It’s too early to be afraid of Omicron, the South African variant

It’s too early to be afraid of Omicron, the South African variant
It’s too early to be afraid of Omicron, the South African variant

A new variant has been identified by researchers in South Africa: it had already been isolated in Asia, Israel and Europe. But too little is known about its epidemiological characteristics. The good news is that global surveillance on Covid holds up

At the time, on these pages I wrote verbatim: “The emergence of more contagious variants, even in the absence of human actions that can exercise selection, is inevitable; more or less quickly, the emergence of more evasive variants of the immunity generated by previous viruses or vaccines is also inevitable “. For this reason, I do not think that the observation of a new variant, identified for the first time by South African researchers, is neither unexpected nor surprising who immediately shared their sequencing data on the Gisaid worldwide database, which raises serious concerns.

Let’s start by saying that the new variant, called B.1.1.529, is not only present in Africa: it has already been isolated in Hong Kong, in Israel and also in Europe, in Belgium. Certainly, right now it seems to be more widespread in South Africa, also considering the relatively low number of sequences done in that country; but it is likely that B.1.1.529 will soon be discovered in many other places around the world. The main cause for concern that this variant arouses is constituted by thevery high number of mutations found, which, often separately, have already been identified as probably advantageous for the virus (and therefore are not produced by a random gene drift). First of all, in the Spike protein: here are 9 mutations already identified in other dangerous variants such as Alpha, Beta, Gamma and Delta, but never all together. There are also three other mutations never found before in the “variants of concern” (Voc), of which two probably confer modest advantages over the original strain, but one – E484A – is precisely at a crucial point for binding to the human receptor. ACE2. Then there are 11 other mutations, never seen or seen very sporadically, of which we know nothing: they could also be disadvantageous for the virus, but it is urgent to characterize their function. Then there are 4 mutations that cause a sequence change of the important protein, because this occurs precisely in the site bound by a monoclonal antibody (Sotrovimab): these are probably immunoevasive mutations.

Again, there are two mutations – S477N and Q498R – never seen together before, known to confer greater affinity with the human ACE2 receptor; and finally, there is an area at one end of the Spike protein where you see many insertions, deletions and mutations, which probably change its structure – in a way we don’t know how its function varies. Besides the Spike protein, there are a multitude of other mutations in other proteins of the virus, including some in the nucleocapsid protein, known to increase the infectivity of the virus; also in this case, finding them all together is the greatest element of novelty.

The profile of these mutations, so, seems to be very threatening; However, we do not yet know what the epidemiological characteristics of this new variant are, nor its ability to induce more or less serious disease, nor whether and to what extent it is able to bypass the vaccine barrier. Fortunately, South African researchers have first-rate research facilities, both in terms of sequencing capacity, and above all in terms of their ability to cultivate the virus in the laboratory and test its resistance to vaccines; they are literally working day and night – we can see this from the flow of messages in Gisaid’s science forums, for example – to get answers, useful to the whole world.

At this moment, we do not know how much and if this variant is really dangerous; but, thanks to the worldwide surveillance network of Covid-19, we have been warned in time and we must take advantage of this window of time to prepare by sequencing, increasing the control of outbreaks, taking some extra precautions regarding the use of masks and unnecessary gatherings and finally strictly monitoring the vaccination status and swabs at airports, as well as blocking certain flights. Perhaps this will be a false alarm; but, fortunately, we will know soon.

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