Suppressed Chinese Covid ‘origins’ data published and reviewed in leading journal

Vital data that sheds light on the origins of the Covid-19 pandemic have been published after peer review in one of the world’s most prestigious scientific journals.

The analysis is based on 800 genetic swabs taken from the Wuhan wet market by the Chinese authorities just days after Covid-19 was first detected and before a pandemic was officially declared.

It shows that the two earliest known strains of Sars-Cov-2 were present in the market and that wild animals known to catch and spread the virus, including racoon dogs and civets, were present.

The researchers were unable to show the animals were themselves infected and caused the outbreak, but it is a strong signal, they argue, that the pandemic had natural origins.

“This paper adds another layer to the accumulating evidence that all points to the same scenario: that infected animals were introduced into the market in mid- to late November 2019, which sparked the pandemic,” said Prof Kristian Andersen, an evolutionary biologist  at Scripps Research in the United States, and a co-author of the report.

The paper is a more considered peer-reviewed analysis of data that emerged in March 2023, which sparked global headlines as scientists argued vociferously over its meaning.

It is based on hundreds of samples collected from walls, floors, metal cages and carts inside Huanan Seafood market by the Chinese Center for Disease Control and Prevention (CDC) on 1 January 2020, just 24 hours after news broke of the first cluster of Covid cases in Wuhan.

China initially withheld the data from international researchers and the World Health Organization (WHO), in a possible bid to deflect blame and create space for the state to construct origins narratives that pointed to the US or other countries.

It only emerged publicly when Dr Florence Débarre, an evolutionary biologist at the Institute of Ecology and Environmental Sciences in Paris, noticed the sequences on the international GISAID data repository, downloaded them and shared them with collaborators for analysis.

The latest study shows early strains of Sars-Cov-2 were present in the market in the early days of the outbreak, together with the “genomic ghosts” or traces of exotic animals being sold there.

It does provide compelling evidence that the pandemic began after spilling over from wildlife but it remains circumstantial, falling short of hard proof.

Critics said the researchers had initially over-stated their conclusions, noting that there was no way of telling if the market animals themselves had been infected.

Others pointed out that, while the first cluster of Covid cases had been announced only 24 hours before the samples were taken, Covid had almost certainly been circulating in Wuhan under the radar for over a month before.

It remains possible, therefore, that a laboratory leak could still explain the first cases.

Dr Débarre said the new paper, published today in Cell, includes no new “scoop”, but is a more refined, more detailed analysis of the original preprint.

“The key message is the same,” Dr Débarre said. “There was wildlife present in Huanan market at the end of 2019, including species like racoon dogs and civics that were previously identified as risky because they were involved in Sars [spillover in 2002], and because it has been shown experimentally that they can be infected with and transmit Sars-Cov-2.”

As well as identifying civets and racoon dogs – known to be able to catch and spread Covid-19 – the study confirmed the presence of animals including the bamboo rats, Malayan porcupines, and Amur hedgehogs in the market.

Importantly, it also includes analysis of the early dynamics of Sars-Cov-2 and found genetic evidence that the early strains were present in the same areas of the market as wildlife.

“The most recent common ancestor of sequences from the market matches the most recent common ancestor of the pandemic, which is consistent with an origin in the market,” Dr Débarre said. “Another way of phrasing it is that early Sars-Cov-2 diversity was represented in the market from the very beginning.

“It’s not possible to prove that the animals were infected or not infected using the data. However, the pattern that we see is consistent with the animals being infected. Likewise, the fact of having both early lineages A and B in the market doesn’t prove that the market is the origin, but it is what you would expect if it were.”

She added: “It is something of a big piece of information, when you consider the scale of the whole city of Wuhan and its 12 million inhabitants.”

Prof Edward Holmes, an evolutionary biologist and virologist at the University of Sydney and co-author of the report, said the fact both the early lineages of Sars-Cov-2 were in the market is consistent with the “multi-jump theory” that Covid jumped from animals to people on several separate occasions.

Other experts not involved in the paper said the data was “as good as it gets”, given how much time has passed since Covid-19 first emerged.

“It does add another layer of evidence that wild animals, being traded inside the Huanan market, were the very likely source and therefore origin of the Sars-CoV2 pandemic,” said Prof Jonathan Ball, deputy vice-chancellor of Liverpool School of Tropical Medicine and professor of molecular virology.

“Finding genetic material from key animal species, like civet cats and racoon dogs … in the same samples as testing positive for the presence of Sars-CoV2 is as good a smoking gun as we are ever likely to get.”

But despite “providing very strong evidence” there remain limitations, noted Prof James Wood, an infectious diseases epidemiologist at the University of Cambridge.

“The limitation of the work is that market samples were not taken before the market closed around 1st January 2020 and the pandemic viruses are thought to have arisen four to six weeks before this date,” he added.

“The virus results are what one might expect to find had the pandemic originally arisen around a wildlife market stall or stalls – but they cannot provide direct evidence of this simply because of the sampling dates.”

He added that the paper – which comes only a few weeks after a study in Nature found a concerning bat coronavirus among 36 novel viruses detected in Chinese fur farms – is an “important” reminder of the threat posed by wet markets.

“While efforts have been made globally to tighten up on laboratory biosecurity to ensure that viruses cannot inadvertently escape … little or nothing has been done to limit either the live trade in wildlife, nor the biodiversity loss or land use changes that are the actual likely drivers of past and future pandemic emergence,” Prof Woo said.