November 30, 2021 11:28 AM
A new variant of sars-cov-2, initially called B.1.1.529 and now renamed omicron, has an unusually high number of mutations and appears to have sparked a recent increase in cases in South Africa.
When was the omicron variant first identified?
It was first identified on November 23 in South Africa, based on samples taken between November 14 and 16. Joe Phaahla, the South African health minister, said on November 25 that he believes the variant is at the origin of the exponential increase in new daily cases of covid-19 recorded across the country in recent days. On the same day the UK Health Security Agency (HSA) cataloged it as a variant under observation, triggering travel restrictions for people headed to the UK from South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia. . The World Health Organization (WHO) had cataloged variant B.1.1.529 as “under observation”, but its technical advisory group on the evolution of the sars-cov-2 virus decided on November 26 to classify it as a disturbing variant .
WHO has labeled it with the Greek letter omicron.
What is happening in South Africa?
The national daily cases went from 274 on 11 November to one thousand fifteen days later. While the rate of growth has been fast, the absolute numbers are still relatively low compared to the UK, where fifty thousand new cases were recorded on 26 November. More than 80 percent of cases in South Africa today are concentrated in the province of Gauteng. All 77 cases sequenced in the province between 12 and 20 November were identified as being caused by this variant. The estimated reproduction rate – the average number of people an individual can infect – is nearly 2 in Gauteng, compared to about 1.5 at the national level.
What do the mutations of variant B.1.1.529 tell us?
The variant has a “very unusual set of mutations,” says Sharon Peacock of the University of Cambridge. There are more than thirty mutations in the spike protein, the part of the virus that interacts with human cells. Other mutations can help the virus bypass our immune system, make it more transmissible and less responsive to treatment, according to the HSA. But the latter also points out that “this has not been proven”.
The real implications of the mutations are for now purely theoretical and are based on the experience of past mutations of sars-cov-2 rather than on laboratory tests. According to Wendy Barclay of Imperial College London, “we really don’t know” whether it will reduce the effectiveness of vaccines. However, he adds that, in theory, the number of mutations on the variant’s spike protein could compromise the efficacy of the antibodies produced by the covid-19 vaccines.
Mutations on part of the virus are similar to those seen in the alpha and delta variants, which could help the variant spread more easily. According to Barclay “it is very plausible from a biological point of view” that the variant B.1.1.529 has a higher transmissibility than the delta.
The mutations also make the new variant more likely to be more resistant to antibody treatments such as those developed by Regeneron, which have been shown to save lives. “This is really a cause for concern,” says Barclay. A small positive clue is the fact that, to date, there are no signs that the variant is causing a more serious disease.
Genomic sequencing has detected this variant in South Africa, Botswana and Hong Kong. Cases have also been reported in Israel, apparently in a traveler from Malawi, and in Belgium, in a person who had been to Egypt. British health secretary Sajid Javid called the possibility that the variant has spread to other countries “highly likely”. Since November 27, two cases have been detected in the UK, where around one fifth of positive cases undergo genomic sequencing. Even in countries with low sequencing levels there may be early warning signs, because the variant is linked to a mutation called s-gene dropout, detected by molecular testing, says Jeffrey Barrett of the Wellcome Sanger Institute in Hinxton in the United Kingdom.
How did the other countries respond?
The UK and the EU have imposed restrictions on people from southern African countries. Javid said the variant is a cause of “enormous international concern”. Prime Minister Boris Johnson on November 27 announced additional travel restrictions.
Is it obvious that this variant prevails over the delta variant?
We do not know. “We have no definitive evidence at the moment that this is more transmissible, but there are hints that it may be,” says Peacock, noting growth in South Africa and the highest base breeding number in the Gauteng region. Some earlier variants failed to catch on in some countries, due to competition from other variants: beta did not spread to the UK, for example, while alpha spread from Europe but never caught up. high levels in South Africa. “If this variant doesn’t turn out to be as transmissible as the delta, it would definitely be good news,” says Barrett.
All the usual social distancing measures, such as hand washing, wearing a face mask, getting vaccinated and having a booster shot of the vaccine still apply. The emergence of a potentially worrying variant is, however, a reminder of how risky it is to have uneven vaccination rates globally: only 24 percent of South Africa’s inhabitants are in fact fully vaccinated.
How much do we really know about this variant?
Most of our knowledge comes from the South African Genomic Surveillance Network and the South African government, both of which have been praised by researchers for taking swift action in sharing variant information. But the things we don’t know are more than what we know. Tulio de Oliveira of the University of Stellenbosch, South Africa, said yesterday that the full understanding of the mutations of the variant “remains uncertain”. And, as Peacock argues, “it’s important to underline how little we know about this new variant.”
(Translation by Federico Ferrone)
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