A woman in Johannesburg, South Africa, receives a nasal swab from a health worker EMMANUEL CROSET/AFP via Getty Images
A new variant of SARS-CoV-2, known first as B.1.1.529 and now named omicron, has an unusually high number of mutations and appears to have triggered a recent surge in cases in South Africa.
When was omicron first identified?
It was first in South Africa using samples taken between 14 and 16 November. Joe Phaahla, South Africa鈥檚 health minister, that he believes the variant is behind an exponential daily rise in covid-19 cases across the country in recent days. The same day, the UK 午夜福利1000集合 Security Agency (HSA) , triggering travel restrictions for people travelling to the UK from South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia. The World 午夜福利1000集合 Organization had listed B.1.1.529 as a variant under monitoring, but its Technical Advisory Group on SARS-CoV-2 Virus Evolution to class it as a variant of concern. The WHO has now named it omicron after the Greek letter.
What is happening in South Africa?
National daily cases have gone from . While the rate of growth has been fast, absolute numbers are still relatively low compared with the UK, on 26 November. More than 80 per cent of South Africa鈥檚 cases are currently in the country鈥檚 Gauteng province. All of the 77 cases sequenced in the province between 12 and 20 November were identified as being caused by the variant. The estimated reproduction number, the average number of people that an individual is likely to infect, is almost 2 in Gauteng compared with nearly 1.5 nationally.
What do B.1.1.529’s mutations tell us?
The variant has a 鈥渧ery unusual constellation of mutations鈥, 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 鈥渢his has not been proven鈥.
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 鈥渨e don鈥檛 really know鈥 if it will reduce the effectiveness of vaccines. Nonetheless, she adds that, in theory, the number of changes across the antigenic sites on the variant鈥檚 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 鈥渋t鈥檚 very biologically plausible鈥 that B.1.1.529 has greater transmissibility than delta.
The mutations also mean that 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. 鈥淭hat is really a cause for concern,鈥 says Barclay. One small bright spot is that, 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 , apparently originating from a traveller from Malawi, and in , from someone who had travelled from Egypt. UK health secretary Sajid Javid said it is 鈥渉ighly likely鈥 that the variant has spread to other countries. As of 27 November, , where about a fifth of positive cases are sent for genomic sequencing. Even in countries with low levels of sequencing, it may be possible to get early warning signs, because the variant is linked to a mutation called S-gene dropout, which is picked up by PCR tests, says Jeffrey Barrett at the Wellcome Sanger Institute in Hinxton, UK.
How have other places responded?
The UK and EU have both imposed restrictions on people travelling from countries in southern Africa, with Javid saying the variant is of 鈥渉uge international concern鈥. Prime minister Boris Johnson .
Is it a given that this will outcompete the delta variant?
We don鈥檛 know. 鈥淲e don鈥檛 have definitive evidence at the moment that this is more transmissible, but there are hints there that it may be,鈥 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 hasn’t become established in the UK, for example, while alpha spread from Europe but never reached high levels in South Africa. 鈥淚f this variant is not as transmissible as delta that would be good news for sure,鈥 says Barrett.
What can I do?
All the usual measures of social distancing, handwashing, mask-wearing, getting vaccinated and having a booster shot still apply. The emergence of such a potentially worrying variant is, however, a reminder of the risk of uneven vaccination rates globally 鈥 .
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 which have been praised by researchers for acting fast to share information on the variant. But there is more that we don鈥檛 know than we do. Tulio de Oliveira at Stellenbosch University, South Africa, that the full significance of the variant鈥檚 mutations 鈥渞emain uncertain.鈥 Peacock adds: 鈥It鈥檚 important to stress how much we don鈥檛 know this new variant.鈥
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