Covid-19: Scientists monitoring new virus variant detected in SA, Botswana

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  • A new variant of the SARS-CoV-2 virus has been detected in three countries, including SA.
  • According to a virologist who posted details about the variant online, it has a significantly high number of mutations.
  • However, it appears the virus is circulating at a low frequency, and scientists are currently assessing its potential impact.

A new variant of the virus that causes Covid-19 has been discovered in three countries, including South Africa.

Known as B.1.1.529, it has 32 mutations in the spike protein – the part of the virus that latches onto human cells, which most vaccines target. Mutations refer to individual changes in the virus' genetic code.

The National Institute for Communicable Diseases (NICD) on Thursday confirmed the detection of a new variant in the country.

In a statement, the NICD said twenty-two positive cases of variant B.1.1.529 have been recorded in South Africa "following genomic sequencing collaborations between the NICD and private laboratories.

"In addition, other NGS-SA laboratories are confirming more cases as sequencing results come out".

READ | As daily Covid-19 cases rise sharply, the question about the fourth wave is not if, but when

According to Dr Tom Peacock, a virologist at Imperial College London, the high number of spike mutations suggests "this could be of real concern". Peacock posted details of the variant on genome-sharing website, GitHub.

At low numbers, must be monitored

In a Twitter thread, Peacock said that because B.1.1.529 had a "really awful spike mutation profile", it should be carefully monitored. However, he also said:

"[It's] worth emphasising this is at super low numbers right now in a region of Africa that is fairly well sampled…"

It is possible that the variant is an "odd cluster" that is not very transmissible, he said.

South Africa has a large collaborative genomic surveillance network, which has been crucial in identifying variants and controlling outbreaks. Krisp (KwaZulu-Natal Research Innovation and Sequencing Platform), located in KwaZulu-Natal, is the principal investigative institute of this network.

Health24 has contacted Krisp for additional information on B.1.1.529, and also understands that an announcement will soon be forthcoming from South African health authorities. 

Variant under monitoring

On 24 November, the World Health Organisation (WHO) classified the B.1.1.529 variant as a variant under monitoring (VUM). A variant receives this label when it has genetic changes that are believed to affect the virus' characteristics, the WHO notes. A VUM presents some indication that it may pose a future risk. However, it requires "enhanced monitoring and repeat assessment, pending new evidence".

Other variant labels listed under the WHO's website include variants of interest (VOI) and variants of concern (VOC). The former receives the classification if it has undergone genetic changes that may allow it to transmit more easily; cause more severe illness; or reduce the effectiveness of vaccines or treatments, among other factors, Health24 previously explained.

When there is increased evidence of it fulfilling at least one of the above criteria, it is elevated to a VOC, such as the Delta variant, which is currently prevalent in South Africa.

There are unknowns

Ravi Gupta, a professor of clinical microbiology at Cambridge University, and Africa Health Research Institute (AHRI) faculty member, has been studying B.1.1.529 in his laboratory.

Gupta told The Guardian that work conducted in his lab established that two of the mutations on the variant increased infectivity and reduced antibody recognition. 

"It does certainly look a significant concern based on the mutations present," he said, but cautioned that there were still unknowns about the variant, including how infectious it was.

"Immune escape is only part of the picture of what may happen," he added.

Focus shouldn't be on number of mutations

While the new VUM has a significantly high number of mutations, it doesn't necessarily mean that the variant is of a greater threat than others, Dr Richard Lessells, a leading infectious diseases expert involved in surveillance for Covid-19 variants, previously told Health24.

He said: "As we go on in this pandemic, and as new variants pop up, each new one that pops up will have more mutations than the last one, because more time has elapsed and the virus had more time to evolve. So, the number of mutations is not really a helpful thing to differentiate," he added.

Instead, the key focus should be on the specific pattern or combination of mutations because that would determine the behaviour of the virus, he explained. 

Reporting suggests that B.1.1.529 is being monitored and studied. Additionally, considering it is currently circulating at a low frequency, it is not possible to conclusively say whether this variant may pose a greater threat to efforts to reach the end of the pandemic than the current VOCs, including Delta.

Viruses change, it's in their nature

Local experts have previously explained that it is in virus' nature to mutate often, and these changes are therefore expected. 

"This is what viruses do. They change continuously, and they try to adapt," Professor Willem Hanekom, director at the AHRI, told News24 in February

He added: "If there's an advantage in their change, then that [variant] with the huge advantage will become much more common in society."

Hanekom added that as long as the epidemic was not under control, variants would continue to emerge. 

In August, Lessells stated that the detection of C.1.2, another VUM, was a reminder of how important vaccination was for everyone. 

"It helps slow the spread of the virus and that's what slows this evolutionary process," he said.

*For more Covid-19 research, science and news, click here. You can also sign up for our Daily Dose newsletter here.

READ | Covid-19: How Africa’s top scientists have tracked emerging variants, ensuring we’re not left behind

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READ | As daily Covid-19 cases rise sharply, the question about the fourth wave is not if, but when

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