Coronavirus and animal origins, does the scientific community agree?

Let us understand briefly

While the Covid-19 epidemic is present on all continents, scientists are still looking for the species that causes human transmission of the Sars-CoV-2 coronavirus.

An investigation essential to understand the emergence of the disease but in which the evidence is not yet conclusive.

On March 3, 2020, the Covid-19 epidemic crossed the barrier of 90,000 infected worldwide. While the number of new daily cases has never been so low in China, the cradle of the epidemic, other countries are seeing the disease spread like wildfire. Faced with this new disease, which no longer spares any inhabited continent, scientists are hard at work to understand the coronavirus Sars-CoV-2, the etiological agent of Covid-19. And the question of its origin is far from being resolved.

Bats, snakes, pangolins, several animal species transiting through the Wuhan market, the starting point of the epidemic, have been implicated, as the natural reservoir or intermediate host of the coronavirus, by researchers.

But each publication posted on Biorvix was accompanied by a following questioning it. As a reminder, the Biorvix site is a pre-publication site, the referenced works have not followed the classic scientific publication path, namely a peer review where errors in methodology or interpretation are raised and then revised by the authors. A long process, but one that enhances the value of the published results. On the other hand, pre-publication, although having its limits, is very useful for communicating scientific results quickly in a situation that evolves as quickly as an epidemic.

The SARS-CoV-2 coronavirus intermediate host in question


In early February, Chinese researchers claimed that Sars-CoV-2 and an isolated pangolin coronavirus shared 99% of their genome. A communication error since their study, published on February 20 on Biorvix, reveals that it is actually only the “receptor-binding domain” of the surface protein S and which does not have that an amino acid different from the protein S domain of the Sars-CoV-2 coronavirus. We are therefore far from a 99% genetic match between the two viruses.

Two other studies, published the same day, suggest that the virus responsible for Covid-19 shares, for one, 90.23% and, for the other, 91.02% of its genome with the strains isolated from the pangolins tested. . This similarity is not enough to make pangolin a host for the virus.

In the case of the Sars epidemic of 2002-2003, Sars-CoV shared 99.8% of its genome with a coronavirus isolated from civets, making this small mammalian Feliform the intermediate host of the virus and the link between its natural reservoir and Man.

The bat, a serious track in the emergence of the epidemic

Bats are still considered the most likely source of Sars-CoV-2. A coronavirus isolated from the flying mammal is genetically closest to the virus circulating between humans, 96% of the genetic material is common. Could the virus have passed from the bat to humans without an intermediate host?

The differences between the famous “receptor-binding domain” of the two viruses suggest that the bat coronavirus could not infect humans without an intermediate host, according to the researchers.

But who is this intermediate host that escapes scientists? The publications on the subject raise more questions than they solve. The investigation still promises to be long.

Coronavirus: pangolin suspected of being the missing link

The pangolin is the most poached species in the world, far ahead of elephants or rhinos. Victim of illegal trafficking, this small mammal, threatened with extinction, is highly prized for its flesh, scales, bones and organs in traditional Asian medicine. It could be the animal that transmitted the virus, this is what Chinese researchers say while others call for caution.

Is the pangolin, a small mammal with scales threatened with extinction, the animal that transmitted the new coronavirus to humans? Chinese researchers advanced the hypothesis on Friday, but other scientists are cautious while awaiting final confirmation.

The animal, which harbors a virus without being sick and can transmit it to other species, is called a “reservoir”. In the case of the new coronavirus, it is certainly a bat: according to a recent study, the genomes of this virus and of those which circulate in this animal are identical to 96%. But as the bat virus is not equipped to attach to human receptors, it probably passed through another species to adapt to humans.

Is the pangolin the missing link?

The identity of this intermediate animal has been the subject of many questions since the beginning of the epidemic. The snake hypothesis was soon swept aside. Friday, the University of Agriculture of southern China ruled that the pangolin could be “a possible intermediate host”, but did not give much details. We only know that the genetic analyzes of viruses taken from pangolins and humans were 99% identical, according to the new Chinese state agency. These elements are “not sufficient to conclude, tempered a British scientist, Professor James Wood. Evidence for the involvement of pangolin has not been published in a scientific journal, “an essential criterion to validate this hypothesis,” he said.

“We would have to look at all the genetic data to know the degree of proximity between the pangolin and human viruses,” added another British scientist, Professor Jonathan Ball. The new virus appeared in December in a market in Wuhan (central China). Despite its name as a Seafood Market, many other animals, including wild mammals, were sold there for food. It is not known if the pangolin was one of them. During the SARS epidemic (2002-2003), also caused by a coronavirus, the intermediary was the civet, a small mammal whose meat is appreciated in China.

How are animal surveys carried out?

Before targeting the pangolin, Chinese researchers tested more than 1,000 samples from wild animals. They probably had to identify all the types of animals sold in the market and test to see if they were carrying the virus. For this, we perform “a pharyngeal sample (in the throat, editor’s note) and a stool sample”, explains to AFP Arnaud Fontanet, from the Pasteur Institute.

Virologist Martine Peeters, from the IRD (Research Institute for Development), investigated in Africa to find the animal reservoir of the Ebola virus. There too, the bat was involved. The researcher describes samples taken from this animal: “We pass them a swab in the mouth and another in the rectum”. If you do not have the animal itself, you must also collect excrement from the wild. “We collected thousands of droppings at many sites in Africa,” said Martine Peeters to AFP.

This is probably also what Chinese researchers did for the new coronavirus, especially since the market in Wuhan was closed at the start of the epidemic. At the end of January, a Chinese team said they had taken 585 samples from stalls and from a garbage truck on the market, and “having found the coronavirus in 33 of them,” says Professor Fontanet. They don’t say which samples it was, but I think it was excrement lying around on the benches. “

The importance of knowing the animal responsible for the epidemic?

Knowing the animal that transmitted the virus to humans can help prevent the virus from re-appearing once the epidemic has been brought under control. “It was by prohibiting the consumption of civets and by closing livestock farms that we could have prevented any reintroduction [of the SARS virus in humans, note],” said Professor Fontanet. If the pangolin hypothesis is confirmed, the quest for the animal responsible for the epidemic caused by the new coronavirus will have been rapid, as for the SARS.

For other illnesses, it can take much longer. “In the case of Ebola, research on the reservoir began in 1976 and the first results were published in 2005”, reminds AFP Eric Leroy, virologist and veterinarian of the IRD. For the AIDS virus, HIV, the investigation lasted twenty years before pointing to the great apes, notes Martine Peeters.

What threats are now hanging over the pangolin?

Nearly 100,000 pangolins are victims each year in Asia and Africa of illegal trafficking which makes it the most poached species in the world, largely in front of elephants or rhinos, according to the NGO WildAid. Their delicate flesh is highly prized by Chinese and Vietnamese gourmets, as are their scales, their bones and their organs in traditional Asian medicine.

In 2016, the International Convention on Trade in Endangered Species (Cites) voted to include pangolins in its appendix 1, which strictly prohibits its trade. Despite this measure, their traffic has only increased, according to NGOs. “It is wild animal-human contacts that are at the origin of these transmissions, so wild animals should be left where they are,” says Professor Fontanet.

At the conclusion of a study published Monday in the medical journal Nature, Chinese researchers recommended “the establishment of a strict legislation against the breeding and the consumption of wild animals”. A transitional measure has already been taken: at the end of January, China banned the trade in all wild animals pending the end of the epidemic.

“Each time, we try to put out a fire and, when it is out, we wait for the next one,” deplores François Renaud, a CNRS researcher. According to him, it would be necessary to “map everything that is potentially liable to transmit infectious agents to humans”, while conceding however that this “inventory of risks” on a global scale would represent a huge work and would require significant funding. .

Bats are the reservoir of the new virus from China

Scientists are struggling to better characterize 2019-nCoV, a new strain of coronavirus that is shaking China. A first hypothesis on its reservoir was put forward a few days ago, here is a second one which favors bats. And which also brings 2019-nCoV closer to the SARS agent.

As the days go by, the 2019-nCoV coronavirus reveals its secrets a little more. In an article published yesterday, we discussed the reservoir of the virus: snakes sold on the Wuhan market, according to the first elements gathered by researchers from the Beijing Medical University. The scientists behind this study suggest that 2019-nCoV is the result of a recombination between two coronaries, one of which is specific to bats.

A new study, pre-published in bioRvix, conducted by researchers from the Chinese Academy of Sciences, seems to confirm the relationship between bats and 2019-nCoV. In addition, it would belong to the same species as SARS-CoV, the agent responsible for an epidemic of pneumonia 18 years ago.

2019-nCoV is close to SARS-CoV

The genomic sequencing work was carried out using viruses isolated from five different patients at an early stage of the disease. By entire comparison of the genome, it appears that 2019-nCoV and a viral strain of bats are 96% identical.

Another new development, 2019-nCoV would also be a close cousin of SARS-CoV, whose reservoir is the bat. These two viruses share 79.5% of their genome, but also the same protein, ACE2, which serves as their gateway into the cells of the respiratory mucosa.

Should we therefore abandon the snake hypothesis? If the natural reservoir of 2019-nCoV seems rather to be bats, the snakes described above could be the intermediate host between bats and humans. In the case of SARS-CoV, humans were infected during close contact with masked palm civets (Paguma larvata), which are also sold and consumed in Chinese markets. Of course, this is only an assumption.

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