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It turned out that spike-negative samples were surging across South Africa, suggesting that Omicron had a competitive advantage over Delta, which until now had been the dominant variant in the country.

“It gives us concern that this variant may already be circulating quite widely in the country,” Richard Lessells, an infectious disease specialist at the University of KwaZulu-Natal in Durban, South Africa, said at Thursday’s news conference.

Dr. de Oliveira warned that South Africa, where less than one-quarter of the population is fully vaccinated, could see a surge of hospitalizations unless the country prevented Omicron from multiplying further in superspreading events. “We really would like to be wrong on some of these predictions,” he said.

Countries in Europe as well as the United States and Canada have been among those banning flights arriving from South Africa and several other African nations. But Omicron has already been spotted in Hong Kong and Belgium, and may well be in other countries outside of Africa as well.

Theodora Hatziioannou, a virologist at Rockefeller University in New York, said that Omicron’s distinctive mutations raise the possibility that it first evolved inside the body of someone with H.I.V., whose immune systems may have been too weak to quickly fight it off. “Your responses are just not as good,” Dr. Hatziioannou said.

Instead of getting cleared away in a matter of days, the virus may have lingered in that person for months, spending the time gaining the ability to evade antibodies. “This virus has seen a lot of antibodies,” Dr. Hatziioannou said.

Dr. Hatziioannou and her colleagues have been able to produce mutant spike proteins in their laboratory that make viruses highly resistant to Covid-19 antibodies. She said that Omicron has many mutations in the same regions of the spike protein pinpointed in their own research. “The overlap is pretty striking,” she said.