With Omicron now detected in more than 50 countries, the world will soon find out whether it will displace Delta
JUST ONE month ago, South Africa’s pandemic appeared to be nearing an end. The country was recording fewer covid-19 cases—and admitting fewer patients to hospitals—than at any point since the beginning of the pandemic. Weekly recorded deaths, from any cause, were down to levels last seen before the pandemic. Tourists were returning. SARS-CoV-2 seemed to be fading into the background to become just another endemic disease.
No longer. Daily diagnosed cases of covid began rising in the middle of November. Shortly thereafter, hospital admissions started to tick up, too. The cause seems clear: Omicron, a mutation first discovered in samples collected on November 8th in South Africa and three days later in neighbouring Botswana. Just how virulent it is remains unclear: some have claimed the variant is less deadly, though evidence of that appears, as yet, inconclusive.
How can Omicron, which has only been confirmed in fewer than 300 cases in South Africa, be responsible for a wave that numbers over 10,000 cases every day? Testing, which has plagued covid data since the pandemic began, remains a problem. Just as covid cases represent only diagnosed infections rather than every infection, “confirmed cases by variant” represent only those patients whose virus. The real number of Omicron infections is thus vastly greater than those confirmed.
Analysing the shifting shares of different variants among sequenced viruses in GISAID, Tom Wenseleers, a professor of biology and biostatistics at KU Leuven, in Belgium, found that Omicron probably overtook Delta in its share of South African cases as early as November 11th. This was just four weeks after the sequencing data suggests the virus started circulating. As of December 7th the total probable number of Omicron cases had reached 88,306.
New variants beat old ones by infecting more people. Omicron is clearly now dominant within South Africa, relative to Delta. Based on the rate at which it overtook Delta, Mr Wenseleers estimates that the reproductive number of the mutation could be three to six times that of Delta. Trevor Bedford, a virologist at the Fred Hutchinson Cancer Research Center in Seattle, puts the most probable reproductive number at three to three-and-a-half, up from around one just before the variant emerged.
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