Just a few days later, the same phenomenon was reported at the Lancet Department of Molecular Pathology in Johannesburg.
Dr Allison Glass, a Lancet pathologist, said the finding coincided with an increase in Covid-19 positive cases in parts of South Africa.
In Gauteng province, which includes Johannesburg, less than 1% of people tested positive in early November, but the number rose to 6% within two weeks and to 16% on Wednesday.
The finding “raises concerns that we’re in for another rally,” Glass told CNN. “Our first thoughts were: Our quiet December and the Christmas break will pass.”
Three weeks later, what the South African scientists stumbled across would be known to the world as the Omicron variant of the coronavirus.
CERI quickly upgraded testing samples in Gauteng and found this variant to appear very often. Tulio later observed on Twitter that in less than two weeks, the new variant “dominated all infections following the devastating Delta wave in South Africa.”
The origin of a mystery
It is not clear where or when Omicron appeared. There is no identifiable “Patient Zero”, the first one known to have been infected with this variant.
As the director of the Africa Centers for Disease Control and Prevention, John Nkengasong, told CNN on November 30, “We can’t judge where this is coming from.”
Nkengasong said: “The first cases were recognized and identified in Botswana and then in South Africa. But he points out: “Identifying a virus, a new strain or a new variant doesn’t mean it came from.”
Michael Head, a senior researcher in global health: “It could be the result of an outbreak, possibly in some parts of sub-Saharan Africa, where there is not a large amount of surveillance activity. close genomics and low vaccination rates. at the University of Southampton, told CNN in a phone interview.
Attempting to trace the origin of Omicron may be futile if it has been in circulation for a while.
Trevor Bedford, from the Department of Epidemiology at the University of Washington, said on Twitter that based on genomic analysis from Botswana and South Africa, “the Omicron variant could be present much earlier than we received the information. newspaper, probably in early October”.
Kristian G. Andersen, a virologist at Andersen Laboratories in California, has a similar view, writing on Twitter: “We can estimate that based on the diversity in the sampled genomes and mostly Most land estimates are ~mid-October (with widespread uncertainty), so we believe relatively young.”
There was also a sharp increase detected in the viral load in wastewater in the Pretoria area in late October and early November.
Speaking to CNN’s Becky Anderson on Wednesday, Michelle Groome of South Africa’s Institute of Infectious Diseases said: “Our wastewater monitoring actually alerted us relatively early to these cases in the country. Pretoria district.”
But virologists admit they are dealing with very preliminary information about the evolution and characteristics of Omicrons.
Passed through travel
The surge in infections in early November may have set the stage for more cases now being identified elsewhere. Most of the international cases tracked by CNN through the end of November involve people who have traveled from or through South Africa or from Mozambique, Malawi, Botswana and Namibia.
For example, on November 11, four foreigners leaving Botswana tested positive for coronavirus – a test that later (on November 24, according to the Botswanan Ministry of Health) showed the Omicron variant.
Also on November 11, a 36-year-old man from Hong Kong returned home from a 20-day trip to South Africa, passing through Qatar. Two days later, while in quarantine, he tested positive. Gene sequencing confirmed Omicron.
Some people who had traveled home to Europe subsequently infected members of their families, including in Germany and Italy.
A CNN analysis of publicly available data shows that about 90% of Omicron infections so far recorded in Europe involve individuals who have traveled through or from southern Africa.
However, sequencing in many countries is still quite limited. Only a very small percentage of Covid tests require sequencing, which takes longer than a simple test. Current data almost certainly underestimate the spread of variation.
Not all roads lead to southern Africa
While some travelers from southern Africa certainly carry this variant, there are other puzzling cases. One involved a Belgian woman who had come to Egypt via Turkey. She arrived home on 11 November – and tested positive for this variant 10 days later.
None of the nine cases reported in Scotland as of 30 November had travel history and all had attended the same event on 20 November Scotland First Minister Nicola Sturgeon says that “the lack of any travel or foreign connection to these cases suggests that there is a community of transmission of Omicron in Scotland.”
She also said it was unlikely the cases were the result of the COP26 climate change conference being held in Glasgow from 31 October to 12 November.
Now it is clear that, however it reached Europe, Omicron was on the continent for most of November. In the Netherlands, the medical institute RIVM said it had found Omicron in samples dating from the date November 19 and 23 – the earliest samples of which more than a week before passengers on a KLM flight arriving from Johannesburg were identified as the first known case of Omicron in the country. .
“It is still unknown who is involved [in the earlier cases] also went to southern Africa,” RIVM said on Tuesday.
There’s still a lot to discover about the new coronavirus variant – how quickly it can spread, whether it can evade or render existing vaccines ineffective, whether it can only be cause mild symptoms for most people who are infected or not.
For now, the Delta variant remains the dominant strain, accounting for 99.8% of global sequences uploaded to the GISAID database, according to the latest WHO bulletin.
But that bulletin also noted that “South Africa, where Omicron was first detected, has seen a recent sharp increase in the number of cases in many provinces, coinciding with the discovery of the Omicron variant. “
Over the past two weeks, South Africa has grown from a weekly average of 290 cases per day to nearly 3,800 daily. On Wednesday, authorities reported 8,561 new cases nationwide. Authorities said three-quarters of the positive tests sequenced in Gauteng province were Omicrons.
“Our cases are growing very rapidly, I think perhaps at the fastest rate we’ve seen since the beginning of the pandemic, but it’s not clear if this is due to an increase in transmission. of the omicron variant or due to an escape from the immune system,” said Michelle Groome. CNN.
“We still have more questions than answers about Omicron’s impact on transmission, disease severity, and effectiveness,” said Tedros Adhanom Ghebreyesus, WHO Director-General, this week. of tests, treatments and vaccines”.
But emerging evidence – although preliminary – indicates that Omicron is off to a good start. The world is still embracing a new variant of the coronavirus that has 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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