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

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.