Wuhan market increasingly likely origin point for COVID-19

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An international team of researchers has found more evidence that COVID-19 came from animals in a Wuhan food market.

The researchers have identified wildlife present at the Huanan Seafood Wholesale Market in early 2020 via traces of their DNA, and say it’s likely that some of these animals were infected with COVID-19.

The study is published in Cell.

‘Extensive epidemiological evidence supports wildlife trade at the Huanan market as the most likely conduit for the COVID-19 pandemic’s origin,’ write the researchers in their paper.

‘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,’ says co-corresponding author Professor Kristian Andersen, a researcher at Scripps Research, USA.

The team used genetic data collected by the Chinese Center for Disease Control and Prevention (CDC) on 1 January 2020, hours after the market had been closed and the animals removed.

A team from the Chinese CDC swabbed surfaces such as floors and walls all over the market, then returned a few days later to investigate stalls selling wildlife more closely, collecting drain samples and swabbing cages and carts as well.

This gave them 923 environmental and 457 environmental samples to examine.

The Chinese CDC team used a technique called metatranscriptomic sequencing on the samples. This method can collect the RNA and DNA of all organisms, from viruses to mammals, present in a swab.

‘This is one of the most important datasets that exists on the origin of the COVID-19 pandemic,’ says co-corresponding author Dr Florence Débarre, from the National Centre for Scientific Research, France.

The Chinese CDC team published their findings on the data, which showed ample evidence of SARS-CoV-2 at the market, in Nature last year. They also shared all of their sequencing data publicly, which allowed an international team to investigate it further.

‘We have analysed, in new and rigorous ways, the vitally important data that the Chinese CDC team collected,’ says co-corresponding author of the Cell paper, Professor Michael Worobey, from the University of Arizona, USA.

‘This is an authoritative analysis of that data and how it fits in with the rest of the huge body of evidence we have about how the pandemic started.’

The researchers used genetic mapping techniques to identify the wildlife present in the market, as well as viruses they were carrying and whether or not SARS-CoV-2 was present in their stalls.

The list of wildlife includes rabbits, dogs, hedgehogs, porcupines, marmots and civets.

Some of the animals’ genetic material was found on the same swabs as SARS-CoV-2 samples.

‘Many of the key animal species had been cleared out before the Chinese CDC teams arrived, so we can’t have direct proof that the animals were infected,’ says Débarre.

‘We are seeing the DNA and RNA ghosts of these animals in the environmental samples, and some are in stalls where SARS-CoV-2 was found, too. This is what you would expect under a scenario in which there were infected animals in the market.’

The team also compared the viral genomes in the data to those in the earliest confirmed COVID-19 patients, and found that only a couple of people, if any at all, were likely to have been infected with the virus before the market outbreak.

‘In this paper, we show that the sequences linked to the market are consistent with a market emergence,’ says Débarre.

‘The main diversity of SARS-CoV-2 was in the market from the very beginning.’

Worobey says that bringing wild animals into the centre of big cities is ‘the most risky thing we can do’.

‘We need to start putting the evidence of how this pandemic started into action by taking serious, concrete action to stop the perilous practice of bringing live animals with potential pandemic pathogens into densely populated urban areas,’ he says.