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SU scientists first to detect new ‘kraken’ Covid variant in SA
Author: FMHS Marketing & Communications / FGGW Bemarking & Kommunikasie – Ilse Bigalke
Published: 16/01/2023

​In Covid-19 history, Prof Tulio de Oliveira and his team at Stellenbosch University (SU), as well as the Network for Genomics Surveillance in South Africa (NGS-SA) under his leadership, will be remembered for first detecting the Beta variant of SARS-CoV-2 and later the Omicron variant.

At the beginning of the year (6 January 2023), it was announced that the team at the Centre for Epidemic Response and Innovation (CERI) at SU and the NGS-SA had also detected the first case of the new “kraken" Omicron subvariant, XBB.1.5, in South Africa. Kraken refers to a legendary sea monster.

The World Health Organisation (WHO) describes it as the most transmissible Covid-19 variant to date, and it has been detected in in more than 30 countries, notably in the United States. Its transmissibility is due to a potent array of mutations that appear to help it evade immune defences and improve its ability to invade cells.

Describing how the subvariant was detected, De Oliveira explained that South Africa has one of the strongest genomic surveillance systems in the world. The NGS-SA, a close collaboration between hundreds of scientists, nine laboratories, the National Health Laboratory Service and the National Institute of Communicable Diseases, have been monitoring changes in SARS-CoV-2 since March 2020, even before the first Covid case hit South Africa.

“We do genomic surveillance every week and select 100 to 200 random samples across the country. The process consists of sequencing the genome of the virus that causes Covid and identifying the mutations that allow us to determine exactly which variant is circulating.

“We recently found the first genome of the new subvariant of Omicron that is currently causing a surge of infections in the east coast of America, especially in New York. The sample was taken late in December."

Explaining the reason for the constant genomic surveillance, the world-renowned bioinformatician said: “It's to make sure that diagnostics and vaccines are still effective and that if we find something unusual that is likely to cause a wave of infection, we have time to prepare the health system.

“Early warnings really save lives, as could be seen in the last wave of Omicron. We had the information early, therefore hospitals could prepare and ensure that enough oxygen was available."

Alerted, but not concerned

The SU professor said there is no concern at present that XBB.1.5 will cause a new wave of infections, due to its low prevalence. “I don't expect a big wave of infections with hospitalisations in South Africa because of the strong immunity of the population and the previous waves of Omicron variants.

“In case of a fast increase in prevalence and hospitalisations, which we consider extremely unlikely, we will ensure that the public will be properly informed via the Department of Science and Innovation and the Department of Health.

“Our communication process is very effective and prevents panic among the population. We release a report every week to the relevant government departments and inform the public three days later, to ensure that scientific information reaches the public directly.

“At the moment we are alerted, but not concerned that XBB.1.5 will cause a new wave."

Are vaccines still effective?

De Oliveira explains that existing vaccines are still very effective, because the new subvariant is not very different from hundreds of other variants of the Omicron lineage.

“The level of population immunity due to vaccinations and previous infection is high. This was illustrated in New York, where there were at least six times less hospitalisations of vaccinated and unvaccinated people.

“But a booster is still important for people who are concerned about another wave of infections. It will prevent severe infection."

Recommendations and measures

Scientists and the WHO have advised South Africa to increase the rate of testing and number of samples sent for genomic sequencing. The surveillance of wastewater to monitor the prevalence of Covid-19 in the population will also be increased.

Advice included “reinvigorating" the vaccination campaign. “Vaccination remains the bedrock to protect us against any subvariant," said Health Minister Joe Phaahla. Covid-19 boosters for adults are also to be rolled out.

However, no restrictions will be put in place for South Africans and restrictions on travellers from countries who are experiencing an increase in cases will also not be implemented.


Additional source: SABC News interview

Photo caption: Prof Tulio de Oliveira with laboratory technologist Lucious Chabuka.

​Photo credit: Stefan Els