A Malayan porcupine from a farm in Dong Nai province, November 2013. (Huong et al, 2020, PLoS ONE)

Early in this unforgettable year, a wet market in Wuhan, China, emerged as a possible step along the way, if not the place of origin, of the outbreak that would seed the pandemic of COVID-19. Prescient researchers have reached back to meat samples collected in 2013 and 2014 and used genetic testing to trace what might have happened again more recently: the magnification of viral infection from wild or farmed meat to large markets to restaurants. The report appears in PLoS ONE.

“This study shows the wildlife supply chain generates a one-two punch when it comes to spillover risk. It is known to increase contact rates between wildlife and people and here we show how it greatly amplifies the number of infected animals along the way,” write Amanda E. Fine from the Wildlife Conservation Society, Viet Nam Country Program in Ha Noi and the Wildlife Conservation Society, Health Program, Bronx, New York, and colleagues.

COVID-19 was not a surprise to anyone familiar with the ways of viruses. A lot of folks weren’t paying attention, even when repeatedly warned.

Collecting Rats

In the study, PCR revealed telltale RNA from six types of coronaviruses in three settings:

  • wild, free-ranging field rats
  • commercial wildlife farms that supply bamboo rats and Malayan porcupines to large markets and restaurants
  • guano farms.

Resembling rows of upside-down brooms, guano “farms” are actually backyard bat roosts created, since encouragement from the Cambodian government in 2004, to earn money, enhance soil fertility, control pests, reduce use of chemical fertilizers, and protect endangered bats. Beneath the excrement-encrusted fringes, gardens grow, livestock wander, and children play. The fact that bats are teeming with viruses, thanks to biological quirks I explained here, wasn’t part of the plan – no PPE suggested.

The researchers sampled animals in 2013 and 2014 “at sites identified as high-risk interfaces for viral spillover from wildlife to humans,” noting that novel coronaviruses have been emerging over the past two decades. Viet Nam is one such site.

They examined 2,164 tissue samples from 1,506 individuals (702 field rats, 429 wildlife farm rodents, and 375 bats) from 70 sites in Dong Thap, Soc Trang, and Dong Nai provinces in the southern region near the Mekong River Delta.

Field rats are popular. People eat them at least once a week in Viet Nam and Cambodia, citing taste, low cost, and the view of rodent meat as “healthy, nutritious, natural, and disease-free,” according to an early version of the new paper. Thousands of tons of field rats are collected for consumption annually.

The investigators swabbed the mouths of the severed heads of the rats, both field and farmed, then plucked tissue samples, mostly from the small intestine but also sometimes from the brain, kidney, or lung, along with urine and feces. They noted that butchering sites at all three points – traders, market vendors, and restaurants – were cleaned only sporadically.

Amplification and Diversification of Coronaviruses Can Fuel a Pandemic

The findings create a narrative of how a coronavirus pandemic starts.

Of 702 field rats, 239 (34%) had coronaviruses. But break the numbers down. “The odds of coronavirus RNA detection significantly increased along the supply chain, from field rats sold by traders (20.7%) to field rats sold in large markets (32.0%), to field rats served in restaurants (55.6%),” the researchers write.

Farmed animals seem safer. About 6% of bamboo rats and Malayan porcupines raised on 17 of 28 surveyed wildlife farms destined for human dinner tables had coronaviruses.

The findings for guano farms were especially unsettling. Of 313 bats in one guano farm close to human homes, 234 (74.8%) carried coronaviruses.

Amplification isn’t the only problem. Perhaps even more alarming is the natural tendency of viruses to swap hunks of their genomes. This recombination happens in host species, their reservoirs, and even in piles of bat dung or bird droppings. Mixing and matching genetic material can easily spawn a novel pathogen that jumps to humans. And that might be what transpired in Wuhan in 2019.

Why China?

Hindsight is critical in understanding how SARS-CoV-2 arose. After SARS (China; 2003), MERS (Middle East; 2012), and Swine Acute Diarrhea Syndrome (China; 2017), many scientists pointed out that it was only a matter of time before another coronavirus (CoV) jumped from bats to humans. Four researchers at the CAS Key Laboratory of Special Pathogens and Biosafety at the Wuhan Institute of Virology warned in a report in Virology in March 2019 that such a zoonosis was likely if not imminent:

“It is generally believed that bat-borne CoVs will re-emerge to cause the next disease outbreak. China is a likely hotspot. The challenge is to predict when and where, so that we can try our best to prevent such outbreaks. …. Investigation of bat coronaviruses becomes an urgent issue for the detection of early warning signs, which in turn minimizes the impact of such future outbreaks in China.”

Apparently those responsible for cutting NIH funding to a bat coronavirus project in April 2020 were unfamiliar with the scientific literature warning of emerging viral diseases, perhaps responding to political pressure based on belief – not data – that the virus came from the Wuhan lab, according to this article in Science.

Conjuring up a conspiracy theory isn’t necessary to hypothesize how and why viral zoonoses might arise in China.

China presents a perfect biological storm. It’s the largest country with the most people, and has climates that support a great diversity of bats and the viruses that they harbor. People live in close contact with bats and/or their droppings, and as in Viet Nam and Cambodia, they like to eat the reservoir species – rats, porcupines, perhaps pangolins. “Chinese food culture maintains that live slaughtered animals are more nutritious, and this belief may enhance viral transmission,” wrote the researchers in 2019.

So it wasn’t much of a surprise that the novel coronavirus’s closest relative is a bat virus, RaTG13. The two genomes are 96% alike, much closer than SARS-CoV-2 is to SARS-CoV, the virus behind SARS from 2003. We know this because researchers in China published the first genome sequence of the new virus on January 11. (I wrote about the 75,000+ SARS-CoV-2 genome sequences posted in a public database two weeks ago here at DNA Science, COVID Genomes Paint a Portrait of an Evolving Pathogen.)

The wet market mentioned early on as the source of the outbreak was more likely the site of “an intermediate host facilitating the emergence of the virus in humans,” wrote a large team from China in The Lancet January 30, 2020.

The Future: End Wet Markets

Dr. Fine and her colleagues call for global “precautionary measures that restrict the killing, commercial breeding, transport, buying, selling, storage, processing and consuming of wild animals” to minimize emergence of pathogenic viruses.

They also ask for building and improving detection capacity; surveillance to identify and describe coronaviruses in humans, wildlife, and livestock; and addressing human behaviors that facilitate transfer of viruses from non-human animals to us.

“The more opportunities we provide for humans to come into direct contact with a multitude of wildlife species, the higher the likelihood of another spillover event. The costs of inaction are astronomically high and we must ensure that future food production and security is sustainable, just, and supports global health.”

It might be a good time to consider a plant-based diet.

The opening photo is a Malayan porcupine from a farm in Dong Nai province, November 2013. Below is a guano farm (Huong et al, 2020, PLOS ONE)