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 be reinfected, we do not know if it will be more dangerous in young children, we do not know if it will escape current vaccines, we do not know if it will spread throughout the planet, but we know that we have to watch her.
The new variant of SARS-CoV-2, B.1.1.529, called Ómicron, has been detected by PCR between November 11 and 23 in South Africa, in Gauteng province (77 cases), Botswana (4 cases), Hong-Kong (one case), Israel (one case) and Belgium (one 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 vaccination rate are higher. But we have to be vigilant.
B.1.1.529 has more than 50 mutations in your genome compared to the original Wuhan sequence. 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. Mutation in the genome is one thing and the effect it may have on the biology of the virus is quite another. The effect does not have to be cumulative, compensation phenomena may occur: the effect of one mutation can be offset by that of another.
But this variant accumulates mutations that have been linked to a possible immune escape and a possible increase in transmissibility.
Took a look at the spike mutations in B.1.1.529 this evening, and colour coded them (details below)…there is…not much green.???? pic.twitter.com/yNHM55oTTH
— Jeffrey Barrett (@jcbarret) November 25, 2021
Nine mutations (in red) appear in other alpha, beta, delta, gamma variants. Eleven (in blue) 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:
First, Nu variant has lot of antigenic change. Below are how mutations relate to escape averaged over 36 human antibodies. Many mutations at peak escape sites, especially E484, G446, K417, & Q493. This means even in polyclonal mix, lot of RBD antibodies will be affected. (2/n) pic.twitter.com/YjSifYojIL
— Bloom Lab (@jbloom_lab) November 25, 2021
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:
This extremely long branch (>1 year) indicates an extended period of circulation in a geography with poor genomic surveillance (certainly not South Africa) or continual evolution in a chronically infected individual before spilling back into the population. 4/16 pic.twitter.com/8mEI46VFMn
— Trevor Bedford (@trvrb) November 26, 2021
Is there cause for widespread alarm and hysteria? 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 to 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 do not actively search for new variants, we will not detect them, but it does not mean that they do not appear. Punishing the one who is doing 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.
Ignacio López Goñi. Professor of Microbiology, University of Navarra.
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