Omicron: How South African scientists discovered the variant and sparked a global chain reaction

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A few days later, the same phenomenon was reported to the Lancet’s Department of Molecular Pathology in Johannesburg.

Lancet pathologist Dr Allison Glass said the discovery coincided with an increase in positive cases of Covid-19 in parts of South Africa.

In Gauteng province, which includes Johannesburg, less than 1% of people tested positive in early November, but this figure rose to 6% in two weeks and to 16% on Wednesday.

The discovery “raised fears of another wave,” Glass told CNN. “Our first thought was: Here is our December calm and the Christmas holidays.”

Three weeks later, what South African scientists had stumbled upon would be known around the world as the Omicron variant of the coronavirus.

The Gauteng spike did not go unnoticed by the Network for Genomics Surveillance in South Africa (NGS-SA). Its director, Tulio de Oliveira, called a meeting for November 23. He tell the New Yorker: “We learned from a member of our network that a private laboratory, Lancet Laboratories, had sent six genomes of a highly mutated virus. probes in PCR tests. ”

CERI quickly stepped up testing of samples in Gauteng and found that the variant appeared very frequently. Tulio then observed on Twitter that in less than two weeks, the new variant “dominates all infections following a devastating Delta wave in South Africa”.

People line up for Covid-19 tests at Lancet Laboratories in Johannesburg, South Africa on Tuesday.

Origin a mystery

It is still unclear where and when Omicron first emerged. There is no identifiable “Patient Zero”, a first person known to have been infected with the variant.

As the director of the African Centers for Disease Control and Prevention, John Nkengasong, told CNN on November 30: “We just cannot assess where this is coming from.”

“The first cases were recognized and identified in Botswana and then in South Africa,” Nkengasong said. But he stressed: “Identifying a virus, a new strain or a new variant does not mean it comes from there.”

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“This could well be the consequence of an epidemic, probably in parts of sub-Saharan Africa, where there is not a lot of genomic surveillance going on and the vaccination rate is low,” Michael Head, senior researcher in global health at the University of Southampton, told CNN in a telephone interview.

Trying to trace the origins of Omicron may be futile if it has already been in circulation for some time.

Trevor Bedford, of the Department of Epidemiology at the University of Washington, said on Twitter that, based on genomic analyzes from Botswana and South Africa, “the Omicron variant probably appeared much earlier than our opinion, probably at the beginning of October “.

Kristian G. Andersen, a virologist at Andersen Lab in California, took a similar point of view, tweeting: “We can estimate this based on the diversity of the genomes sampled and most estimates land ~ mid-October (with a large uncertainty), so we think it’s relatively young. “

A sharp increase in the viral load of wastewater was also detected in the Pretoria region at the very end of October and the beginning of November.

Speaking to CNN’s Becky Anderson on Wednesday, Michelle Groome of the South African Institute of Communicable Diseases said: “Our sewage surveillance actually alerted us quite early to these cases in the Pretoria district.”

But virologists admit that they are currently dealing with very preliminary information on the evolution and characteristics of Omicron.

Transmitted by trip

The surge in infections in early November may have paved the way for the many cases now identified elsewhere. Most of the international cases followed by CNN through the end of November involved people who had traveled to or via South Africa or from Mozambique, Malawi, Botswana and Namibia.

For example, on November 11, four foreigners leaving Botswana tested positive for the coronavirus – tests which later (on November 24, according to the Botswana Ministry of Health) would reveal the Omicron variant.

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Also on November 11, a 36-year-old Hong Kong man returned home after a 20-day trip to South Africa, via Qatar. Two days later, while in quarantine, he tested positive. Genome sequencing confirmed Omicron.

Several people who traveled to their homes in Europe then infected members of their households, notably in Germany and Italy.

CNN’s analysis of publicly available data shows that around 90% of Omicron infections recorded in Europe so far have been in people who have traveled through or from southern Africa.

However, sequencing in many countries is quite limited. Only a very small percentage of Covid tests go through sequencing, which takes longer than a simple test. Current data almost certainly underestimates the spread of the variant.

Not all roads lead to southern Africa

While some travelers from southern Africa certainly wore the variant, there are other puzzling cases. One concerns a Belgian woman who had traveled to Egypt via Turkey. She arrived home on November 11 and tested positive for the variant 10 days later.

Several confirmed cases in Canada are linked to travelers from Nigeria. The case identified in Saudi Arabia on December 1 was that of a traveler from North Africa. And an Israeli doctor tested positive on his return from a conference in London. He had not been to South Africa.

None of the nine cases reported in Scotland as of November 30 had a travel history, and all had witnessed the same event on November 20. is the community transmission of Omicron in Scotland. “

She also said the cases were unlikely to be the result of the COP26 climate change conference held in Glasgow from October 31 to November 12.

It is now becoming clear that regardless of how it reached Europe, Omicron was on the continent for much of November. In the Netherlands, the RIVM health institute said it found Omicron in samples dating from November 19 and 23 – the oldest of them more than a week before passengers on a KLM flight arriving from Johannesburg could only be identified as the first known Omicron cases in the country. .

“It is not yet clear whether the people concerned [in the earlier cases] have also been to southern Africa, ”RIVM said on Tuesday.

Netherlands claims Omicron variant was already in country earlier than previously thought

There is still so much to discover about the new variant of the coronavirus – how quickly it can spread, whether it can escape or blunt existing vaccines, whether it will only cause mild symptoms for the majority of those infected.

For now, the Delta variant remains the dominant strain, accounting for 99.8% of the global sequences uploaded to the GISAID database, according to the latest WHO bulletin.

But this bulletin also notes that “South Africa, where Omicron was first detected, has recently seen a sharp increase in the number of cases in several provinces, coinciding with the detection of the Omicron variant”.

Over the past 15 weeks, South Africa has grown from a weekly average of 290 cases per day to almost 3,800 cases per day. Authorities reported 8,561 new cases nationwide on Wednesday. Authorities said three-quarters of the positive tests sequenced in Gauteng province were Omicron.

“Our cases are increasing very rapidly, I am thinking probably of the fastest rate we have seen since the start of the pandemic, but it is not known whether this is due to increased transmissibility of the omicron variant or to an immune breakout,” Michelle Groome said. CNN.

WHO Director-General Tedros Adhanom Ghebreyesus said this week that “We still have more questions than answers about Omicron’s effect on transmission, disease severity and testing effectiveness, therapies and vaccines, ”he added.

But emerging evidence – albeit preliminary – indicates that Omicron is ahead of the game. The world is still grappling with a new variant of the coronavirus that has already spread to nearly thirty countries on four continents.

CNN’s Ghazi Balkiz contributed to this report from Johannesburg and Zeena Saifi from Abu Dhabi.


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