Analysis of the genomes of Covid-19 would have revealed a dual origin of the virus. It is not yet known whether this recombination took place in a pangolin or a bat, or under what conditions it took place.
- Scientists have analyzed the SARS-CoV-2 genome to find its origin
- The bat would be a reservoir of this virus
Pangolin, bat, snake… While all scientists agree that Covid-19 was transmitted to us by an animal, the very nature of the latter remains uncertain. The situation would be all the more complex as the analysis of the genomes would have revealed a dual origin of the virus, explained the academic Alexandre Hassanin (lecturer at the Sorbonne and researcher at the Natural History Museum), on March 17 in The Conversation.
According to the WHO, China would have started reporting cases of coronavirus to it on December 31, 2019. However, the onset of symptoms for patients would have started on December 8. If the majority of the first infected had in common to frequent the wholesale fish market of Huanan, located in the city of Wuhan, 850 km west of Shanghai, it was finally shown that the very first human case of Covid-19 had never been to this establishment. What’s more, the molecular dating estimated from genomic sequences of SARS-CoV-2 rather point to an origin in November.
The virus genome was quickly sequenced by Chinese researchers. It is an RNA molecule of about 30,000 bases containing 15 genes. Based on comparative genomic analyses, this virus belongs to the group of Betacoronavirus and looks a lot like SARS-CoV which caused acute pneumonia in November 2002 in the Chinese province of Guangdong. It then spread to 29 countries, including France. In all, 8,098 people had been infected and 774 had died. At the time, the WHO had issued a global alert strongly encouraging the isolation and quarantine of those affected to stop the epidemic.
What is a reservoir?
A posteriori, scientists understood that bats of the genus Rhinolophus were the source of the virus and that the palm civet, a small carnivore widely sold in markets and consumed by many Chinese, had probably served as an intermediate host between bats and the first human cases.
Since then, many Betacoronavirus have been discovered, in bats but also in humans. Recently, the RaTG13 virus, isolated from a bat of the species Rhinolophus affinis which comes from China’s Yunana province, has been described as 96% similar to SARS-CoV2. Thus, bats would be a reservoir of the SARS-CoV and SARS-CoV-2 viruses.
For the author of this paper, a reservoir is defined by “one or more animal species, little or not sensitive to the virus, which will naturally harbor one or more viruses. The absence of symptoms of the disease is explained by the effectiveness of their immune system which allows them to fight against excessive viral proliferation..
A recombination between two different viruses
However, in early February, scientists revealed that a virus even closer (99%) to SARS-CoV-2 had been identified in pangolin. However, according to an even more recent study, currently being assessed, the situation is more complex than that. According to this new research, the genome of the coronavirus isolated from the Malayan pangolin would in fact only be 90% similar to SARS-Cov-2. It would therefore not be responsible for the current epidemic.
In detail, the virus isolated from the pangolin represents 99% identity with SARS-CoV-2 “if we compare the 74 amino acids of a particular region of protein S, the ACE2 receptor binding domain (Angiotensin Converting Enzyme 2) which allows the virus to enter human cells to infect them”explains Alexandre Hassanin.
Thus, the coronavirus isolated in the pangolin can enter human cells, unlike that isolated in the bat. The SARS-CoV-2 virus is therefore the result of a recombination between two different viruses: one close to that of the bat and the other of the pangolin. For recombination to occur, the two divergent viruses must have infected the same organism concurrently. It was already through this recombination mechanism that SARS-Cov appeared. The author of the paper concludes: “Two questions remain unanswered: in which organism did this recombination take place? (a bat, a pangolin or another species?) And above all, under what conditions did this recombination take place?”
If Alexandre Hassanin refers to the disease as SARS-CoV-2, the WHO refuses to use this name so as not to link Covid-19 and SARS. She therefore prefers to mention “the virus responsible for the disease ‘Covid-19‘”. Currently, more than 318,000 cases have been reported worldwide (13,600 deaths worldwide). In France, more than 16,000 cases are confirmed. The disease has killed 674 people, including a doctor.
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