The new omicron variant has an “extremely” high number of mutations in the coronavirus. They found 32 mutations only in the S protein or in the spike. In comparison, the delta variant, which is considered highly infectious, has eight mutations.
Fernando Gonzalez Candelas, Valencia University
The identification of a new variant of SARS-CoV-2 in South Africa, characterized by a large number of mutations (55 in the entire genome, 32 in the S protein or spike) and the dizzying increase in its relative incidence in this population triggered more once alerts on a global scale. Several countries have closed air traffic with South Africa and there are experts who indicate that it is “the most worrying variant we’ve seen so far”. O who it elevated it to the category of “concerning variant” and designated it with the Greek letter “micron”.
But with the available data, can we accept the relevance of these claims? Are they based on demonstrations or are they conjecture? When can we define a new variant as worrisome and what consequences does this have for our strategy in the face of the pandemic? I will try in the following paragraphs to shed some light on these questions.
The genomic sequence of the omicron variant (Lineage B.1.1.529 in the PANGO system, or 21K Lineage by NextStrain) shows 55 mutations in relation to the original Wuhan virus, 32 of them located in the S protein or spike, the most important for its role in cell infection and immune response.
Many of these mutations have previously been detected in variants of concern (VOCs) or of interest (VOIs) of the virus, such as the N501Y mutations (present in alpha, beta, and gamma VOCs), the T95I, T478K, and G142D (all in delta), or their role in the interaction with the ACE2 cell receptor (S477N, Q498R), or are found in binding regions of some antibodies (G339D, S371L, S373P, S375F).
This accumulation of mutations with known effects is already a matter of interest and concern, but adequate experiments still need to be carried out to demonstrate their effects when found simultaneously.
The effects of two mutations are not always additive and the interactions (epistasias in technical language) can be positive (increasing the effect of each) and negative (decreasing).
As long as we do not have laboratory results and epidemiological and genomic surveillance data that show us greater transmissibility or greater possibilities of escape from the immune response, it is not reasonable to move from surveillance to alert or, even less, to alarm.
The reason given by WHO for declaring it a VOC is that it may be associated with an increased risk of infection, although there is still no public information to support this claim.
South African genomic surveillance
However, warning signs were triggered by the rapid increase in cases detected in South Africa with this variant. It is not strange that a new variant is detected in this country, one of those with the best SARS-CoV-2 genomic surveillance system and in which, as in almost all countries on the African continent, vaccination has not progressed in the same way.
Thanks to his surveillance, the sequence of the virus responsible for the Covid-19 outbreak observed in Gauteng province was quickly obtained, at a time with a very low cumulative incidence of infection (about 10 cases per 100,000 inhabitants). Under these circumstances, any variant associated with an outbreak quickly reaches a high relative frequency, which may indicate greater transmissibility, but also that it grows where it hardly existed.
If the main cause of the alarm is transmissibility, other properties associated with spike mutations do not leave much room for guarantees, as indicated above. Once again, we ask ourselves how a virus with so many mutations arises. The answer is not definitive, but the main suspicion is that it evolved in a patient with a weakened immune system infected for a long period of time, after which it was transmitted to other people in a chain that we are not aware of until now. .
@tuliodna / Center for Epidemic Response & innovation, South Africa
What can we do about a disturbing new variant?
At the moment, we have the same tools as the others: vaccinate, use masks, maintain distances, ventilate closed rooms, that is, reduce as much as possible the exposure and circulation of the virus, increase the immunized population in every country on the planet, limiting the opportunities for new mutations to appear in the virus.
Although we thought that after the delta variant it would be difficult for worrisome variants to appear, the omicron variant surprised us again. Regardless of whether or not it has the serious consequences that justify its declaration as a VOC, it is clear that the evolution of SARS-CoV-2 could continue to bring surprises. The sooner we reduce these possibilities, the better for everyone.
Fernando Gonzalez Candelas, Professor of Genetics. Head of the Joint Research Unit “Infection and Public Health” FISABIO-Universitat de València I2SysBio. CIBER Epidemiology and Public Health, Valencia University
This article was originally published in The conversation. read the original.