A new variant of the coronavirus responsible for Covid-19 has been identified in Botswana and South Africa, where it has been linked to a significant increase in new cases. The strain, originally known as B.1.1.529 and later renamed omicron, poses a “very high” risk, according to the World Health Organization, which added it to its list of potentially dangerous variants. Governments around the world have begun to prohibit travelers from South Africa and neighboring countries, fearing that omicron will evade vaccine-induced protection, causing another Covid surge and thwarting efforts to reopen economies.
According to the European Centre for Disease Prevention and Control, the omicron variant of SARS-CoV-2 has 30 or more changes, three small deletions, and one small insertion in the spike protein. The receptor binding domain accounts for half of the changes– the part of the spike protein used to bind to human ACE-2, which is the enzyme the coronavirus targets to enter cells and cause an infection.
Mutations in this region can render the spike protein unrecognizable to antibodies produced in response to vaccination or a natural infection.
At least three mutations have been linked to the virus evading detection by antibodies, according to Vinod Balasubramaniam, a virologist at Monash University’s Jeffrey Cheah School of Medicine & Health Sciences in Malaysia. Another mutation appears to improve the virus’s ability to enter human cells, making it more transmissible, he said. According to the ECDC, Omicron is the most divergent variant detected in large numbers thus far, raising concerns that it may result in increased transmissibility, a significant reduction in vaccine effectiveness, and an increased risk of reinfections. However, researchers do not yet know for certain.
The WHO received the first report on November 24 from South Africa, though the agency stated that the first known confirmed infection was from a specimen collected on November 9. According to the ECDC, it was also discovered on November 11 in Botswana. According to a scientist at the University College London Genetics Institute, it most likely evolved during a chronic infection of an immunocompromised person, possibly in an untreated HIV/AIDS patient. In such a case, a long-term SARS-CoV-2 infection could allow the virus to undergo genetic changes in the patient that are beneficial to the pathogen. South Africa has the most HIV-infected people in the world, with 8.2 million people infected. The beta variant, discovered last year in South Africa, could have come from an HIV-infected person as well.
According to Tulio de Oliveira, a bio-informatics professor who runs gene-sequencing institutions at two universities, early PCR test results showed that 90 percent of the 1,100 new cases reported Nov. 24 in the South African province that includes Johannesburg were caused by the new variant. South Africa’s President Cyril Ramaphosa announced on November 28 that the average daily case count in his country had risen to around 1,600 from 500 the previous week and 275 the week before that.
In less than a week, the proportion of Covid tests that were positive increased from about 2% to 9%. In South Africa, only 36% of adults are fully vaccinated. On Nov. 22, officials in neighboring Botswana recorded four cases in people who were fully vaccinated. A traveler from South Africa was found to have the variant in Hong Kong, and another case was discovered in a person quarantined in a hotel room across the hall.
The United Kingdom has temporarily banned flights from South Africa and several other countries after detecting three Covid cases caused by omicron. Other countries have since followed suit. Singapore is restricting entry for people who have visited South Africa or neighboring countries, and the launch of vaccinated travel lanes with three Middle Eastern hubs has been delayed. The European Union has proposed that member countries suspend air travel from southern Africa. Australia tightened border controls for visitors from southern Africa, while India increased screening of visitors from South Africa, Botswana, and Hong Kong. For the next 14 days, Israel is prohibiting foreign nationals from entering the country.