DOI: 10.5061/dryad.7h44j0zrj
title: Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014

description: 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.
description: 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.
description: <strong>Column name    Field
 description</strong><br> Country    Country<br>
 SiteName    The name of the site where the samples were
 collected<br> District    District within Vietnam<br>
 StateProv    Province within Vietnam<br> SiteLatitude    Site
 latitude rounded up to 2 decimal places <br> SiteLongitude    Site
 longitude rounded up to 2 decimal places <br> EventName    Generated
 as sitename + event date<br> DomesticAnimals    List of domestic and
 other animals observed at a site (if observed if not blank)<br>
 AnimalID    Country defined animal ID<br> TaxaGroup    Taxonomic
 description of the animal sampled 4 categories (Bats, Carnivores,
 Non-human Primates, Rodents & Shrews)<br>
 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)<br>
 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..<br> 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.<br>
 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.<br> Order    Taxonomic
 order<br> Family     Taxonomic family (if known)<br> Genus  
  Taxonomic genus (if known)<br> SampleDate    The date the animal
 was sampled in the field MM/DD/YY<br> SpecimenID    The text value
 of the ID of the specimen, which matches the label on the physical
 specimen.<br> SpecimenType    The type of specimen
 collected<br> TestType    The type of PCR that the PCR was performed
 for<br> TestRequested    The viral family that the PCR was performed
 for<br> TestRequestedProtocol    The testing assay used to perform
 the PCR test<br> ConfirmationResult    The confirmation test result
 (Negative or Positive)<br> Sequence    The genetic sequence (if
 positive otherwise NULL)<br> GenbankAccessionNumber    The Genbank
 accession number (if positive otherwise NULL)<br> Virus    Which
 viruses were associated with each specimen x test combination (if positive
 otherwise NULL) - long version<br> VirusGroup    Which viruses were
 associated with each specimen x test combination (if positive otherwise
 NULL) - short version