Scientists race to unravel the secrets of a new Covid-19 variant first identified in South Africa

Bioinformatician Professor Tulio de Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform at the University of KwaZulu-Natal. (Photo: Amy Gibbings / News24)

The National Coronavirus Command Council met on Saturday to assess developments in the Covid-19 pandemic, including scientific updates around the newly detected coronavirus variant. The meeting was brought forward as a matter of urgency after being originally scheduled for Sunday.

Scientists are in a race against time to analyse hundreds of recently collected samples to get a sense of how far a new variant has spread in South Africa, and to get a handle on disease severity and the impact of vaccines.

On Friday evening, the World Health Organization (WHO) said the new variant was “of concern” and gave it the name Omicron. “This variant has a large number of mutations, some of which are concerning,” the WHO said in its official description. “Preliminary evidence suggests an increased risk of reinfection with this variant, as compared with other [variants].”

The National Coronavirus Command Council will now meet on Saturday instead of Sunday, the presidency announced on Friday night. According to the presidency, the council will “assess developments in the Covid-19 pandemic, including scientific updates around the newly detected coronavirus variant”.

Gauteng’s number of new positive Covid-19 cases almost doubled overnight between 24 November and 25 November as a team of scientists revealed that the new variant had been identified in this country.

There had been concerns that people dropped their guard in Level 1 lockdown, with possible drivers being electioneering and the political rallies in the run-up to the 1 November elections. Big crowds, including those at Black Friday sales and at festive season gatherings, add to the pressure to flatten the rising curve.

The director of the KwaZulu-Natal Research Innovation and Sequencing Platform (Krisp), Tulio de Oliveira, said in a tweet that, by PCR proxy testing, an estimated 90% of cases in Gauteng (at least 1,000 a day) are caused by this variant.

Dr Ridhwaan Suliman, who tracks the Covid numbers on his Twitter feed, noted 1,950 new cases as the biggest single-day increase since 13 August in the province – a 308% week-on-week increase. Suliman, a CSIR senior researcher, added: “Here we go again Gauteng!”

The dreaded fourth wave now seems very likely.

The Gauteng Department of Health released information this week, in response to questions in the legislature from the DA, showing one-third of the province’s healthcare workers are unvaccinated.

The 31,521 unvaccinated employees means about 36% of staffers have not had the jab.

Also, since the start of the pandemic, 111 healthcare workers in the department have died from the virus and another 1,908 were hospitalised.

In Gauteng, there was a cluster outbreak at the Tshwane University of Technology (TUT) Pretoria West campus.

The City of Tshwane also identified other cluster outbreaks in Hatfield, Atteridgeville, Mamelodi East, Centurion and Soshanguve.

The TUT authorities met to address the outbreak, to confirm the number of students and staff affected, and to tighten up protocols.

TUT confirmed on Friday that 86 students have so far tested positive in this outbreak. A TUT spokesperson said the university currently doesn’t have a vaccination mandate policy but runs a permanent onsite vaccination site on campus and continues with its vaccination drive.

The spokesperson said a university team, alongside Department of Health officials, had embarked on a ramped-up screening and testing drive at its Gauteng campuses to get a “clearer picture of the extent of the outbreak”.

CEO of Higher Health Professor Ramneek Ahluwalia said there was no data yet to suggest current vaccines would not be effective against the new variant, but the high infection rates in Gauteng showed signs of the probable high transmissibility. “The 30 to 32 spike protein mutations … are far more than we have seen with the previous variants in South Africa,” he said. The new variant could become dominant quickly, taking over from Delta, which caused the third wave.

“The choices we make now and during the holiday period will have a major impact on the coming academic year. And the first choice we want is every student and all eligible family members of students to get vaccinated as soon as possible.”

In Waverley, Johannesburg, a 70th birthday garden party held at an open-air venue in the suburb on 21 November has so far returned three positive cases among the 40-odd guests. It includes the host, Theresa Giorza, and her husband Maurice Smithers, whose birthday they were celebrating.

Giorza and Smithers have suffered mild symptoms that developed two days after the party, which had an “RSVP via vaccination card” stipulation. Smithers said: “We took every precaution, from being outdoors, limiting guest numbers, asking people to confirm their vaccinations, and even making paper snack cones so people didn’t have to touch the same snack bowls, but it just shows that you can’t be too careful and clearly Covid-19 was there as an uninvited guest … either we caught it at the party or we carried it to the party.”

He added that the venue wasn’t thorough with temperature checks and sanitising at its multiple entry points and that, as people relaxed, he admitted, less physical distancing was practised.

“I guess there was a false sense of security with the infection numbers being so low at the time. I’m sure that if we weren’t fully vaccinated the symptoms would be worse,” he said.

Smithers’s doctor has ordered blood tests to check for clotting and risk of secondary infections. The doctor has not disclosed what variant he was infected with.

Already, the rise in cases has seen travel restrictions imposed on South Africa. The UK has once again placed South Africa on the red list of countries blocked from entry.

The Netherlands national cricket team, which had been playing the Proteas at Supersport Park in Pretoria, said their ODI tour would be cut short as they fly out of the country as soon as possible.

The Omicron variant was first identified in samples collected between 12 November and 20 November from Gauteng (77 samples), Botswana (four samples) and Hong Kong (one traveller from SA).

De Oliveira said the new variant had several concerning mutations but the “good news” was that it can be detected by a PCR test and does not need whole-genome sequencing to be identified.

Cases in neighbouring North West and Limpopo provinces showed significant increases.

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

According to the National Institute for Communicable Diseases’ latest update, issued late on 25 November, 2,465 new Covid-19 cases have been identified in South Africa.

The WHO regards anything higher than a 5% positivity rate as “too high”. In the past 10 days, South Africa’s positivity rate went from about 1% to 6.5% by the night of 25 November, with 114 deaths resulting from Covid-19 being reported.

The bulk of new cases – 1,950 – were identified in Gauteng.

On the afternoon of 25 November, scientists from the Network for Genomics Surveillance in South Africa (NGS-SA) recounted their race against time as they hunted for the variant, which has an alarming number of mutations.

NGS-SA includes teams from the National Institute for Communicable Diseases (NICD), Krisp, the universities of Cape Town, Stellenbosch, the Free State, Pretoria, the Witwatersrand, and the National Health Laboratory Service.

The Omicron variant was found on 23 November at 2pm in samples from Lancet private laboratories. The samples were taken between 14 November and 16 November, when cases started to spike in Gauteng.

Flags were raised because the virus in these samples produced different results in PCR testing.

An hour later, the network’s scientists met and an urgent message was sent to the Department of Health.

By 24 November, more tests were done and more messages sent to government departments that this variant was “concerning”.

At 8am on Thursday, 25 November, the ministers of health and science met for an urgent briefing. That night, flights from SA and neighbouring countries to the UK were banned by the UK.

“It is not surprising that a new variant has been detected in South Africa,” NICD acting executive director Professor Adrian Puren said. “Although the data are limited, our experts are working overtime … 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.”

Dr Michelle Groome, head of the Division of Public Health Surveillance and Response at the NICD, says that provincial health authorities remain on high alert and are prioritising the sequencing of Covid-19 positive samples.

“Detected cases and percentages testing positive are both increasing quickly, particularly in Gauteng, North West and Limpopo.” She stresses that, regardless of the emergence of new Covid-19 variants, the importance of non-pharmaceutical interventions remains unchanged and members of the public are urged to be responsible.

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

According to De Oliveira, the Omicron variant is “very unusual” and clearly different from other circulating variants of the virus.

Many of the mutations have been “rarely observed until now”, he said, adding that their “full significance remains uncertain”.

The mutations that have been seen before are associated with the virus’s resistance to neutralising antibodies, enhanced transmissibility and increased infectivity.

On Friday, 26 November, the NICD said that at this stage there are no unusual symptoms being associated with the new variant of the virus.

The WHO’s Maria van Kerkhove said not much is known yet about the new variant but the concern was that unknown mutations could have an impact on how the virus behaves.

She said scientists worldwide will study the impact of vaccines on the variant and how it behaves in the coming weeks.

To prevent place names from being used, the WHO gives variants of concern names using letters from the Greek alphabet.

A variant of concern is one that is thought to have a significant impact on public health, such as Delta.

On 25 November, Minister of Health Dr Joe Phaahla said South Africa’s uptake of the vaccine remained low, with fewer than 130,000 people being vaccinated each day. The department was aiming for 300,000 a day. He said it was particularly concerning that the uptake was very low among young people – the age group in which the new variant and outbreak was first identified. DM168

Additional reporting by Ufrieda Ho.

This story first appeared in our weekly Daily Maverick 168 newspaper which is available for R25 at Pick n Pay, Exclusive Books and airport bookstores. For your nearest stockist, please click here.


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