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‘The world is watching South Africa’: medical experts sift through Omicron’s clues

Health officials worldwide are closely monitoring the rapidly rising wave of coronavirus infections in South Africa for clues to explain the dramatic spike. Omicron variant.

While the virus has been detected in countries from the UK to Canada and Hong Kong, South Africa and the neighboring countries where the outbreak was first detected show they are looking for much-needed data on the virus. new variant.

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

Of particular interest are the 50 highly unusual mutations for the virus that could have allowed Omicron to spread more quickly, while also helping it avoid the immune protection provided by vaccines and previous infection. Others have debated the severity of symptoms associated with the new strain of bacteria.

Infections in South Africa have skyrocketed in recent days, driven by a surge in cases in Gauteng province, which includes Johannesburg and Tshwane. According to data from South Africa’s National Institute of Infectious Diseases (NICD), the number of Covid-19 infections has more than tripled in the past week, from less than 4,000 cases in the seven days to November 21 to 13,828. into the next week.

The graph shows that Covid cases are growing faster in South Africa's Gauteng province than in previous waves and hospitalizations are also faster than in previous peaks

Most of them were tagged with Omicron, which thanks to a genetic abnormality could be picked up from a conventional PCR test without sequencing the gene.

But experts insist more actual data are needed on its transmissibility, adding that there is no confirmed evidence of its severity despite anecdotal reports over the weekend that Omicron causes it. milder symptoms.

“There’s a lot we think we know about Omicron. . . South Africa will be the first place where we can test some of our hypotheses,” Pillay added.

Few expected that new infections would continue to increase. By analyzing samples from a wastewater treatment facility in Gauteng, the researchers were able to show that by the middle of this month, traces of the virus detected had almost reached the level found. during the Delta wave crest in July.

The graph shows the level of coronavirus in wastewater in Gauteng province rising to the highest level during the Delta wave

Salim Abdool Kalim, an epidemiologist and former head of South Africa’s ministerial advisory panel on Covid-19, said: “We’ll be getting more cases very quickly, and we’re already seeing the evidence very soon. about this”.

He predicts that regardless of the virulence of the virus, South Africa will “come under pressure on hospitals in the next two weeks”. The number of Covid-related hospitalizations doubled in a week, to 580 in the seven days to November 28, according to the NICD.

At the same time, immunity is thought to be very high in South Africa, with the majority of the population estimated to have been infected with Covid-19 since the pandemic began, based on excess mortality figures, as well as 29 percent of the population has received at least one dose of the vaccine.

Image showing key mutations forming the Covid-19 Omicron variant.  Omicron has 10 times more mutations in the mutant protein than the Delta variant, raising concerns about its transmissibility, symptoms and whether it could evade vaccines more easily.  The graphic shows six points where this strain differs from previous versions of the virus.

Tom Wenseleers, professor of evolutionary biology at the University of Leuven, predicts that Omicron’s R0, the basic reproductive number in a population with no immunity and no containment, is “in the playing field.” of the Delta variant, between 6 and 7.

But he suggests that Omicron’s mutations have given it “extra powers” that allow it to “compete” with Delta. “We can tell from the genetics of the virus and the rapid spread in South Africa that Omicron will cause problems for every country,” he said.

Despite the increase in hospitalizations, some doctors working there expressed hope that Omicron could lead to less serious illness.

“At the moment there does not appear to be any signal of an increase in severity, but it is premature. [In fact]“The proportion of patients with severe illness is quite low and lower than what we have seen in the rest of the pandemic,” said Waasila Jassat, NICD physician and specialist, Waasila Jassat, NICD physician and specialist. , adds that the majority of hospitalized patients have not been vaccinated. .

Elsewhere in South Africa’s health system, “it’s still early days for us as general practitioners,” said Unben Pillay, a physician in private practice in Gauteng, He also noted that he has seen a “very strong increase” in the past 10 days, often with mild flu-like symptoms.

David Stuart, professor of structural biology at the University of Oxford, said, in the best case scenario: “What we all hope for is because there are so many changes to the virus and those changes are close. as will definitely affect the relationship with [receptors in the human body], that omicron can cause less serious illness. “

Other experts cautioned against placing too much faith in an estimate of Omicron’s severity before extensive research on the new strain has been completed. “The anecdotes haven’t raised any red flags, although we don’t know for sure,” said Abdool Karim.

UCL’s Pillay also cautions against reading too much into reports of mild symptoms because of South Africa’s young population and because some of the early outbreaks centered on universities in Pretoria.

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

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

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

Additional reporting by Donato Paolo Mancini in London

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