We entered the laboratory in South Africa that studies the omicron variant 3:03
Johannesburg, South Africa (CNN) -
In early November, Lancet Laboratories laboratory technicians who discovered the omicron variant in South Africa found unusual characteristics in the samples they were testing for the coronavirus.
Basically, a gene was missing in what would be a normal genomic profile of the virus.
The PCR tests missed one of their expected targets, a sign that something had changed in the virus.
A few days later, the same phenomenon was reported at the Lancet Department of Molecular Pathology in Johannesburg.
Lancet pathologist Dr. Allison Glass said the discovery coincided with an increase in positive COVID-19 cases in parts of South Africa.
In Gauteng province, which includes Johannesburg, less than 1% of people tested positive in early November, but this increased to 6% in a fortnight and 16% on December 1.
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The discovery "raised concerns that another increase awaited us," Glass told CNN.
"Our first thought was: here goes our quiet December and the Christmas holidays."
Three weeks later, what South African scientists had found would become known around the world as the omicron variant of the coronavirus.
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Variant cases on the rise in South Africa
The increase in Gauteng did not go unnoticed by the Network for Genomic Surveillance in South Africa (NGS-SA).
Its director, Tulio de Oliveira, called a meeting for November 23.
He told The New Yorker: "A member of our network informed us that a private laboratory, Lancet Laboratories, had submitted six genomes of a highly mutated virus. And, when we looked at the genomes, we were quite concerned because they discovered a flaw in one of the probes in the PCR test. "
The South African Center for Response and Innovation (CERI) rapidly increased sample testing 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 after a devastating wave the delta variant in South Africa."
The origin of the omicron variant is a mystery
Where and when the omicron variant first emerged is still unknown.
There is no identifiable "patient zero," the 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 cannot assess where this originated."
"The first cases were recognized and identified in Botswana and later in South Africa," said Nkengasong.
But he noted: "Identifying a virus, a new strain or a new variant does not mean that it came from there."
"It could well be a consequence of an outbreak, probably in some parts of sub-Saharan Africa, where there is not a lot of genomic surveillance and the vaccination rate is low," Michael Head, lead researcher in the world health in the University of Southampton, in a telephone interview.
Trying to trace the origins of the omicron variant can be futile if it has already 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 of Botswana and South Africa, "the omicron variant probably emerged much earlier than when we realized it, probably in early October."
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Kristian G. Andersen, a virologist at the Andersen Laboratory in California, took a similar view, tweeting: "We can estimate that based on the diversity of genomes sampled and most estimates come in mid-October (with wide uncertainty), so We believe it is relatively young. "
A sharp increase in sewage viral load was also detected in the Pretoria area in late October and early November.
Speaking with CNN's Becky Anderson on Wednesday, Michelle Groome of the Communicable Diseases Institute of South Africa said: "Our sewage surveillance alerted us relatively early to these cases in the Pretoria district."
But virologists acknowledge that they are dealing with very preliminary information at the moment about the evolution and characteristics of omicron.
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Ómicron may have been transmitted through travel
The surge in infections in early November may have laid the groundwork for the many cases now being identified elsewhere.
Most of the international cases tracked by CNN through the end of November involved people who traveled to or from South Africa or from Mozambique, Malawi, Botswana and Namibia.
For example, on November 11, four foreigners leaving Botswana tested positive for coronavirus, tests that would later (on November 24, according to the Botswana Ministry of Health) reveal the Omicron variant.
Also on November 11, a 36-year-old man from Hong Kong came home from a 20-day trip to South Africa, traveling via Qatar.
Two days later, while he was in quarantine, he tested positive.
Genome sequencing confirmed that it is the omicron variant.
Several people who traveled to Europe later infected members of their household, including in Germany and Italy.
A CNN analysis of publicly available data shows that around 90% of omicron infections recorded so far in Europe involved people who had traveled through or from southern Africa.
However, sequencing is quite limited in many countries.
Only a very small percentage of covid tests are subject to sequencing, which takes more time than a simple test.
Current data almost certainly underestimates the spread of the variant.
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Not all roads lead to southern Africa
While some travelers from southern Africa certainly carried the variant, there are other puzzling cases.
One involves a Belgian woman who had traveled to Egypt via Turkey.
He came home on November 11 and tested positive for the variant 10 days later.
Several confirmed cases in Canada are related 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 when he came home 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 attended the same event on November 20.
Scottish Prime Minister Nicola Sturgeon said "the lack of known travel or overseas connection to these cases suggests that there is community transmission of omicron in Scotland."
He 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 clear that no matter how it got to Europe, the omicron variant was on the continent for much of November.
In the Netherlands, the RIVM health institute said it found omicron in samples dating back to November 19 and 23, the first of them more than a week before passengers on a KLM flight arriving from Johannesburg were identified as the first known cases of this variant in the country.
"It is not yet clear whether the people affected [in the previous cases] have also been to southern Africa," RIVM said on Tuesday.
The doubts it leaves in the world
Much remains to be discovered about the new variant of the coronavirus: how quickly it can spread, whether it can evade or weaken existing vaccines, whether it will only result in mild symptoms for the majority of those infected.
For now, the delta variant remains the dominant strain and represents 99.8% of the global sequences uploaded to the GISAID database, according to the latest WHO bulletin.
But that bulletin also notes that "South Africa, where omicron was first detected, has seen a recent sharp increase in the number of cases in several provinces, coinciding with the detection of the omicron variant."
In the last fortnight, South Africa has gone from a weekly average of 290 cases a day to almost 3,800 cases a day.
This Wednesday, the authorities reported 8,561 new cases nationwide.
Authorities said three-quarters of the positive tests sequenced in Gauteng province were omicron.
"Our cases are increasing very rapidly, I think probably at the fastest rate that we have seen since the beginning of the pandemic, but it is not clear if this is due to increased transmissibility of the omicron variant or due to immune escape," he said. Michelle Groome told CNN.
WHO Director General Tedros Adhanom Ghebreyesus said this week that "we still have more questions than answers about the effect of omicron on transmission, the severity of the disease and the efficacy of tests, therapeutics and vaccines." added.
But emerging evidence, albeit preliminary, indicates that omicron has an advantage.
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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