New Chinese Research on Bat Coronaviruses & Wuhan Markets Published Ahead of US-EU Meeting Asking for Answers on SARS-CoV2 Origins  
Some of the first SARS-COV-2 cases emerged around Wuhan’s “wet markets” selling wild animals for slaughter and meat consumption; such markets can be a flashpoint for pathogen transmission to humans.

Chinese researchers have this week published two papers that shed new light into the likely bat origins of SARS-CoV2 and related foodborne risks – even as pressures from the United States and the European Union grow for a more complete investigation into the origins of SARS-CoV2. 

The US and EU are expected to issue a joint statement on the issue next week calling for “progress on a transparent, evidence-based and expert-led WHO -convened Phase 2 study on the origins of Covid-19, that is free from interference.” 

Speaking at a Thursday press conference ahead of this weekend’s G7 Summit, European Council President Charles Michel set the stage with a declaration that “the world has the right to know exactly what happened in order to be able to learn the lessons.”

Added European Commission President Ursula von der Leyen: “Investigators need complete access to the information and to the sites” to “develop the right tools to make sure that this will never happen again.”

Preemptive Chinese Moves? 

The EU statements followed this week’s release of two papers by Chinese academics in peer-reviewed journals on bat coronaviruses and Wuhan market pathogen risks.  

One study, published in the journal Cell,  reviews previously unreported data on the genome sequences of about two dozen novel coronaviruses harborned by bat species in southwestern China’s Yunnan province, including one that may be the most similar yet, genetically speaking, to SARS-CoV2.

A second paper, published in Scientific Reports highlights the poor hygiene and animal market conditions, and a range of pathogen risks associated with Wuhan’s live animal markets, which included many illegally traded species, in a survey of 47,000 live animals sold at 17 Wuhan markets between May 2017 and November 2019.  During the two-and-half years, one of the study’s co-authors conducted monthly surveys of all 17 shops in Wuhan markets that sold live wild animals for food and pets. Seven of the shops were at the Huanan seafood market, one of the first sites around which a cluster of novel coronavirus cases was first identified in December 2019 and early 2020. 

No Smoking Guns – But… 

Experts contacted by Health Policy Watched noted that papers add weight and nuance to the origins investigation, although neither resolves the polarized debate over whether the virus emerged via “natural” contact between bats and humans, or bats and another  intermediate food or animal host.  

“This shows why we should fully examine the natural spillover origin hypothesis, but it’s in no way the ‘smoking gun’ that Bob Gerry described as in the Wall Street Journal,” said Jamie Metzl, a senior fellow at the Atlantic Council. Metzl is one of the co-authors of a series of open scientific letters that have criticized the WHO-led investigation as inadequately exploring the possibility that the SARS-CoV2 could have “escaped” from the Wuhan Institute of Virology, where scientists were studying horseshoe bat coronaviruses from Yunnan Province, just prior to the pandemic.

Another scientist expressed doubt that the timing of the publications represented any kind of a trend by Beijing to drive the narrative against US and European pressures, saying other studies of bat coronavirus sequences have been published previously and: “this is just science, slowly and methodically being published. I have no doubt more will come out.” 

Twenty-four Full-Length Coronavirus Genomes 

Infographic describing research published in the journal Cell, in June 2021, which mapped the genomes of 24 coronaviruses harborned by bats in China’s Yunnan province, including four close relatives of SARS-CoV2, the virus that causes COVID-19.

The paper on the new set of bat coronaviruses, published in Cell by 15 Chinese and Australian researchers, sequenced 24 full-length coronavirus genomes out of a collection of 411 bat saliva and excrement samples collected in Yunnan province between May 2019 and November 2020 – including four novel viruses that researchers said were closely related to SARS-CoV2.  

One virus, dubbed “Rhinolophus pusillus virus” (RpYN06), was found to be the  closest relative of SARS-CoV-2 in most of its genome, among the group of viruses collected “although it possessed a more divergent spike gene. 

“The other three SARS-CoV-2 related coronaviruses carried a 41 genetically distinct spike gene that could weakly bind to the hACE2 receptor in vitro” – referring to the receptor in humans to which SARS-CoV2 attaches so effectively. 

None of the samples, however, appeared to be quite as genetically similar to SARS-CoV2 as a previously identified bat virus (Rhinolophus affinis) RaTG13 – which the researchers admitted still “shares the greatest sequence identity with SARS-CoV-2 across the viral genome as a whole (Zhou et al., 2020b).” That  coronavirus, as well, is believed to have been harbored by bats in remote parts of Yunnan province in southwestern China, bordering Myanmar. 

The study suggests that “bats across a broad swathe of Asia harbor coronaviruses that are closely related to SARS-CoV-2 and that the phylogenetic and genomic diversity of these viruses has likely been underestimated.

“Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species, with the largest contiguous hotspots extending from South Laos and Vietnam to southern China. Our study highlights the remarkable diversity of bat coronaviruses at 45 the local scale, including close relatives of both SARS-CoV-2 and SARS-CoV.” 

Market Risks Abounded – But Pangolins Not Among Species Sold 

Wuhan’s shuttered live animal markets in April 2020, including (a) Huanan Seafood market, (b) Qiyimen live animal market, (c) Baishazhou market and (d) Dijiao outdoor pet market.

The second study, conducted by scientists from the China West Normal University, as well as Oxford University and the University of British Columbia, found 47,000 live animals sold in Wuhan’s live animal markets between May 2017 and November 2019,

“Serendipitously, prior to the COVID-19 outbreak, over the period May 2017–Nov 2019, we were conducting unrelated routine monthly surveys of all 17 wet market shops selling live wild animals for food and pets across Wuhan City,” the authors report. 

“This was intended to identify the source of the tick-borne (no human-to-human transmission) Severe Fever with Thrombocytopenia Syndrome (SFTS), following an outbreak in Hubei Province in 2009–2010 in which there was an unusually high initial case fatality rate of 30%.”

“While we caution against the misattribution of Covid-19’s origins, the wild animals on sale in Wuhan suffered poor welfare and hygiene conditions and we detail a range of other zoonotic infections they can potentially vector,” lead author Xiao Xiao, from the Lab Animal Research Centre at Hubei University of Chinese Medicine in Wuhan,wrote.

No Pangolins At Wuhan’s Markets 

Significantly, while some 38 species were sold in 17 markets in Wuhan between May 2017 and November 2019, no pangolins were sold in the markets at all, the study also found.

That, the authors conclude, rules out pangolin, an endangered species known to be a carrier of coronaviruses, as a potential host of the first SARS-CoV2 virus cases transmitted to humans.  

“Circumstantially, the absence of pangolins (and bats, not typically eaten in Central China; media footage generally depicts Indonesia) from our comprehensive survey data corroborates that pangolins are unlikely implicated as spill-over hosts in the COVID-19 outbreak. This is unsurprising because live pangolin trading has largely ceased in China.”

However, badgers, porcupines, red foxes, masked palm civets, raccoon dogs, Siberian weasels, snakes, Siamese crocodiles and Chinese bamboo rats were among 38 animal species sold at the Huanan seafood and fresh produce market in central Wuhan. Almost all of the animals were “sold alive, caged, stacked and in poor condition,” and were often butchered on site, the researchers wrote.

Masked palm civets were discovered to be the host of the SARS-COV virus that caused the 2003 SARS outbreak, the authors acknowledge, warning against “false attribution” of the virus to any species, as of yet. 

“We should therefore not be complacent, because the original source of COVID-19 does not seem to have been established,” the authors wrote. “This is doubly important because false attribution can lead to extreme and irresponsible animal persecution. For instance, civets were killed en masse following the SARS-CoV outbreak, and any unwarranted vilification or persecution of pangolins and bats in relation to COVID-19 would risk undermining otherwise very successful efforts to better protect and conserve wildlife in China.”

Animals Sold at Wet Markets Kept in Poor Conditions 

Caged animals held for sale and slaughter in unsanitary conditions at Wuhan’s Huanan Seafood Market, prior to the outbreak of COVID-19, including: (a) King rat snake (Elaphe carinata), (b) Chinese bamboo rat (Rhizomys sinensis), (c) Amur hedgehog (Erinaceus amurensis) (the finger points to a tick), (d) Raccoon dog (Nyctereutes procyonoides), (e) Marmot (Marmota himalayana) (beneath the marmots is a cage containing hedgehogs), and (f) Hog badger (Arctonyx albogularis).

None of the 17 vendors in Wuhan selling the wild-caught and farmed non-domesticated species posted required origin or quarantine certificates, “so all wildlife trade was fundamentally illegal”, they said.

Along with the sale of the animals as luxury meat items,  some of the wild animals were also sold as pets – another prestige item in China, the authors noted. 

“We thus make an ethical distinction here between the subsistence consumption of bush meat in poorer nations, versus the sort of cachet attached to wild animal consumption in parts of the developed world, notably China, but also Japan,” the authors stated. 

Although the survey pre-dates the discovery of SARS-CoV2, other “potentially lethal viruses” were found in the wildlife tested, including rabies, SFTS, H5N1, as well as common bacterial infections that, nevertheless, represent a risk to human health (e.g., Streptococcus). 

Many of the earliest cases of human COVID-19 infection were linked to the Huanan seafood market, initially identified as where SARS-CoV-2 first crossed to humans. However, other early clusters of cases elsewhere in the city also suggest that the novel coronavirus did not exclusively emerge from the Huanan marketplace either. 

The study challenges some of the assumptions in a recent WHO report on its mission to Wuhan noting that: “The WHO reports that market authorities claimed all live and frozen animals sold in the Huanan market were acquired from farms officially licensed for breeding and quarantine, and as such no illegal wildlife trade was identified.” 

“In reality, however, because China has no regulatory authority regulating animal trading conducted by small-scale vendors or individuals it is impossible to make this determination.”

The authors also note the gunshot and trapping wounds found on the bodies of live animals or their carcasses following slaughter, suggesting illegal hunting and trapping of many of the species sold in the market. 

China Crackdown – But More Steps Needed

After the first COVID-19 outbreak in Wuhan, China cracked down on wildlife trafficking, banning the consumption and trading of wild animals for food in February 2020, although it still allows some animals to be reared for fur or traditional Chinese medicine.

However, the study cites a series of other measures that still may be needed, stating that: “Legislative reform is also vital to clarify unequivocally which species are considered ‘wild’ and cannot be traded legally and safely.”

Another problem, as encountered by the WHO report is that, retrospectively, it proved difficult to ascertain which species were on sale, even to the genus level, relying solely on the responsible market authority’s official sales records and disclosures. 

Sales of wild animals, including squirrels, birds and turtles, as pets, are another concern, the authors note, saying, “While not currently the vector of any major viral epidemics, it would be naive to imagine that unconventional pets do not still also pose a serious concern for public health26. This potential for disease is likely exacerbated by poor sanitary and welfare conditions.

The authors also cite physical infrastructure reforms in China’s open air markets, and other hygienic practices, in line with new WHO co-authored guidance, on “Reducing public health risks associated with the sale of live animals on mammalian species in traditional food markets’, stating that, “adopting these more responsible practices has the potential to save countless lives in the future.”

Origins of COVID-19 Unsolved: More Investigations Needed

More than a year into the pandemic, the question of the virus’s origins remains largely unresolved.

A World Health Organization-led research mission in March found that SARS-CoV-2 most likely spilled over to humans from a live animal — either directly through a bat infection, or via another mammal, possibly one sold at Wuhan’s wet markets. 

But other scientists have charged that the virus may instead have escaped from the Wuhan Institute of Virology – and calling for further exploration of that hypothesis.

Last month President Joe Biden administration asked US scientists to “redouble efforts” to find the origins of the virus, asking for another update in 90 days.

Image Credits: Breaking Asia, , Scientific Reports, Nature .

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