Friday, January 7 2022

Health officials around the world are closely following the growing wave of coronavirus infections in South Africa looking for clues to explain the highly mutated Omicron variant.

While the strain has been detected in countries ranging from the UK to Canada and Hong Kong, it is in South Africa and its neighbors where the outbreak was first detected that they are looking for much needed data. on the new variant.

“The world is watching South Africa,” said Deenan Pillay, professor of virology at University College London.

Of particular concern is that the virus’s 50 highly unusual mutations may allow Omicron to spread faster, while also helping it evade the immune protection provided by vaccines and past infections. Others have debated the severity of symptoms associated with the new strain.

Infections in South Africa have jumped in recent days, driven by an increase in cases in Gauteng province, which includes the cities of Johannesburg and Tshwane. Covid-19 cases have more than tripled in the past week, from less than 4,000 in seven days as of November 21 to 13,828 the following week, according to data from the South African National Institute of Communicable Diseases (NICD).

Most of them have been linked to Omicron, which, thanks to a genetic quirk, can be detected from regular PCR tests without the need for genomic sequencing.

But experts insisted more real-world data was needed on transmissibility, adding that there was no confirmed evidence yet of its severity despite anecdotal reports over the weekend that Omicron produced milder disease symptoms.

“There is a lot we don’t know about Omicron. Real-world clinical data from South Africa will give us some of the early answers, ”added Pillay.

Few people doubt that new infections will continue to increase. By analyzing samples from a wastewater treatment facility in Gauteng, researchers were able to show that by mid-this month, traces of the virus detected had almost reached levels found before the peak of the Delta wave in July.

Graph showing coronavirus levels in Gauteng province wastewater are climbing to peak during the delta wave

Salim Abdool Karim, epidemiologist and former head of the South African Ministerial Advisory Committee on Covid, said: “We are going to get more cases quickly, and we are already seeing the first evidence. ”

He predicted that no matter how virulent the strain, South Africa “would see pressure on hospitals over the next two weeks.” Covid-related hospital admissions in Gauteng province have already doubled in one week, to 580 in seven days through November 28, according to the NICD.

At the same time, immunity is said to be at a very high level in South Africa, with the vast majority of the population estimated to have been infected with Covid since the start of the pandemic, based on excessive death figures, as well as 29% of the population having received at least one dose of vaccine.

Graphic showing the key mutations that shape the Omicron variant

Tom Wenseleers, professor of evolutionary biology at the University of Louvain in Belgium, predicted that Omicron’s R0, the basic reproduction number in a population without immunity and without containment measures, was “in the stage” of Delta variant, between 6 and Sept.

But he suggested that Omicron’s mutations gave him “extra strength” that would allow him to “outdo” Delta. “We can say from the genetics of the virus and the rapid spread in South Africa that Omicron will be a problem for all countries,” he said.

Despite the increase in hospital admissions, some doctors working in the field have expressed hope that Omicron may lead to less severe illness.

“There doesn’t seem to be any sign of increased severity at this time, but it’s early. [In fact], the proportion of patients admitted with severe illness is quite low and lower than what we have seen in the rest of the pandemic, ”said Waasila Jassat, physician and NICD specialist, adding that the vast majority of admissions had not been vaccinated.

Elsewhere in the South African health system, “it is still early days for us as general practitioners,” said Unben Pillay, a private practitioner from Gauteng, while noting that he had detected a “very large increase” in cases. in the past 10 days, often with mild flu-like symptoms.

David Stuart, professor of structural biology at the University of Oxford, said: ‘What we are all hoping for is because there are so many changes in the virus, and those changes will almost certainly affect the affinity with [receptors in the human body], that Omicron may cause somewhat less serious illness.

Other experts urged caution not to place too much faith in Omicron’s estimate of severity until extensive research into the new strain is completed. “The anecdotes do not raise red flags yet, although we are not sure,” said Abdool Karim.

Pillay of UCL also warned against over-reading reports of mild symptoms due to South Africa’s young population and the fact that some of the early outbreaks focused on universities in Pretoria.

Meanwhile, scientists studying the new variant are grateful for South Africa’s transparency and scientific expertise.

“They’re way ahead of us on the epidemic curve and we’ll learn a lot from what’s going on there,” Stuart said.

“South Africa was extremely open and made all the information [on Omicron] available to the global community in a timely manner. For that, we should be extremely grateful, ”he added.

Additional reporting by Donato Paolo Mancini in London

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