Raccoon dogs, lab leaks and Chinese secrecy have made for high drama as scientists who think they may have found the elusive “Animal X” that passed SARS-CoV2 were excluded from a data-sharing platform for “scooping” Chinese scientists.

Nineteen scientists, including world-renowned figures such as Dr Michael Worobey and Dr Angela Rasmussen – have published a report detailing how they had been scolded and falsely accused of rules violations by the data-sharing platform, GISAID, after reporting that they had found genetic material of wild animals intermingled with environmental samples collected by the Chinese Center for Disease Control in January and February of 2020 from the Huanan Seafood Wholesale Market in Wuhan – ground zero of the COVID-19 outbreak.

This co-mingling of SARS-CoV-2 virus and animal RNA/ DNA from five animal species “identifies these species, particularly the common raccoon dog, as the most likely conduits for the emergence of SARS-CoV-2 in late 2019”, the authors concluded in their study, published on the pre-print research server base Zenodo on Monday. 

This is the first time that scientists have proposed that the elusive “animal X” responsible for virus spillover from animals to humans might have been found.

Later on Tuesday, it appeared that GISAID had removed all the authors’ access to its platform. The platform is a public-private partnership that is hosted by the German government that allows scientists to share data about infectious diseases.

Important update: I cannot access GlSAlD anymore. And it seems that my coauthors cannot either. pic.twitter.com/m4oY5uUeQq

— Flo Débarre (@flodebarre) March 21, 2023

Report co-author and French evolutionary biologist Florence Débarre accidentally found the Chinese Center for Disease Control and Prevention (CCDC) environmental samples on the GISAID infectious diseases database on 4 March 2023.

The samples had apparently been posted to support a CCDC preprint article published on 25 February by a group of Chinese scientists affiliated with CCDC and other governmental resaerch institutions.

In the preprint article, the Chinese authors asserted that of the 1,380 samples collected from the environment and the animals in the market in early 2020, “No virus was detected in the animal swabs covering 18 species of animals in the market” – exactly the opposite of what Worobey and his colleagues said they have found.

Of the environmental samples taken from the marketplace in the early days of the pandemic, only 73 tested positive for SARS-CoV-2 and three live viruses were successfully isolated – which 99.9% related to the genetic forms of virus strains circulating among humans in those early days, according to the Chinese authors.  

Genetic footprints of ‘multiple animal species’ co-mingling in SARS-CoV2 environmental samples 

In contrast, the Worobey-led research group, in their analysis of the same GSAID data, said they found genetic evidence of “multiple animal species” co-mingling among the SARS-CoV-2 positive environmental samples collected at the marketplace.

In particular, they identified mitochondrial genomes for the common raccoon dog; Malayan porcupine; Amur hedgehog; masked palm civet; and hoary bamboo rat “from wildlife stalls positive for SARS-CoV-2”. 

This is important, they assert, because although live mammals had been observed in the market in late 2019, an area where many COVID-19 patients with the earliest-known onset of symptoms worked, the animals’ presence and “exact locations were not conclusively known” at the time when SARS-CoV2 first surfaced in the marketplace.

The most recent data posted on GSAID, therefore, raises the likelihood that wild animals kept caged in the market could have been a conduit for passing the coronavirus, which originates amongst bats, to humans, the authors state. 

In another explosive finding, some of the animals they identified – such as the fox-like raccoon dogs – are known to be susceptible to  SARS-CoV-2 but “were not included in the list of live or dead animals tested at the Huanan market, as reported in the 2021 WHO-China joint report on the origin of the COVID-19 pandemic”, the authors state. 

Even more crucially, in some cases, there was more animal genetic material than human material “consistent with the presence of SARS-CoV-2 in these samples being due to animal infections”, say the authors.

In 2021, an international team assembled by the World Health Organization (WHO) to investigate the origins of SARS-CoV-2 identified animal transmission – through an elusive ‘Animal X’ – as the most likely route of infection in their report. But the theory stalled due to a lack of actual evidence in the WHO report about the exposure of wild animals in the marketplace at the time to the virus. 

Those who have concluded that zoonotic origin at Huanan market is most likely did so by weighing the mounting evidence, taking a scientific approach.

Those who promote the lab leak hypothesis despite no evidence have taken a political approach from the start. https://t.co/4Jl0BBIaED

— Dr. Angela Rasmussen (@angie_rasmussen) March 20, 2023

Chinese secrecy – data withdrawn

The controversy around the data, and its implications, has been heightened by the fact that it has now been withdrawn from the GSAID site.

This happened shortly after the scientists said that they had contacted one of the Chinese preprint authors, on 9 March, and were told they could conduct an independent analysis of the CCDC data.

But on 11 March,  a day after the Worobey group told the Chinese colleague that they had found animal genetic material in the samples, the data was pulled from the site “at the request of the submitter”. 

Not only that, but the GISAID Secretariat sent emails to the scientists “admonishing us to comply with the GISAID terms of use, or in some cases falsely accusing us of having breached the GISAID terms of use”, wrote the Worobey group. 

“We are well aware of these terms of use, have not breached them, and have no intention of breaching them,” they wrote.

While the GISAID website makes no mention of a secretariat, its business affairs are run by the executive board of the Friends of GISAID, the members of which are not named, and advised by an 11-person scientific advisory council that includes US, Chinese, European, Japanese and Singaporean representatives.

However, GISAID released a statement on Tuesday accusing the Worobey group of “scooping” the Chinese group by using its data and publishing it before the Chinese scientists had done so.

“Unfortunately, GISAID learned that select users published an analysis report in direct contravention of the terms they agreed to as a condition to accessing the data, and despite having knowledge that the data generators are undergoing peer review assessment of their own publication,” according to the statement.

GISAID said it had asked the Chinese researchers whether “best efforts to collaborate have been made in this case”, and were told the Worobey group had communicated “only their intent to publish their analysis of the generators’ data. As such, the best efforts requirement has not been met”.

“GISAID’s goal is to incentivize timely and transparent data sharing by providing a trusted place for data contributors to see their rights respected.  It should be apparent to everyone that the data generators [Chinese researchers] are the ones most familiar with the details surrounding their submitted data and the context in which it was collected,” added the platform, stressing that the Chinese research should have been published first.

WHO involvement

However, it is unclear whether the international scientific community will agree, as China has long been accused of withholding data and access to Wuhan sites.

The WHO confirmed late last week that it had been informed both about the findings and the CCDC’s actions on 12 March, and it reached out to its Scientific Advisory Group for the Origins on Novel Pathogens (SAGO) and the CCDC.

After calls between SAGO and the CCDC, the CCDC confirmed that “DNA from wild raccoon dogs, Malaysian porcupine, and bamboo rats among others” had been found “in SARS-CoV-2 positive environmental samples”, according to a SAGO statement released last Friday.

“These results provide potential leads to identifying intermediate hosts of SARS-CoV-2 and potential sources of human infections in the market,” according to SAGO.

This is despite the CCDC’s assertions to the contrary, which mention 18 animals, none of which are raccoon dogs.

But, said SAGO, “the presence of high levels of raccoon dog mitochondrial DNA in the metagenomics data from environmental samples identified in the new analysis, suggest that raccoon dog and other animals may have been present before the market was cleaned as part of the public health intervention”.

Late on Friday afternoon, WHO Director-General Dr Tedros Adhanom Ghebreysus did not mince his words at a media briefing when he appealed to China for transparency, adding that these samples could have been shared three years ago.

China has consistently refused to accept that COVID-19 might have originated on its shores, and has asserted that the virus could have been spread from imported frozen fish sold at the market – the frozen food chain hypothesis.

However, the independent origins group report stated that “there is no conclusive evidence for foodborne transmission of SARS-CoV-2 and the probability of cold-chain contamination with the virus from a reservoir is very low”. 

Lab leak revival

In early March, the Republican-dominated US House Subcommittee on the Coronavirus Pandemic convened its first hearing to examine COVID-19’s origins, focusing almost entirely on the theory that COVID-19 originated from a laboratory “leak” at the Wuhan facility studying coronaviruses. 

Dr Robert Redfield, former head of the US CDC, told the hearing that he found it implausible that a virus could jump from animals in the Wuhan wet market to humans.

The lab leak theory was initially pushed by then-US president Donald Trump and his allies in 2020.

The impetus for the lab leak theory has grown this year, particularly as the US ramps up its anti-China rhetoric – and China’s secrecy and refusal to share data has fueled it.

“The FBI has for quite some time now assessed that the origins of the pandemic are most likely a potential lab incident in Wuhan,” Christopher Wray, the head of the US Federal Bureau of Investigation (FBI) told Fox News in late February.

The Trump-appointed Wray added that “we’re talking about a potential leak from a Chinese- government-controlled lab that killed millions of Americans”.

However, the origins report described this hypothesis as “extremely unlikely”, saying that “the deliberate bioengineering of SARS-CoV-2 for release has been ruled out by other scientists following analyses of the genome”. In addition, the SARS-CoV-2 from bats and pangolin that were being studied at the Wuhan lab “are evolutionarily distant from SARS-CoV-2 in humans”. 

Meanwhile, recent polls show that roughly two-thirds of Americans believe that Covid probably started in a lab, according to the New York Times.

Image Credits: Bernd Schwabe/ Wikipedia, Ryzhkov-Sergey/ Wikipedia, CSPAN.