Where exactly was the first human infected with Covid-19? Is it really an infection linked to an animal? When exactly did the epidemic start? A CNRS study published this Thursday, September 19, sheds light on mysteries of more than four years about this global disease.
This is the story of a major scientific discovery made “by chance” in March 2023 and made inaudible in France by the hubbub over pension reform. One of the mysteries of the origin of Covid-19 has been solved by a French woman. This Thursday, September 19, an international research team, led by Florence Débarre, a researcher in evolutionary biology at the CNRS, published the conclusions of an unprecedented study on this virus that has confined the planet.
It all begins in Wuhan, China, in the Huanan market. It is in the rows of this market teeming with the city’s 12 million inhabitants that the most devastating modern virus is said to have first reached humans. There, among the thousand vendors in the immense area, some illegally offer wild animals, in dubious hygienic conditions.
“Huanan market was the most frequent location for wildlife vendors in Wuhan (…) Several were identified as illegally offering live animals such as raccoon dogs, civet cats, bamboo rats, Malayan porcupines, Amur hedgehogs, and Asian badgers in late fall 2019,” the researchers wrote in the scientific journal Cell.
In addition to exotic animals, smaller and unwanted guests are also present on the shelves: viruses. Hepatitis C, kobuvirus, betacoronavirus… And even a strain of the bird fluH9N2, transmissible to humans, were identified by researchers in samples taken on site at the start of the pandemic.
“There are viruses everywhere, all the time. But most of them don’t have any harmful consequences,” Florence Débarre told BFMTV.com. “However, some of them have zoonotic potential, being able to pass from animals to humans.”
A date of infection of patient zero
A virus that jumped from animals to humans? This investigation clearly suggests that it was in the confines of this wet market that SARS-CoV-2 first crossed the species barrier to infect humans. By studying the genealogy of the virus, it is even possible to date patient zero, “between mid- and late November” 2019.
“Thanks to this study, we are gradually getting closer to understanding how this can happen and how it could have happened,” comments virologist Bruno Lina, member of Covars, the new scientific council.
“We see that the progression of this virus was gradual. Animals were infected, then some humans, probably with a transmission that was not very rapid at the beginning, in the first days of December,” he notes, observing in the data a “small amplification” halfway through the month.
As a reminder, it was only on January 5, 2020, two weeks later, that the World Health Organization (WHO) first mentioned “pneumonia of unknown cause” in the city.
The study also allows us to understand the beginning of the evolution of the virus in humans, with its separation into two lineages, A and B. The first died out, the second took the world by storm, before subdividing into the numerous variants that are still circulating everywhere today.
Knowing the evolution of the virus, and in particular the common ancestor of the two lineages, allows us to certify that it did not exist before November 2019, contrary to certain dated and already disproven assertions or theories.
This animal that transmitted the virus to humans
Scientists know where and when the contact took place. But they can also, with great reliability, determine through whom. At least, a list of potential suspects. Suspicions fall on the civet, the bamboo rat, the porcupine and the raccoon dog.
It is the latter, a kind of adorable mix between a raccoon, a dog and a fox, who is now presented as the number one suspect. “Raccoon dogs are a species for which it has been experimentally demonstrated that they can not only be infected and have their version of Covid, but also transmit it. This makes them an important suspect,” summarizes Florence Débarre.
“This is a species that was already involved in the SARS epidemic (another coronavirus, editor’s note) between 2002 and 2004 (…) We knew that they represented a risk for the transmission of coronaviruses to humans,” she adds.
The study does have its limitations, however. First, because of the method used to reach these conclusions. For example, the animals present five years ago on this market were never directly tested, only their environment. “With the data we have, it is impossible to demonstrate the source of the viruses that are found,” whether they are of human or animal origin, the researcher specifies.
But the analysis shows a correspondence between the places where traces of Covid-19 were found and the location where sick people were in this market. The rate thus appears much higher where wild animals were sold, in the southwest area, than in the rest of the market.
Finally, the last downside: the lack of data on the ability of certain animals present to transmit to receive and transmit the virus to humans. So, perhaps an arctic fox or a Reeves’ Muntjac present in Wuhan at the time could also be a serious candidate.
These other exotic beasts “are not excluded”, but “we do not have knowledge of their capacity to infect and transmit” in the absence of experimental data – analyses that the researchers recommend carrying out to refine their hypotheses.
Elements that will remain mysterious
The raccoon dog, whose “guilt” has been questioned since the beginning of the pandemic, and whose presence on site was identified by an initial study by the researcher published “in the middle of the conflict over pension reform”, contrasts with some of the first options repeated at the beginning of the epidemic. Thus, neither pangolins nor bats were present at the market at the time of the events. Are they therefore completely unrelated to this epidemic? Not necessarily.
The CNRS study looks at the appearance of Covid-19 in humans. But these species could have played a role in the long history of this zoonosis, having probably traveled hundreds of kilometers and several species before reaching humans in China.
“Bats remain high on the list of potential distant sources of the virus, because there are similar viruses circulating (among them),” the author explains. “With the data from the Huanan market, we cannot describe the long chain of events that lead from bats in the South to the presence of the virus in the market.”
Episode 6: The origins of COVID-19
The pangolin is not whitewashed either. Viruses similar to SARS-CoV-2 have been detected in the small animal on several occasions. It is therefore conceivable that at some point in the long chain of events, it was a host. But like the bat, it is unlikely to have directly infected humans.
The hope of a detailed knowledge of the virus’s path from its birth to today is rather slim. Or even non-existent. “We will not know the precise list of events. On the other hand, we will be able to have better ideas of the potential species involved,” adds the evolutionary biology researcher at the CNRS.
Lab leak hypothesis deflates
In this case, scientists are progressing slowly, and are careful not to draw definitive conclusions based on their data. But it is clear that the sequence of elements, while not allowing one hypothesis to be 100% confirmed, has the merit of eluding others. Including the one that has stirred up part of the public debate, that of the “laboratory leak”.
In Wuhan, a highly sensitive virology laboratory has indeed been the focus of much attention. Could this be where the pandemic originated? A hypothesis that was initially “legitimate” by the researchers’ own admission. But faced with evidence supporting the zoonosis trail, the idea of a scientific accident is deflating.
Moreover, it would be difficult to say that this hypothesis had not been seriously studied. Seven American intelligence agencies conducted the investigation and, according to documents declassified in June 2023, the vast majority considered the “zoonotic” hypothesis “very probable.”
“This clearly puts paid to some other hypotheses,” says Bruno Lina. “We see that we have all the elements that support the fact that this is indeed a natural appearance of the virus” transmitted from animals to humans without (in)voluntary intervention. The only error of our species would therefore be to have encroached on nature.
