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

Citation

Olson, Sarah H. et al. (2020), Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014, Dryad, Dataset, https://doi.org/10.5061/dryad.7h44j0zrj

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.

Methods

PREDICT data associated with event, sample, specimen, test, and sequence result finding were collected on paper field forms, project-standardized excel templates, or online forms and uploaded in the EIDITH database. EIDITH helped clean and curate this data and provided an extract on 23 March, 2020 of the dataset with fields used in this publication.

Usage Notes

Column name    Field description
Country    Country
SiteName    The name of the site where the samples were collected
District    District within Vietnam
StateProv    Province within Vietnam
SiteLatitude    Site latitude rounded up to 2 decimal places 
SiteLongitude    Site longitude rounded up to 2 decimal places 
EventName    Generated as sitename + event date
DomesticAnimals    List of domestic and other animals observed at a site (if observed if not blank)
AnimalID    Country defined animal ID
TaxaGroup    Taxonomic description of the animal sampled 4 categories (Bats, Carnivores, Non-human Primates, Rodents & Shrews)
SpeciesScientificName    The scientific name of the animal sampled. If complete genus species is unknown, this will be the next known level of taxonomic classification (i.e. genus, subfamily, family)
CommonName    The english common name of the animal sampled. If the complete geenus species is unknown, the english name will be set to Unidentified long-fingered bat in the Miniopterus genus, as an example for Miniopterus sp..
CommonNameFieldMorphology    When an animal is barcoded this is set to the species_scientific_name as defined in the field before the species_scientific_name is updated with the barcoding results. If the barcoding test did not result in a species identification or the animal was not barcoded, this field will be left blank.
IDCertainty    If the animal was barcoded, the certainty corresponds to the barcoding results and indicates the percent of sequence match. For animals not barcoded, the certainty is based on the field team's confidence in the species identification.
Order    Taxonomic order
Family     Taxonomic family (if known)
Genus    Taxonomic genus (if known)
SampleDate    The date the animal was sampled in the field MM/DD/YY
SpecimenID    The text value of the ID of the specimen, which matches the label on the physical specimen.
SpecimenType    The type of specimen collected
TestType    The type of PCR that the PCR was performed for
TestRequested    The viral family that the PCR was performed for
TestRequestedProtocol    The testing assay used to perform the PCR test
ConfirmationResult    The confirmation test result (Negative or Positive)
Sequence    The genetic sequence (if positive otherwise NULL)
GenbankAccessionNumber    The Genbank accession number (if positive otherwise NULL)
Virus    Which viruses were associated with each specimen x test combination (if positive otherwise NULL) - long version
VirusGroup    Which viruses were associated with each specimen x test combination (if positive otherwise NULL) - short version

Funding

United States Agency for International Development, Award: GHN-A-OO-09-00010-00 and AID-OAA-A-14-00102