A new international study published in the journal Cell provides new evidence to support the hypothesis that the virus causing the COVID-19 pandemic originated from wild animals that were sold at the Huanan market in the Chinese city of Wuhan.
This new information does not, however, allow us to definitively eliminate the scenario of a leak from the research laboratory present in the city, which is however not supported by any scientific data, says the researcher who led this study.
In this study, the researchers carried out an in-depth analysis of all available genetic data: on the one hand, those obtained from the sequencing of environmental samples from the Huanan market, that is, samples that were collected during sampling of the cages, carts, tables, doors and floor of the market after its closure at the very beginning of January 2020. These samples were subjected to a PCR test that detected the presence of the SARS-CoV-2 virus — which is responsible for the COVID-19 pandemic — as well as metatranscriptomic sequencing, which consisted of sequencing all the genetic material present in the samples that could contain that of viruses, bacteria, fungi, plants, animals or even humans.
In addition, the researchers had access to the genetic sequences of viruses taken from the first human cases of COVID-19 in China and other countries.
Among the genetic data from the environmental samples, the researchers found snippets of DNA that matched reference sequences in the genomes of particular animals. They were able to identify various animal species, such as the civet, raccoon dog, bamboo rat and Malayan porcupine, that were present at the market.
Along with the DNA of these animals, they also found the sequence of SARS-CoV-2. “These results are compatible with the hypothesis that the animals were infected, but we cannot prove it,” because it was not possible to take samples from the wild animals on sale at the market since they had been evacuated when the market closed.
“We will never be able to have a definitive answer,” says Florence Débarre, a researcher at the Institute of Ecology and Environmental Sciences in Paris, at the National Center for Scientific Research (CNRS).
These results still suggest that some of these animal species were probably intermediate hosts of the virus — that is, between bats, the initial reservoir of the virus, and humans. According to the authors of the study, the civet and the raccoon dog are at the top of the list of suspect animal species “because they had been identified, even before the COVID-19 pandemic, as representing a risk of transmission of coronavirus to humans, and also because they were involved in the SARS epidemic in 2002,” underlines Ms. Débarre.
The natural hypothesis reinforced
Analysis of the genome of viruses taken from the first COVID-19 patients, as well as those found in environmental samples, has also helped to strengthen the scenario of a natural origin at the Huanan market, rather than that of a virus escaping from the Wuhan research center.
Researchers have confirmed that two lineages of SARS-CoV-2 circulated early in the pandemic. Several of the initial patients, who reported frequenting the Huanan market for shopping or as vendors, were infected with lineage B viruses. A few other patients who had no direct contact with the market were infected with lineage A viruses.
“The fact that some of the first COVID-19 cases were unrelated to the market gave rise to the idea that the outbreak may have started elsewhere. […] And that the market would have played the role of secondary amplification rather than being the initial source,” recalls the researcher. This scenario seemed all the more plausible since no lineage A virus – which these cases with no link to the market carried – had been discovered in the first samples taken at the market.
It was not until 2022 that it was revealed that lineage A had been detected in an environmental sample from the market by the Chinese Center for Disease Control and Prevention. “With this new information, the scenario of an origin at the market, which had been a bit complicated to explain until then, suddenly became simple and coherent,” notes Ms. Débarre. In addition, “the patients who had not frequented the market nevertheless lived near it.” [Qui plus est]people who had gone to the market subsequently came into contact with other people, particularly on transport, and when they returned home and saw their families. They had multiple opportunities to transmit the virus – contracted at the market – to others.
Do all these observations further undermine the hypothesis that the virus came from a research laboratory? “The possibility that the pandemic is linked to research activities is a legitimate hypothesis to consider and that we have considered, but our scientific conclusions, which are based on an analysis of different types of data, do not point in this direction,” says Ms. Débarre.
The most plausible scenario
“However, I doubt that the debate is closed. People who are firmly convinced that the origin [de la pandémie] “It is the laboratory’s, I don’t think we will be able to convince them with this study,” the evolutionary biology specialist admits lucidly.
“Our study mainly provides arguments that are in favor of the market. For the lab, it is more the absence of data; apart from that, [cette hypothèse] is based solely on speculation. Whereas for the natural hypothesis, it is data that shows that the first human cases frequented the market or otherwise resided around the market. It is the fact of having found the two early lineages (A and B) of the virus at the market. And it is the fact that, of all the places in this city of 12 million inhabitants, this market which sold wild animals is the place most likely to be a source of transmission of the virus from animals to humans,” she summarizes.
“Our results thus provide arguments for the hypothesis that the first human cases were infected by animals that were sold at the market. None of these arguments in themselves provides a definitive answer, but it is their convergence that suggests that this is a very plausible scenario. It is at least the simplest scenario that can explain the data. We cannot affirm that this is the true story: there is no way to conclude this. But given the current state of the data, this is what is simplest and most compatible with the data,” she argues.
