A new variant of the novel Coronavirus is spreading rapidly in South Africa and leaving behind other variants faster than previous ones.
The new variant, B.1.1.529 in South Africa, is detected in Gauteng province, and the positivity rates in Tshwane (part of Gauteng) have increased in the last three weeks from less than 1 per cent to over 30 per cent.
The new COVID-19 variant sequencing has been concentrated on samples from Gauteng. Almost all recent samples from Gauteng (77) have found this new variant outstripping the previous Delta variant. This coincides with a wider rise in cases in South Africa. Although the numbers are small (both of B.1.1.529 and cases in South Africa overall), but there's a clear upward trend.
Despite being tracked for only the past three days, the virus has been identified as having 32 different mutations concerning predicted immune invasion and transmissibility.
The variant was identified this week and has been found in three countries so far: Botswana, South Africa and Hong Kong (returning traveller from South Africa).
"Gauteng saw a rapid increase in test positivity last week. Notwithstanding the potential for bias in sequencing, the B.1.1.529 variant seemingly is becoming dominant (almost 0 to 75 per cent in 2 weeks) in South Africa," Vinod Scaria, Scientist, Institute of Genomics & Integrative Biology, said in a tweet.
Of the 59 laboratory-confirmed cases of the new variant, three were in Botswana, two were in Hong Kong among people who had travelled from South Africa, and the rest were from South Africa.
The strain has an unusually large number of mutations and is clearly very different from previous variants, said Tulio de Oliveira, Director, Centre for Epidemic Response & innovation, South Africa, in a press briefing.
B.1.1.529 genome was collected from 77 samples from Gauteng, South Africa, four samples from Botswana, and one sample from Hong Kong (through a traveller from South Africa) from 12-20 November.
Early signs from diagnostic labs show that B.1.1.529 has rapidly increased in Gauteng and may already be present in most provinces.
"We can make some predictions about the impact of mutations in this variant, but the full significance is uncertain, and the vaccines remain the critical tool to protect us from severe diseases. While the number of people infected with the B.1.1.529 strain is still small, caution has to be exercised due to the very unusual constellation" of mutations," said Oliveira.
The mutations contain features seen in all of the other variants but also traits that have not been seen before. The B.1.1.529 variant has an unprecedented number of mutations in the spike protein gene. This protein is the target of most vaccines and has a greater potential to escape prior immunity than previous variants.