Omicron is already dominant in South Africa


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ONLY A MONTH AGO, the pandemic in South Africa appeared to be nearing its end. The country recorded fewer Covid-19 cases – and admitted fewer patients to hospitals than it has ever done since the pandemic began. The deaths recorded weekly, whatever the cause, had returned to levels last seen before the pandemic. Tourists came back. SARS-CoV-2 seemed to be fading into the background and becoming just another endemic disease.

No longer. In mid-November, daily diagnosed cases of Covid began to rise. Shortly thereafter, hospital admissions began to rise too. The cause seems clear: Omicron, a mutation first discovered in samples collected on November 8 in South Africa and three days later in neighboring Botswana. How virulent it is remains unclear: some have claimed the variant is less fatal, although the evidence is still inconclusive.

How can Omicron, which has only been confirmed in fewer than 300 cases in South Africa, be responsible for a wave of over 10,000 cases a day? The tests that have plagued Covid data since the beginning of the pandemic remain a problem. Just as Covid cases only represent diagnosed infections and not every infection, “confirmed cases by variant” only represent those patients whose virus samples have been sequenced. The actual number of Omicron infections is thus far higher than the confirmed number. Since November 26th, not a single sample collected in South Africa and sent to GISAID, an initiative for data exchange for corona and influenza virus sequences, contains the previously dominant Delta variant. All were Omicron.

Tom Wenseleers, Professor of Biology and Biostatistics at the KU Leuven in Belgium, analyzed the changing proportions of different variants among sequenced viruses in GISAID and found that Omicron Delta probably already overtook Delta on November 11 in the proportion of South African cases. This was just four weeks after sequencing data suggested the virus began to circulate. By December 7th, the total probable number of Omicron cases had reached 88,306. In previous waves, modeling by Imperial College London has shown that confirmed cases represent around one in ten infections in South Africa. This suggests that Omicron infections do not go into the hundreds overall, but into the hundreds of thousands.

New variants beat old ones by infecting more people. Omicron is now clearly dominant within South Africa compared to Delta. Based on the speed at which it has overtaken Delta, Mr. Wenseleers estimates that the mutation’s reproductive number could be three to six times higher than Delta’s. Trevor Bedford, a virologist at the Fred Hutchinson Cancer Research Center in Seattle, estimates the most likely reproductive number to be three to three and a half, up from about one just before the variant appeared. However, some SARS-CoV-2 mutations appear to have a limited benefit in a specific context. The alpha variant first discovered in the UK never caught on in southern Africa, just as beta, which was first discovered in South Africa, never became dominant outside the region, according to sequencing data from GISAID (although it temporarily caught on in the Philippines). . Delta, on the other hand, became dominant everywhere.

With Omicron now discovered in more than 50 countries, the world will soon find out if it will displace Delta elsewhere as well. The evidence available so far seems to suggest that it will. In the UK and several other countries, Omicron is already responsible for more than 0.2% of cases by variant. â– 

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