Explainer: What we know about the COVID-19 variant detected in South Africa

Reuters
By Alexander Winning and Alistair Smout

JOHANNESBURG/LONDON, Nov 26 (Reuters) – Global authorities have reacted with alarm to a coronavirus variant detected in South Africa, with the EU, Britain and India among those announcing stricter border controls as scientists seek to determine if the mutation is vaccine-resistant.

WHERE AND WHEN WAS NEW VARIANT FOUND?

South African scientists detected a small number of the variant – called B.1.1.529 – on Tuesday, in samples from Nov. 14-16.

On Wednesday South African scientists sequenced more genomes, informed the government that they were concerned and asked the World Health Organization to convene its technical working group on virus evolution for Friday.

The country has identified around 100 cases of the variant, mostly from its most populated province, Gauteng.

WHERE ELSE HAS IT BEEN IDENTIFIED?

South African scientists say early signs from diagnostic laboratories suggest it has spread rapidly in Gauteng and may already be present in the country’s other eight provinces.

The country’s daily infection rate nearly doubled on Thursday to 2,465. The South Africa’s National Institute for Communicable Diseases (NICD) did not attribute the resurgence to the new variant, though local scientists suspect it is the cause.

Botswana detected four cases, all foreigners who arrived on a diplomatic mission and have since left the country.

Hong Kong has one case, in a traveller from South Africa and Israel one in a traveller returning from Malawi.

The variant is relatively easy to distinguish in PCR tests from Delta, the dominant COVID-19 variant and the most infectious so far. Unlike Delta, it has a mutation known as the S-gene drop-out.

WHY IS IT WORRYING SCIENTISTS?

All viruses – including SARS-CoV-2, the virus that causes COVID-19 – change over time. Most changes have little or no impact on their properties.

However, some changes may affect how easily they spread, the their severity or the performance of vaccines against them.

This one has drawn scrutiny because it has more than 30 mutations of the spike protein that viruses use to get into human cells, UK health officials say.

That is about double the number of Delta, and makes this variant substantially different from the original coronavirus that current COVID vaccines were designed to counteract.

South African scientists say some of the mutations are associated with resistance to neutralising antibodies and enhanced transmissibility, but others are not well understood, so its full significance is not yet clear.

UK Health Security Agency Chief Medical Advisor Dr Susan Hopkins told BBC radio some mutations had not been seen before, so it was not known how they would interact with the other ones, making it the most complex variant seen so far.

So more tests will be needed to confirm if it’s more transmissible, infectious or can evade vaccines.

The work will take a few weeks, the World Health Organization’s technical lead on COVID-19, Maria van Kerkhove, said on Thursday. In the meantime, vaccines remain a critical tool to contain the virus.

No unusual symptoms have been reported following infection with the B.1.1.529 variant and, as with other variants some individuals are asymptomatic, South Africa’s NICD said.

WHAT HAS THE WORLD HEALTH ORGANIZATION SAID?

The UN agency will decide if it should be designated a variant of interest or variant of concern. The latter label would be applied if there is evidence that it is more contagious and vaccines work less well against it, and it would be given a Greek name.

The WHO has so far identified four variants “of concern” – Alpha, Beta, Gamma and Delta.

Two variants of interest are Lambda, identified in Peru in December 2020, and Mu, in Colombia in January.

Reporting by Alistair Smout in London, Alexander Winning, Tim Cocks and Olivia Kumwenda-Mtambo in Johannesburg, Stephanie Nebehay in Geneva and Ari Rabinovitch in Jerusalem Writing by Josephine Mason; editing by John Stonestreet