Omicron: How South African scientists discovered the variant and set off a global chain reactiony

Johannesburg, South Africa CNN — 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. “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. 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 on the diversity in sampled genomes and most estimates land ~mid October, so we believe it’s relatively young.” There was also a sharp increase detected in the viral load of wastewater in the Pretoria area at the very end of October and the beginning of November. Speaking to CNN’s Becky Anderson on Wednesday, Michelle Groome of South Africa’s Institute for Communicable Diseases said: “Our wastewater surveillance actually alerted us as relatively early to these cases in the Pretoria district.” But virologists acknowledge they are dealing with very preliminary information at the moment on the evolution and characteristics of Omicron. But that bulletin also notes that “South Africa, where Omicron was first detected, has experienced a recent sharp increase in the number of cases in multiple provinces, coinciding with the detection of the Omicron variant.” In the past fortnight, South Africa has gone from a weekly average of 290 cases per day to almost 3,800 daily cases.