Who is Omicron variant patient zero?
Detected for the first time in South Africa, this B.1.1.529 variant, by its scientific name, immediately aroused concern in the international community.
And for good reason: with its thirty mutations compared to the original strain of Covid-19 - a record - it poses two threats: that of being particularly contagious and, above all, that of being resistant to vaccines.
While states are stepping up restrictive measures to try to limit its spread, scientists are trying to trace the trail back to its origin to understand how this "super mutant" variant could have appeared.
Among the hypotheses put forward, the researchers are looking for mutations that have appeared in an immunocompromised patient.
For several months, they have been studying a possible link between people whose immune system is weakened - waiting for a transplant, cancer patients, or even suffering from unsupported HIV - and the emergence of most disturbing variants.
"When a patient is immunocompromised, the virus will stay in his body for a very long time, sometimes several months, against only a few days for an average person," Morgane Bomsel, virologist at the CNRS and at the Institut Cochin, in Paris explains to France 24. .
"His immune system is too weak and he cannot get rid of the virus."
Selection pressure
According to a study published in the journal Nature Communications on November 4, a 58-year-old man with kidney disease and on treatment with immunosuppressive drugs thus remained positive for Covid-19 for more than six months. In December 2020, American doctors noted, in the same way, the case of a patient on immunosuppressants, who died after being infected with Covid-19 for 154 days. "However, throughout this period, the virus can accumulate a whole series of mutations and create a variant", continues the virologist.
As a reminder, the Sars-CoV-2 virus, like all viruses, has a genetic heritage that replicates.
But sometimes errors appear in this process.
This is called a mutation.
In the majority of cases, this has no effect, but some can modify the contagiousness or the dangerousness of the virus.
The variant is thus this new version of the virus which takes these different modifications into account.
"In immunocompromised patients, the immune system will not succeed in defeating the virus, but it will all the same fight against it. This will cause what is called selection pressure", continues Vincent Maréchal, professor of virology at the Sorbonne University, contacted by France 24.
In short, in this fight between the immune system and the virus, the latter will be forced to evolve and will only keep its mutations which allow it to continue to reproduce and to resist.
Result: only the most dangerous mutations will remain, capable of escaping the neutralizing power of antibodies.
And it is this virus, with these mutations, which will be transmitted if the patient infects another person.
"With this impressive number of mutations, it is therefore highly probable that an immunocompromised patient is the source of the Omicron variant", considers Vincent Maréchal.
"But this is not the first for which this hypothesis is raised. It is also the case for the British and Beta variants", specifies Morgane Bomsel.
South Africa, fertile ground
However, South Africa could be a fertile ground for this type of process. In question, the AIDS epidemic. In total, seven million people live with this disease in the country, or 12% of the population and 19% of 15-45 year olds. But above all, the rate of people treated remains very low, reaching 57% in 2017. "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. "This is clearly a situation where variants can appear."
This is not the first time that the country has been the first to detect a new variant.
Before Omicron, two had taken the name, since modified, of "South African variants": the Beta and the C.1.2.
"But this is explained, in the first place, by the fact that the country carries out a lot of sequencing, which allows it to identify the variants on its territory", nuance Vincent Maréchal.
"That doesn't necessarily mean patient zero is in South Africa."
If the geographical origin of Omicron remains unclear for the moment - several states, particularly in Europe, identifying cases on their territory prior to the announcement of its discovery - an article published in Science on September 9 suggests that the Beta variant is itself , well and truly appeared in South Africa.
According to this study, the Beta variant, isolated for the first time in October 2020, would have appeared in people sick with AIDS in Nelson-Mandela Bay.
And the process would have been facilitated by the lack of resources allocated to treatment in this metropolis.
This is indeed one of the regions of the world where the concentration of people both infected with HIV and deprived of appropriate treatment is the highest.
By comparing, through computer analyzes, all Beta line variants collected from around the world, the study authors found that 90% of the ancestors of these variants were from South Africa.
The first of the line had therefore probably appeared in this bay.
The virus then spread rapidly to other provinces in South Africa, then reaching neighboring countries.
In March 2021, it became the dominant virus in southern Africa as well as Mayotte and Reunion.
"Variants can appear anywhere"
However, we should not point the finger at South Africa, insists the virologist.
"This highlights above all what happens when two pandemics meet and the need not to forget the fight against AIDS for the benefit of Covid-19."
"But we have seen, these last two years, that the variants can appear everywhere. From Brittany to India, passing by the United Kingdom", he insists.
"There are certainly many factors to consider. There is still a lot about variants that we don't understand."
While research continues to try to elucidate the mechanisms of emergence of these variants, the virologist is launching a final hypothesis.
"Perhaps variants emerge more easily in certain places depending on socio-cultural and health contexts," he raises.
"We must then identify these areas and put in place a surveillance in order to see things coming."
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