Why are SARS-CoV-2 variants emerging now?

While the emergence of viral variants is a perfectly normal process during an epidemic, we do not know exactly why these variants appeared concomitantly in different parts of the world. Let’s take stock of the assumptions currently being formulated.

The emergence of variants, a natural mechanism

Like all viruses, the SARS-CoV-2 coronavirus constantly mutates: by multiplying, it copies its genetic material and, in doing so, sometimes makes errors, or mutations. Its genome is therefore constantly modified, which can have three kinds of consequences.

Some of these mutations, which occur spontaneously, are deleterious. The viruses that carry them suffer a prejudice compared to others (they are transmitted less well, for example). They are then “against-selected”: the viruses which do not carry them, are transmitted better and therefore invade the population.

Other mutations do not have “observable” consequences: they do not modify the capacities of the virus, which continues to be transmitted in the same way, to infect the same age groups, to cause symptoms of similar severity to. those generated by unmutated viruses, etc. These “neutral” mutations are transmitted randomly, since they offer no particular advantage to the virus that carries them.

Finally, conversely, spontaneous mutations can sometimes prove to be “beneficial” for the virus, for example by allowing it to be transmitted more easily. This new virus – which we can call a “variant” – will infect more people more quickly and will therefore become the dominant virus in the population. These beneficial mutations are then said to be “selected”.

In fact, these variants are practically new viruses since they behave differently from that of the virus from which they originate. They can thus be transmitted in different ways, in terms of contagiousness or age of infected people, or even, in the worst case, cause a more serious illness.

Currently, the variant that evolved in England appears to be more transmissible than viruses that circulated before its emergence. As for the variants initially detected in South Africa or Brazil, they could be capable of re-infect people who have already contracted an infection with SARS-CoV-2 viruses that circulated before their emergence. In other words, a large proportion of individuals who have already contracted the virus may not be fully protected against these variants.

Why are variants now appearing?

First hypothesis, the detection capacities of these new variants have greatly increased in recent months, thus making their identification easier. The first variant identified was in Great Britain, where virus sequencing capacities are beyond comparison with the rest of the world.

Second hypothesis, the increase in selection pressures on the virus. The Brazilian variant first appeared in the city of Manaus, where a study suggested that mass immunity could have been achieved, which implies that more than 66% of the population would have been infected.

However, spontaneous mutations become beneficial in a particular environment. In other words, if certain mutations change the phenotype of the virus carrying them sufficiently (that is to say its “observable” characteristics: its appearance or its capacities) so that it is not recognized by the antibodies produced during the first epidemic wave, said virus will be transmitted much more efficiently than the historical variant, and will thus become dominant.

Finally, a third hypothesis, that of the implication of what is called “CoVID-longs”. Some patients infected with Covid-19, especially those with compromised immune systems, develop relatively long forms of the disease. This means that they keep the virus for several weeks or even months in their body.

But if the virus evolves when it is transmitted, it also evolves within the organisms it infects. Since long-CoVIDs may have appeared around the world at around the same time, this intra-individual evolution could explain the apparently simultaneous emergence of the different variants.

It is important to note that the three hypotheses are not necessarily independent, each of the mechanisms having contributed to a greater or lesser extent to the emergence of each of the variants.

What implications for the current pandemic? And for the future?

These variants could be expected to emerge, since this is a normal process. Others could appear in the coming weeks or in the coming months. These emergences must be closely monitored, as they can radically change the epidemiology of SARS-CoV-2. It also seems that the main new variants are transmitted much more efficiently than the historical variant.

While the basic reproduction number (the famous R0, which corresponds to the number of people that an infected individual infects in the absence of transmission control measures) of SARS-CoV-2 was around 3 at the start of the epidemic, those of the British and South African variants would rather be between 4 and 5.

If these estimates hold true – they should be viewed with great caution for now, as data is being acquired – the speed of the virus’s spread would be greatly changed. After 10 chains of transmission without social distancing, the South African variant could thus infect up to 10 million people, where the historical variant would infect “only” 60,000!

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