By our editor Sander Voormolen
Amsterdam. South African researchers have discovered a new variant of the coronavirus with a worrying amount of mutations. There are fears that this new variant, coded B.1.1.529, is even more contagious than the delta variant that is now predominant almost everywhere in the world. Britain and Israel closed all air traffic with southern Africa on Thursday as a precaution. The Dutch government also issued a flight ban on Friday and the European Union is considering the same.
B.1.1.529 has more than thirty mutations in the gene that contains the information for the virus’s spike protein. The spike protein is the protuberance on the outside of the virus that is essential for entering human cells. Changes in this protein can drastically change properties such as infectivity and escape from previously built up defenses.
Never before has there been a variant with so many mutations in this protein as this new variant. Previous variants such as alpha and delta have only a little more than ten. “Unprecedented”, that a variant has so many mutations, says virologist Chantal Reusken of the RIVM. “We see many mutations that we have seen before in the alpha, beta, gamma and lambda variants. Plus a few new ones.”
Binding site for antibodies
The B.1.1.529 variant contains changes at sites that are important for the binding of antibodies. This may mean that the virus can break through previously built up resistance to an infection or vaccination. In any case, some therapeutic monoclonal antibodies will also be less effective against this variant, because the sites where they bind have been changed.
There are also changes where the spike protein cleaves before entering the cell. Reusken: “Probably this affects the efficiency with which the virus can enter a cell, and thus increases the infectivity.”
A piece of hereditary code (a deletion) is also missing, which would allow the virus to better evade the innate defense system (the interferon response).
And then there are also mutations in the genetic code for the virus’s coat protein, which have also been shown to possibly contribute to increased infectivity.
The profile of all those mutations in B.1.1.529 therefore looks bad, but it remains to be seen how they turn out in reality in conjunction. Laboratory tests can provide a definitive answer, but the results are still a long way off.
“The first signs of how quickly this new variant seems to be emerging are very disturbing,” says Reusken. “In the province where this variant is most common, the reproduction number has risen in a short time from 1.5 to 1.9. If this is correct and the virus starts circulating more widely, it would mean that a major step needs to be taken to keep the corona infections under control.”
Just like the alpha variant, the new variant lacks a specific piece of RNA, which means that it fails detection with a specific PCR test, a so-called spike gene dropout. This means that this variant can be tracked approximately because detection with a combination of PCR tests is sufficient and the entire virus does not have to be sequenced first. In this way, the researchers were able to quickly find out that the variant is also increasingly occurring in other provinces in South Africa.
Independent of delta
It is striking that the new variant did not arise from the delta variant which now dominates almost everywhere in the world, as well as in South Africa. “Genetically, this new variant is more similar to virus strains we saw in 2020,” says Reusken. “So this variant arose independently of delta.”
How exactly the virus originated is, according to Reusken, “looking at coffee grounds”, but it is likely that it started in a patient who was chronically infected with SARS-CoV-2, which gave the virus the chance to accumulate mutations. Another scenario is that the virus jumped to an animal and then back to humans, taking the genetic adaptations to the new host with it.
There is also uncertainty about where the variant originated. B.1.1.529 has a wider distribution in South Africa and was also seen in Botswana, but it may well have come from elsewhere in Africa. “Usually, these types of variants are noticed first where they are most searched for. But since this variant is no longer very local in southern Africa, I think it has been present unnoticed for a while.”
According to Reusken, a no-fly zone can help delay the introduction of a new virus variant and hopefully prevent it from settling here. “But with the delta variant that became dominant all over the world in a relatively short time, it turned out that it is very difficult in practice to contain a more contagious variant. You can stop air traffic immediately, but there is a chance that it will still find its way through detours via third countries.”
Although the intervention is not watertight, the necessity is there. Reusken: „It is clear that we cannot have this in the Netherlands at the moment. Hopefully we can delay it until more favorable seasons arrive.”
On Friday, experts from the World Health Organization will meet to discuss whether B.1.1.529 will replace the predicate variant of interest gets or that from variant of concern. In the latter case, the new variant will also be assigned a Greek letter to facilitate communication about it.
Vaccination coverage in South Africa is still low, with only 35 percent of the adult population fully vaccinated. The number of corona infections has been low in recent months, but the arrival of B.1.1.529 seems to herald the fourth wave in the country.
Previously, experts warned that in areas of the world with low vaccination coverage there is a greater risk for the evolution of new virus variants, which in turn can threaten the rest of the world. That predicted scenario now appears to have come true.