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

Nguyen Quynh Huong, Nguyen Thi Thanh Nga, Nguyen Van Long, Bach Duc Luu, Alice Latinne, Mathieu Pruvot, Nguyen Thanh Phuong, Le Tin Vinh Quang, Vo Van Hung, Nguyen Thi Lan, Nguyen Thi Hoa, Phan Quang Minh, Nguyen Thi Diep, Nguyen Tung, Van Dang Ky, Scott I. Roberton, Hoang Bich Thuy, Nguyen Van Long, Martin Gilbert, Leanne Wicker, Jonna A. K. Mazet, Christine Kreuder Johnson, Tracey Goldstein, Alex Tremeau-Bravard, Victoria Ontiveros, Damien O. Joly, Chris Walzer, Amanda E. Fine, View ORCID ProfileSarah H. Olson
doi: https://doi.org/10.1101/2020.06.05.098590
Nguyen Quynh Huong
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
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Nguyen Thi Thanh Nga
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
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Nguyen Van Long
2Department of Animal Health, Ministry of Agricultural and Rural Development of Viet Nam, Ha Noi, Viet Nam
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Bach Duc Luu
2Department of Animal Health, Ministry of Agricultural and Rural Development of Viet Nam, Ha Noi, Viet Nam
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Alice Latinne
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
3Wildlife Conservation Society, Health Program, Bronx, New York, United States of America
4EcoHealth Alliance, New York, New York, United States of America
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Mathieu Pruvot
3Wildlife Conservation Society, Health Program, Bronx, New York, United States of America
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Nguyen Thanh Phuong
5Regional Animal Health Office No. 6, Ho Chi Minh City, Viet Nam
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Le Tin Vinh Quang
5Regional Animal Health Office No. 6, Ho Chi Minh City, Viet Nam
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Vo Van Hung
5Regional Animal Health Office No. 6, Ho Chi Minh City, Viet Nam
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Nguyen Thi Lan
6Viet Nam National University of Agriculture, Faculty of Veterinary Medicine, Ha Noi, Viet Nam
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Nguyen Thi Hoa
6Viet Nam National University of Agriculture, Faculty of Veterinary Medicine, Ha Noi, Viet Nam
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Phan Quang Minh
2Department of Animal Health, Ministry of Agricultural and Rural Development of Viet Nam, Ha Noi, Viet Nam
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Nguyen Thi Diep
2Department of Animal Health, Ministry of Agricultural and Rural Development of Viet Nam, Ha Noi, Viet Nam
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Nguyen Tung
2Department of Animal Health, Ministry of Agricultural and Rural Development of Viet Nam, Ha Noi, Viet Nam
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Van Dang Ky
2Department of Animal Health, Ministry of Agricultural and Rural Development of Viet Nam, Ha Noi, Viet Nam
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Scott I. Roberton
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
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Hoang Bich Thuy
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
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Nguyen Van Long
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
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Martin Gilbert
3Wildlife Conservation Society, Health Program, Bronx, New York, United States of America
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Leanne Wicker
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
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Jonna A. K. Mazet
7One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Christine Kreuder Johnson
7One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Tracey Goldstein
7One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Alex Tremeau-Bravard
7One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Victoria Ontiveros
7One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Damien O. Joly
3Wildlife Conservation Society, Health Program, Bronx, New York, United States of America
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Chris Walzer
3Wildlife Conservation Society, Health Program, Bronx, New York, United States of America
8Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
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Amanda E. Fine
1Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
3Wildlife Conservation Society, Health Program, Bronx, New York, United States of America
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  • For correspondence: afine@wcs.org
Sarah H. Olson
3Wildlife Conservation Society, Health Program, Bronx, New York, United States of America
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  • ORCID record for Sarah H. Olson
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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 detected in the majority of wildlife farms (60.7%, 17/28) and in the Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are farmed. 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 in the trade. 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Added missing department information for co-authors from Viet Nam National University of Agriculture; corrected superscript formatting error in Table 1 by submitting pdf; corrected total count and percentage of sites positive (failed to reflect unique sites) which is consistent with remainder of text.

  • https://datadryad.org/stash/share/pk3wVUxFNzTuCYZ9t8haKRPmx7V8YhTDBuHpG8JJ9kU

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014
Nguyen Quynh Huong, Nguyen Thi Thanh Nga, Nguyen Van Long, Bach Duc Luu, Alice Latinne, Mathieu Pruvot, Nguyen Thanh Phuong, Le Tin Vinh Quang, Vo Van Hung, Nguyen Thi Lan, Nguyen Thi Hoa, Phan Quang Minh, Nguyen Thi Diep, Nguyen Tung, Van Dang Ky, Scott I. Roberton, Hoang Bich Thuy, Nguyen Van Long, Martin Gilbert, Leanne Wicker, Jonna A. K. Mazet, Christine Kreuder Johnson, Tracey Goldstein, Alex Tremeau-Bravard, Victoria Ontiveros, Damien O. Joly, Chris Walzer, Amanda E. Fine, Sarah H. Olson
bioRxiv 2020.06.05.098590; doi: https://doi.org/10.1101/2020.06.05.098590
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Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014
Nguyen Quynh Huong, Nguyen Thi Thanh Nga, Nguyen Van Long, Bach Duc Luu, Alice Latinne, Mathieu Pruvot, Nguyen Thanh Phuong, Le Tin Vinh Quang, Vo Van Hung, Nguyen Thi Lan, Nguyen Thi Hoa, Phan Quang Minh, Nguyen Thi Diep, Nguyen Tung, Van Dang Ky, Scott I. Roberton, Hoang Bich Thuy, Nguyen Van Long, Martin Gilbert, Leanne Wicker, Jonna A. K. Mazet, Christine Kreuder Johnson, Tracey Goldstein, Alex Tremeau-Bravard, Victoria Ontiveros, Damien O. Joly, Chris Walzer, Amanda E. Fine, Sarah H. Olson
bioRxiv 2020.06.05.098590; doi: https://doi.org/10.1101/2020.06.05.098590

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