“This variant did surprise us, it has a big jump in evolution, many more mutations than we expected, especially after a very severe third wave of Delta,” said Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform.

The B1.1.529 variant has a “very unusual constellation of mutations,” with more than 30 mutations in the spike protein alone, Mr. de Oliveira said. On the ACE2 receptor — the protein that helps to create an entry point for the coronavirus to infect human cells — the new variant has 10 mutations. In comparison, the Beta variant has three, the Delta variant has two, said Mr. de Oliveira.

Displaying mutations that might resist neutralization, scientists are also still unclear how effective existing vaccines will be against the new variant. The variant shares similarities with the Lambda and Beta variants, which are associated with an innate evasion of immunity, said Richard Lessells, an infectious diseases specialist at the KwaZulu-Natal Research and Innovation Sequencing Platform.

“All these things are what give us some concern that this variant might have not just enhanced transmissibility, so spread more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system,” Mr. Lessells said.

The new variant has largely been detected among young people, the cohort that also has the lowest vaccination rate in South Africa. Just over a quarter of those ages between 18 and 34 in South Africa are vaccinated, said Dr. Joe Phaahla, the country’s minister of health.

While cases of the new variant are mainly concentrated in the country’s economic hub, particularly in the capital Pretoria, it is “only a matter of time” before the virus spreads across the country as schools close and families prepare to travel for the holiday season, Mr. Phaahla said.

Alexandra E. Petri contributed reporting.