South African scientists detect new Covid ‘super-variant’

South Africa Covid test

A nurse in Richmond, Johannesburg takes a mouth swab for Covid-19 testing South African scientists sequencing the genetic profile of Covid-19 have detected a new ‘super-variant’ with multiple mutations.

Photo credit: Luca Sola | AFP

South African scientists sequencing the genetic profile of Covid-19 have detected a new ‘super-variant’ with multiple mutations.

Evidence so far shows it may be yet more infectious than the Delta variant that has spread around the world.

The announcement was made today in a virtual briefing by leading South African scientists, who have become alarmed at the rapid spread of the new ‘super variant’, designated B.1.1.529, mainly in the greater Johannesburg region in the last week.

Working off recent discoveries derived from genomic sequencing, including in the past 48 hours, concerned scientists have said they can make “some predictions” about the new variant’s likely spread, which would likely be “very rapid”.

At least 1,000 cases have been found in greater Johannesburg and surrounding areas in Gauteng province in about a week, but internationally, four cases have been detected in Botswana and one, a traveller from South Africa, in Hong Kong.

Spreading rapidly

A few cases have also been found in other South African provinces, indicating that the virus is spreading rapidly – even faster than the previous Delta variant that drove the country’s third wave earlier this year.

The new super-variant, with 10 significant mutations to the spike protein that allows the Covid virus to bind with human cells, may well be much more infectious than even the Delta variant has proved to be.

But the scientific community involved in tracking it through South Africa’s world-class Network for Genomic Surveillance (NGS-SA) says it is too early to say exactly how infectious it is.

The new super-variant was detected and sequenced by a team led by Prof Tulio de Oliveira, of South Africa’s world-leading KRISP laboratory in KwaZulu-Natal province.

Dominant version

Prof De Oliveria and his team discovered the Beta variant about this time last year, a version of Covid that drove South Africa’s deadly second wave of infections, later eclipsed by the Delta variant, which remains the dominant version of Covid-19.

He said that in the last 48 hours, scientists had determined that though the data on it is only about a week old, it should go to government and the public in general.

It is not certain whether the new variant originated in South Africa or not.

It is mainly spreading among younger people, with campus outbreaks coming just as the study year draws to a close.

All indications, De Oliveira’s team said, were that the new super-variant may well have developed the means to defeat not only neutralising antibodies, as produced through vaccination or by natural immunity through infection, but could also bypass other immune system protections such as T-cells.

Work was underway to establish more precisely how severe and tenacious infections with the new variant would likely be.

Since the Covid-19 outbreak, leading virological researchers have thought that the human body’s ability to fight invading organisms such as the Covid virus is vital for those who are naturally able to beat off the infection.

Serious concerns

But the possibility that the new super-variant could bypass even these immune system defences has raised serious concerns among government leaders.

They must now decide, as South Africa faces yet another holiday season in full viral outbreak mode, what public health measures to take next.

South Africa is currently in the lowest of lockdown levels, but the new Covid version seems likely to change that status sooner than later.

 “One of the few good things to report is that we found this new variant very early,” said Prof De Oliveira.

“We can make some predictions on what we already know about this variant, but we would really like to be wrong about those predictions. The next few days should tell us a lot more.”

He and others involved in sequencing genomic samples have found around 100 confirmed cases of the new variant with full sequencing completed, and are expected to complete 200 to 300 more in the next day or two.

One fortunate aspect of the new variant is that it is easy to detect from a single assay element of the genetics-based PCR tests used to confirm Covid-19 infections.