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The ‘incredibly transmissible’ Kraken could take over as dominant Covid-19 strain in South Africa

The ‘incredibly transmissible’ Kraken could take over as dominant Covid-19 strain in South Africa
The 'Kraken' subvariant of the Sars-CoV-2 virus has been described as “incredibly transmissible” by the World Health Organization but little data is available on its severity. (Image: iStock)

Looking at information from the US, the ‘incredibly transmissible’ XBB.1.5 subvariant of Omicron might become the dominant Covid-19 strain in South Africa, the National Institute for Communicable Diseases said on Wednesday. 

The XBB.1.5 subvariant of the Sars-CoV-2 virus might become the dominant strain in South Africa as US data shows that it has a “growth advantage” due to increased transmissibility, the National Institute for Communicable Diseases (NICD) said in a statement on Wednesday.

An article published in Nature highlights that this subvariant had a rare amino acid change that makes it easier to bind to human cells, making it more transmissible.

However, an update by the NICD on the Covid-19 situation in South Africa states that the weekly incidence risk in South Africa remains low. It is still well below the World Health Organization’s (WHO’s) guideline that a risk of more than five cases per 100,000 of the population shows that the outbreak is not under control. 

In the past week, Western Cape reported the highest weekly incidence risk (2.7 cases per 100,000 persons), followed by KwaZulu-Natal (2.5 cases per 100,000 persons) and Gauteng and Eastern Cape (1.4 cases per 100,000 persons). The other provinces reported weekly incidences below one case per 100,000 persons.

Those over 80 remain at the highest risk, and young children are at the lowest risk.

South Africa’s testing rates remain low, at around 12 tests for every 100,000 people. On average, the positivity rate (the percentage of positive tests out of all the tests done that week) was 8.6%

Highest positivity rate for Eastern Cape and Western Cape

The highest positivity rate was in the Eastern Cape (11.5%), followed by the Western Cape (11.1%). 

In Motherwell, Gqeberha, three staff members at a clinic and one patient tested positive for the infection, Eastern Cape Department of Health spokesperson Yonela Dekeda confirmed. 

“None of them are showing any life-threatening symptoms, with some not experiencing any symptoms. 

“Those cases are nowhere linked to the newly discovered XBB.1.5 variant. The department decontaminated [the clinic] and debriefed the staff on Friday, 6 January, for an hour, after which operations resumed immediately,” she added.

Outreach teams will trace the contacts of those who tested positive.

XBB.1.5 is one of more than 650 sublineages of Omicron that have been identified worldwide. Of those, more than 200 have been detected in South Africa. 

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Where did XBB.1.5 come from?

“In September 2022, a new sublineage, XBB, was identified in the United States of America (US) and Singapore. XBB is a recombinant of two BA.2 sublineages. It contains the genetic material of both parent sublineages,” the statement from the NICD reads.

Data shows that the original XBB sublineage has increased transmissibility. This sublineage has also produced more sublineages, XBB.1, XBB.2, and XBB.3, that have been circulating in South Africa since October 2022. 

The XBB.1.5 sublineage was first detected in October 2022 in the US and has since been identified in several other countries. It was identified in South Africa in early January from a sample collected late in December 2022. 

“US data shows that it has a growing advantage which does mean it can replace the other sublineages of Omicron currently in circulation,” the statement continues.

This growth advantage, the NICD explained, was due to a genetic change in the spike protein that increases the binding of the virus to human cells and makes it more transmissible.

No data can confirm whether XBB.1.5 will cause more severe disease than the other Omicron sublineages.

But the NICD added that South Africa has a lot that counts in its favour.

“Due to the widespread circulation of other Omicron sublineages, and the overall high population immunity in South Africa, the introduction of XBB.1.5 in South Africa may not necessarily result in a large wave of infections. Ongoing surveillance to track variants will continue to [monitor] the growth of XBB.1.5 in South Africa,” the statement reads. 

More testing

On Tuesday, Health Minister Dr Joe Phaahla said new guidelines that will increase the testing of possible cases were sent to the provinces on Monday night. 

Western Cape is currently testing the most people, with a testing rate of about 18 for every 100,000. Gauteng’s rate is 17 per 100,000 and Limpopo has the lowest testing rate at one per 100,000.

The NICD’s Dr Michelle Groome confirmed on Tuesday that they would increase wastewater surveillance in the country’s sewer systems, which provides an early indication of a spike in infections.

She added that the NICD would also start testing wastewater from aeroplanes from countries with high numbers of infections. 

Why no new name?

While the new subvariant was named “Kraken” by the international media, this specific sublineage has not been given a new designation by the WHO.

The technical lead for the WHO’s Covid-19 response, Dr Maria van Kerkhove, said on Wednesday afternoon during a press conference called by the organisation that XBB.1.5 so far behaves like all the other sublineages of Omicron.

She said data on XBB.1.5 was minimal and mainly from the US, but it was clear that it is “incredibly transmissible”.

“We don’t have data on severity,” she said. 

Van Kerkhove urged people to get a booster shot and protect themselves by ensuring areas are well-ventilated, wearing a mask if necessary and knowing their own risk. 

Dr Michael Ryan, executive director of the WHO’s Health Emergencies Programme, said they had had engagements with their colleagues in China but still needed adequate information to do a comprehensive risk assessment of the situation. DM/MC


"Information pertaining to Covid-19, vaccines, how to control the spread of the virus and potential treatments is ever-changing. Under the South African Disaster Management Act Regulation 11(5)(c) it is prohibited to publish information through any medium with the intention to deceive people on government measures to address COVID-19. We are therefore disabling the comment section on this article in order to protect both the commenting member and ourselves from potential liability. Should you have additional information that you think we should know, please email [email protected]"

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