A new variant of SARS-CoV-2 with an unusually high number of mutations has been detected in South Africa and appears to have triggered a recent surge in cases there.
When was B.1.1.529 first identified?
It was first detected on 23 November in South Africa using samples taken between 14 and 16 November. Joe Phaahla, South Africa’s health minister, said yesterday that he believes the variant is behind an exponential daily rise in covid-19 cases across the country in recent days. Yesterday, the UK Health Security Agency (HSA) designated it a variant under investigation, triggering travel restrictions for people travelling to the UK from South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia. The World Health Organization lists B.1.1.529 as a variant under monitoring, but is expected to elevate it to a variant of interest after a meeting of its Technical Advisory Group on SARS-CoV-2 Virus Evolution. It will then probably officially get the Greek letter “Nu” as its name.
What is happening in South Africa?
National daily cases have gone from 274 on 11 November to 1000 a fortnight later. While the rate of growth has been fast, absolute numbers are still relatively low compared to the UK, which saw 50,000 cases on 26 November. More than 80 per cent of South Africa’s cases are currently in the country’s Gauteng province. All of the 77 cases sequenced in the province between 12 and 20 November were identified as the variant. The estimated reproduction number, the average number of people one person will likely infect, is almost 2 in Gauteng compared to nearly 1.5 nationally.
What do B.1.1.529’s mutations tell us?
The variant has a “very unusual constellation of mutations,” says Sharon Peacock at the University of Cambridge. There are more than 30 mutations in the spike protein, the part of the virus that interacts with human cells. Other mutations may help the virus bypass our immune systems, make it more transmissible and less susceptible to treatments, according to the HSA. But the body notes “this has not been proven”.
What the mutations mean is currently theoretical and based on experience of past mutations of SARS-CoV-2 rather than lab tests. Wendy Barclay at Imperial College London says “we don’t really know” if it will reduce the effectiveness of vaccines. Nonetheless, she says that in theory the number of changes across the antigenic sites on the variant’s spike means the effectiveness of antibodies produced by covid-19 vaccines would be compromised.
Mutations on a part of the virus known as the furin cleavage site are similar to those seen in the Alpha and Delta variants, which could help the variant spread more easily. Barclay says “it’s very biologically plausible” that B.1.1.529 has greater transmissibility than Delta.
The mutations also mean the new variant is likely to be more resistant to antibody treatments such as those developed by Regeneron, which have been shown to save lives. “That is really a cause for concern”, says Barclay. One small bright spot is, to date, there are no signs that the variant causes more severe disease.
How far has it spread?
Genomic sequencing has found the variant in South Africa, Botswana and Hong Kong. There are also reported cases in Israel, apparently originating from a traveller from Malawi, and in Belgium, from someone who had travelled from Egypt. UK health secretary Sajid Javid said it is “highly likely” the variant has spread to other countries. No cases have been detected in the UK yet, where about a fifth of positive cases are sent for genomic sequencing. Even in countries with low levels of sequencing, there may be some early warning signs for countries, as the variant is linked to S-gene dropout which is picked up by PCR tests, says Jeffrey Barret at the Wellcome Sanger Institute.
How have other countries responded?
The UK and EU have both imposed restrictions on people travelling from countries in southern Africa, with Javid saying the variant is of “huge international concern”.
Is it a given that this will outcompete Delta?
We don’t know. “We don’t have definitive evidence at the moment that this is more transmissible, but there are hints there that it may be,” says Peacock, pointing to the growth in South Africa and the higher R number in Gauteng. Some earlier variants have failed to get a toehold in certain countries because of the competition from other variants: Beta has not become established in the UK, for example, while Alpha spread from Europe but never reached high levels in South Africa. “If this variant is not as transmissible as Delta that would be good news for sure,” says Barrett.
What can I do?
All the usual measures of social distancing, handwashing, mask-wearing, getting vaccinated and having a booster all still apply. The emergence of such a potentially worrying variant is, however, a reminder of the risk of uneven vaccination rates globally – only 24 per cent of people are fully vaccinated in South Africa – and why helping low and middle income countries access vaccines is important.
How much do we really know about this variant?
Most of our knowledge is from the Network for Genomic Surveillance in South Africa, and the South African government, both of whom have been praised by researchers for acting fast to share information on the variant. But there is still more we don’t know than we do. Tulio de Oliveira at Stellenbosch University, South Africa, said yesterday that the full significance of the variant’s mutations “remain uncertain.” Peacock adds: “It’s important to stress how much we don’t know this new variant.“
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