet Nam. These coronaviruses were found in the Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are raised on wildlife farms for human consumption as food.

Method: consensus Polymerase Chain Reactions
Sample type: wildlife farm specimens
Geographic raw: Viet Nam
Country inferred: VNM

OVE4034 Viral Detection

Key finding

Amplification of multiple coronaviruses along the wildlife supply chain involving field rats in Viet Nam is suggested to facilitate zoonotic spillover to people consuming wildlife in restaurants.

Virus

Host

Location

Supporting text

Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014. The mixing of multiple coronaviruses, and their apparent amplification along the wildlife supply chain into restaurants, suggests maximal risk for end consumers and likely underpins the mechanisms of zoonotic spillover to people.

Method: consensus Polymerase Chain Reaction | coronavirus RNA detection | supply chain risk analysis
Geographic raw: Viet Nam

OVE4032 Viral Detection

Key finding

Bat and avian coronaviruses were detected in rodent feces on wildlife farms, suggesting interspecies transmission among non-human hosts.

Virus

Host

bats Chiroptera Natural host

birds Aves Natural host

rodents Rodentia Natural host

Location

Supporting text

Our analysis also suggested either mixing of animal excreta in the environment or interspecies transmission of coronaviruses, as both bat and avian coronaviruses were detected in rodent feces on wildlife farms.

Method: consensus Polymerase Chain Reaction (PCR) | coronavirus sequence detection

Evidence type Reservoir Ecology

1 records

OVE4031 Reservoir Ecology

Key finding

Coronavirus RNA detection frequency increased along the field rat wildlife supply chain in Viet Nam, indicating ecological amplification of viral circulation toward end-consumer settings.

Virus

Host

Location

Supporting text

To gain a better understanding of coronavirus presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet Nam 2013-2014, we used consensus Polymerase Chain Reactions to detect coronavirus sequences. Most notably among field rats, the odds of coronavirus RNA detection significantly increased along the supply chain from field rats sold by traders (reference group; 20.7% positivity, 39/188) by a factor of 2.2 for field rats sold in large markets (32.0%, 116/363) and 10.0 for field rats sold and served in restaurants (55.6%, 84/151).

Method: consensus Polymerase Chain Reaction (PCR) | odds ratio analysis of detection frequency
Sample type: field rat samples
Geographic raw: Viet Nam
Country inferred: VNM

Genomic Evolution

1 records · 1 evidence types

Evidence type Phylogenetic Evolution

1 records

OVE4033 Phylogenetic Evolution

Key finding

Sequences from coronaviruses detected in bats and rodents in Viet Nam clustered phylogenetically within the Alpha-, Beta-, and Gammacoronavirus genera.

Virus

Host

Location

Supporting text

We identified six known coronaviruses in bats and rodents, clustered in three Coronaviridae genera, including the Alpha-, Beta-, and Gammacoronaviruses.

Analysis methods: phylogenetic clustering

References

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