It is a seemingly endless race between man and the virus. Appeared in the fall of 2019, Sars-CoV-2 continues to challenge scientists by mutating regularly. For more than a year, several variants have come to undermine the strategies of different countries to contain the epidemic, like the Delta variant which has become the majority. The youngest, the variant B.1.1.529, called Omicron by the Health Organization (WHO), once again worries the world health authorities, in particular because of its 32 mutations which are located in the spike protein, the key allowing the virus to enter the body.
More than a week after the announcement by South Africa of its discovery on November 24, this new variant has been identified in 38 countries and is blowing a wind of panic on the planet, pushing many countries to toughen their measures. health but also to close their borders. Is it more contagious? Is it resistant to the vaccine? Can it make the epidemic worse? Many questions remain unanswered, and among them, that of knowing where the variant appeared for the first time.
More and more cases on the planet
Because if South Africa is the first country to have alerted the WHO to the existence of this variant with a record number of mutations, other cases have since been detected elsewhere, the contaminations of which predate the first alert. This is particularly the case in the Netherlands, which announced that two positive samples, dated November 19 and 23, were positive for the Omicron variant, but also in Sweden, the first case of which dates from November 19, from Israel (20 November) or the United Kingdom (November 23). Four first contaminations were also tested positive from November 14 in Botswana, without the country of origin having been identified. Each country tracks its Omicron zero patient in order to retrace its journey.
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“When sequencing the virus, we always see many mutations, but it is not always clear whether they make a virus a new variant”, explains the virologist Emma Hodcroft quoted by Switzerland info. In the case of Omikron, a virologist from London was the first to draw attention to the fact that B.1.1.529 had an unusually high number of mutations in the spike protein. It was only then that the search teams began to dig the trail and the South African team found a large number of mutations.
“This explains why country after country is announcing that they have cases of Omicron, some of which predate those in South Africa,” explains the virologist. These cases only show “that the mutation has already been around the world before being discovered”.
Circulation prior to its sequencing
“When South Africans sounded the alarm last week, it was because they had noticed a warning signal and this means that this virus emerged a priori a few weeks earlier”, abounds Etienne Simon-Lorière , head of the RNA virus evolutionary genomics unit at the Institut Pasteur, in The Parisian. “It is possible that the international spread (of the Omicron variant) started around the end of October”, said for his part to Guardian Prof. Olivier Pybus, expert in genomics.
A position shared by Dr Richard Lessells, an infectious disease physician at the University of KwaZulu-Natal in Durban, South Africa. He believes, still in the British daily, that the emergence in October was “plausible” given that it was the end of the Delta wave in South Africa. “This is consistent with how and when we saw other variants of concern emerge: for example, the Beta variant appeared last year towards the end of our first wave,” he explained.
The difficulty of tracing back to the first case is such that one might in the end never know its origin. “It is unlikely that we will ever know precisely where and when Omicron appeared,” warns the head of the BBC’s health service, in an analysis. “Not all countries have the capacity to perform genome sequencing,” she explains. In fact, to spot the Omicron, specific tools are needed, which is not within the reach of all countries, which are uneven in the face of the development of scientific research.
The hypothesis of an immunocompromised patient
However, the most probable hypothesis put forward by the researchers is that of the appearance of the virus in an immunocompromised person. This was certainly already the case for the variant detected in the United Kingdom, the variant B.1.1.7, called “Alpha”. “He probably had time to replicate in the body of this patient with weak immune capacities”, explained to L’Express Professor Vincent Calvez, head of the virology department at the Pitié Salpêtrière hospital in Paris, last January.
A scenario that could be repeated with the Omicron. “Some patients infected with Covid-19, especially those with weakened immune systems, develop relatively long forms of the disease. This means that they keep the virus in their body for several weeks, or even months. virus evolves when it is transmitted, it also evolves within the organisms it infects“, explained to L’Express Samuel Alizon, one of the main French experts in phylodynamics, CNRS research director in the Theoretical and Experimental Evolution team of the MIVEGEC laboratory in Montpellier.
If the variant started well in South Africa, the hypothesis of the immunocompromised patient fits with the health context of the country, affected by an HIV epidemic, which precisely weakens the immune system. “We therefore have a high proportion of immunocompromised people, in a country with low vaccination coverage where the virus circulates a lot, analyzes Vincent Maréchal interviewed by France 24. This is clearly a situation where variants can appear. ”
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This theory nevertheless remains a hypothesis. And the world has not finished seeing variants appear. “It is probable that they multiply ad infinitum, in a more or less dangerous way, one cannot predict it. Besides, it is very difficult to know exactly where they really come from. The variants travel with them. people “, explained Vincent Calvez at the start of the year.
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