We do not know if it is more transmissible, we do not know if it will replace other variants, we do not know if it is more virulent and will cause more serious disease, we do not know if it will be easier to get reinfected, we do not know if it will be more dangerous in young children, we do not know if it will escape the current vaccinesWe do not know if it will spread throughout the planet, but we know that we have to watch it.
The new variant of the SARS-CoV-2, B.1.1.529, called omicron, was detected by PCR between November 11 and 23 in South Africa, in the province of Gauteng (77 cases), Botswana (4 cases), Hong-Kong (A case), Israel (one case) and Belgium (A case).
It seems that it has spread very quickly in the Gauteng region, but it must be taken into account that it is an area with very few cases of covid-19 and with a very low vaccination rate. That has been able to influence.
Is it really more transmissible or is it an effect of the population in which it has been isolated? It is not known how this variant will behave in another population in which the incidence and the vaccination rate are older. But we have to be vigilant.
B.1.1.529 has more than 50 mutations in its genome with respect to the original sequence of Wuhan. Thirty-two of them in the region of protein S.
What worries scientists is the accumulation of mutations in that region, because some of these mutations had already been detected in other variants, but not all together in the same variant. Therefore, this variant has already been classified as a variant of concern. More than the number of mutations, what should be analyzed is the effect that they can all have together. One thing is the mutation in the genome and quite another the effect it may have on the biology of the virus. The effect does not have to be cumulative, there may be compensation phenomena: the effect of one mutation can be offset by that of another.
But this variant accumulates mutations that have been related to a possible immune escape and a possible increase in transmissibility.
Nine mutations appear in other alpha, beta, delta, gamma variants. Eleven are new. Fifteen mutations are in the receptor binding site (RBD) and some (N440K, S477N, Q498R) affect binding to the ACE2 receptor and could influence its ability to infect cells. Others can affect the transmissibility (H655Y, N679K, P681H), and there are those that can cause changes in the protein and affect its reactivity with antibodies:
Antigenic effects of the mutations of the new variant. On the other hand, a phylogenetic analysis of the genomes of this variant suggests that it has probably been circulating for months but has not been detected until now:
Is there a reason for a alarm and hysteria generalized? Currently not. It is more what we do not know than what we know. But you have to remain vigilant.
Do we cancel all flights with South Africa? It doesn’t make a lot of sense for a number of reasons. South Africa is probably the only African country doing “homework” and genomic tracking for the virus. That is why it detects it. If we are not actively looking for new variants, we will not detect them, but it does not mean that they do not arise. Punishing the one who is doing it well is a mistake. We cannot rule out, surely it is most likely, that new variants will emerge in other areas where they are not being sought. So do we cancel all flights to Africa? This variant has already been detected in Hong Kong and Belgium, and most likely, as has been suggested, has been around for a long time in other places on the planet.
We need time to learn more about this variant. But what this shows once again is that we are in a global pandemic and what happens in other countries affects us. The more infected there are in the world, the more viruses there will be, the more variants can emerge. Vaccination must be global. And in Africa just over 7% of the population is vaccinated. That is what should alarm us.
* Author: Professor of Microbiology, University of Navarra
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