In the early days of November, laboratory technicians at Lancet Laboratories in Pretoria, South Africa, found unusual features in samples they were testing for the coronavirus.
Essentially, a gene was missing in what would be a normal genome profile of the virus. PCR tests weren’t detecting one of their expected targets, a signal that something about the virus had changed.
Just a few days later, the same phenomenon was reported at Lancet’s Molecular Pathology Department in Johannesburg.
Dr. Allison Glass, a pathologist with Lancet, said the discovery coincided with an increase in positive cases of Covid-19 in parts of South Africa.
In the province of Gauteng, which includes Johannesburg, fewer than 1% of people were testing positive at the start of November, but this rose to 6% within a fortnight and to 16% by Wednesday.
The discovery “raised concerns that we were in for another surge,” Glass told CNN. “Our first thought was: There goes our quiet December and a Christmas break.”
Three weeks later, what the South African scientists had stumbled across would be known worldwide as the Omicron variant of the coronavirus.
The spike in Gauteng didn’t go unnoticed at the Network for Genomics Surveillance in South Africa (NGS-SA). Its director, Tulio de Oliveira, called a meeting for November 23. He told the New Yorker: “We heard from one member in our network that a private lab, Lancet Laboratories, had sent in six genomes of a very mutated virus. And, when we looked at the genomes, we got quite worried because they discovered a failure of one of the probes in the P.C.R. testing.”
CERI rapidly upscaled testing of samples in Gauteng and found the variant appearing very frequently. Tulio later observed on Twitter that in less than two weeks the new variant “dominates all infections following a devastating Delta wave in South Africa.”
Origin a mystery
Just where and when Omicron first emerged is still unknown. There is no identifiable “Patient Zero,” a first person known to have been infected with the variant.
As the director of the Africa Centres for Disease Control and Prevention, John Nkengasong, told CNN on November 30, “We just cannot assess where this originated.”
“The first cases were recognized and identified in Botswana and subsequently in South Africa,” Nkengasong said. But he pointed out: “Identifying a virus, a new strain or a new variant doesn’t mean it came from there.”
“It might well be a consequence of an outbreak, probably in some parts of sub-Saharan Africa, where there’s not a huge amount of genomic surveillance going on and the vaccination rate is low,” Michael Head, a senior research fellow in global health at the University of Southampton, told CNN in a phone interview.
Trying to trace Omicron’s origins may 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 from Botswana and South Africa, “the Omicron variant likely arose much earlier than when it came to our notice, probably in early October.”
Kristian G. Andersen, a virologist at the Andersen Lab in California, took a similar view, tweeting: “We can estimate that based