south african new covid-19 variant
The NCID has confirmed a new Covid-19 variant detected in South Africa. Photo: NCID

The National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, has confirmed that through collaborative efforts with private laboratories and the NGS-SA members, a new COVID-19 variant, B.1.1.529, has been detected in South Africa. Unfortunately it appears to have over 30 mutations (Delta only had two) and there are concerns it could spread rather rapidly.

The NICD says that 22 positive cases of variant B.1.1.529 have been recorded in SA following genomic sequencing collaborations. In addition, other NGS-SA laboratories are confirming more cases as sequencing results come out.

According to the renowned bioinformatician, Professor Tulio de Oliveira, the variant has also been identified in Botswana, and Hong Kong involving a traveller from South Africa.

New Cases Increasing ‘Quickly’

It was just a couple of days ago that a rapid increase of Covid-19 cases in Gauteng made news. South Africa’s Health Minister, Dr Joe Phaahla, said in a media briefing on Thursday that he believes Gauteng’s recent cluster outbreaks may have been tied to this new variant.


Scientists said today that the number of detected cases with the new variant, and the percentage testing positive with it, are both increasing quickly, especially in Gauteng, North West and Limpopo… although it’s believed that the variant is probably already in other provinces, and Dr Phaahla warned that in the coming weeks leading up to Christmas – as people move around the country – the variant “will be all over” SA.

Infectious Diseases Specialist, Dr Richard Lessells, said the variant has been found in Gauteng, because that is where they have been focusing sampling and sequencing.

“However, this is not isolated to Gauteng at this moment,” he said.

In addition, he said the Lancet and National Health Laboratory Service have also noticed the rapid rise in tests that are positive in recent weeks, but also this mutation in the spike protein.

“It gives us concern that this variant may already be circulating quite widely in the country.”

Provincial health authorities have been placed on high alert and are prioritising the sequencing of COVID-19 positives samples.

New variant has a high number of mutations

Prof de Oliveira said: “What we see is this very unusual constellation of mutations, multiple mutations across the genome with more than 30 mutations.”

According to the Professor, the Delta variant, which was responsible for the deadly third wave, had two mutations, while the Beta had three.

Prof de Oliveira said the latest variant’s far larger number of mutations is “concerning for predicted immune evasion and transmissibility“… but that the full significance of it is not yet certain.

Infectious Diseases Specialist Dr Lessells, said: “When this variant was detected, we [could] see this large number of mutations across all the different proteins of this virus.”

While some of them are familiar, many of them are not. “We see a lot of mutations in the spike protein that might affect how well the virus is neutralised,” Lessells said.

Evasion and Transmissibility

He also raised an alarm that mutations may give the virus enhanced transmissibility from one person to the next (ie. make it more contagious). On top of that concern – that it can spread more efficiently – Lessells said it also might “be able to get around parts of the immune system and the protection that we have in our immune system”.

Effect on Vaccines

One of the key questions, according to the scientists, is around vaccines and whether this variant affects that protection, and if for those who are vaccinated it is “still predominantly a milder disease”.

“We can make predictions but we will only know for real by doing the studies in the laboratory,” said Lessells.

However, he emphasised that vaccines remain the critical tool for protecting citizens from severe disease and protecting the health system from another surge in cases.

Call for vaccinations, wearing masks, washing hands and sanitising

“While we had hoped for a very long recess in terms of low infections so that we can have a lot of more opening up of activities, this has just descended on us,” the Health Minister said.

“this has just descended on us” – SA Health Minister

Phaahla urged citizens to avoid crowds, wear masks, wash hands, sanitise and vaccinate.

“The fact of the matter is that we also have an additional tool, which is the vaccination, which will help us to avert serious illness and ending up in hospitals, ICU and succumbing to this virus,” said the Minister.

Dr Michelle Groome, the NICD’s Head of Public Health Surveillance and Response, stresses that regardless of the emergence of new COVID-19 variants, the importance of non-pharmaceutical interventions remains unchanged and the public are urged to be responsible.

“This means that individuals should get vaccinated, wear masks, practice healthy hand hygiene, maintain social distancing, and gather in well ventilated spaces,” she says, adding: “Individual compliance to preventative measures can have a great collective impact in limiting the spread of the new variant.”

Meeting WHO and Assigning a Greek Name to the Variant

The team will be meeting with the World Health Organisation (WHO) on Friday and are expecting to assign a Greek name for this variant, as with the others.

“It’s very important to understand that even though the variant was detected here [it] doesn’t mean that this variant is from South Africa,” said Prof Oliveira.

“It is not surprising that a new variant has been detected in South Africa,” says Prof Adrian Puren, NICD Acting Executive Director. He says that although the data is limited, “our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be. Developments are occurring at a rapid pace and the public has our assurance that we will keep them up to date.”

Sources: NICD and SANews.gov.za