New COVID variant with ‘unusual constellation’ of mutations is already more dominant than Delta in South Africa

November 26, 2021, 6:31 AM UTC

South African scientists have discovered a new COVID-19 variantt Omicron that may be more transmissible and more capable of evading vaccines due to its high number of mutations, sparking concern that it could spread rapidly throughout the country and world.

Currently identified as the B.1.1.529 variant, the new strain has a “very unusual constellation” of new mutations, Tulio de Oliveira, director of South Africa’s Centre of Epidemic Response and Innovation, said during a Thursday media briefing.

B.1.1.529 has more mutations to the “spike protein” than past variants, meaning that it could hamper the body’s immune response and spread more easily. The variant has 50 mutations overall and 32 in the spike protein, the vehicle by which the virus penetrates the body’s cells and the key target of the majority of vaccines. The highly contagious Delta strain, by contrast, had several mutations in its spike protein structure that make Delta particularly adept at allowing latching onto its host, more so than previous strains.

The Delta strain’s receptor binding domain (RBI)—where the virus first makes contact and binds to the body’s cells—had two mutations; compared to B.1.1.529’s ten RBI mutations.

News of the new variant roiled markets in Asia on Friday, with “investors spooked by… B.1.1.529,” wrote Jeffrey Halley, senior market analyst for Asia Pacific at FX data provider OANDA. In morning trading in Asia, the Nikkei plunged 2.75% while South Korea’s Kospi dropped 1.10%. Hong Kong’s Hang Seng dipped 2.15%, hit by fears over the new variant and ongoing China property sector woes. Mainland China fared slightly better with the Shanghai Composite and the CSI 300 down 0.45% and 0.35%. Dow futures dropped 400 points in overnight trading. U.S. markets were closed on Thursday for the Thanksgiving holiday.

De Oliveira wrote on Twitter yesterday that “B.1.1.529 seems to spread very quick! In less than two weeks, [it] now dominates all infections following a devastating Delta wave in South Africa.” In the past week, South African virologists have identified almost 100 cases in the country to-date, with most infections clustered in the Gauteng province, one of the nation’s wealthiest and most economically vibrant regions.

Scientists and health officials acknowledged that little is currently known about the new variant. But its “export to Asia implies that this might be more widespread than sequences alone would imply,” wrote Thomas Peacock, a virologist at Imperial College London, on Github.

The new variant has been detected in vaccinated people in Botswana, South Africa’s neighbor to the north, and in Hong Kong. On Thursday, Hong Kong’s Centre for Health Protection announced that two B.1.1.529 infections were found in two men undergoing hotel quarantine in the city. One man had flown into Hong Kong from South Africa on Nov. 11 and likely spread the virus via airborne transmission to the second man, who was in the room across the hall, the health agency said. Mandatory testing is a component of Hong Kong’s strict quarantine rules that require all arrivals to isolate in designated hotels for as long as three weeks.

The World Health Organization (WHO) announced on Thursday that it will hold a special meeting on Friday to discuss what B.1.1.529 will mean for vaccines, treatments, and diagnostics, according to Dr. Maria Van Kerhove, the WHO’s COVID-19 technical lead and an infectious disease epidemiologist.

Van Kerhove said that monitoring is underway, with researchers working together to “understand what these mutations are,” but that it will take at least a few weeks to determine the variant’s mutations on vaccine efficacy and virus transmissibility.

The organization’s working group on Friday will also discuss if the new variant should be classified as a variant of interest or concern; if it’s designated as such, the WHO will give it a Greek name, likely ‘Nu.’

Some countries are already enacting new restrictions on travelers from South Africa and neighboring countries due to the new variant.

The U.K. has suspended flights from six African countries—South Africa, Botswana, Eswatini, Lesotho, Namibia and Zimbabwe—starting Friday. The six nations have also been added to England’s travel “red list,” meaning that U.K. citizens arriving home from the countries will be required to undergo a 10-day hotel quarantine. Singapore likewise banned travelers from those six countries—plus Mozambique—on Friday over variant fears.

Australia announced on Friday that it’s investigating B.1.1.529 and could close its borders to the African nation. Australia health minister Greg Hunt said that the country “won’t hesitate” to respond if the WHO classifies it as a major new variant, whether that means closing borders or enforcing quarantine.

The discovery of the new variant coincides with a renewed surge in COVID-19 infections in Europe. In Germany, COVID-19 deaths have now surpassed 100,000, including 351 fatalities in 24 hours on Thursday. Germany’s health system is stretched thin as cases skyrocket and intensive care units fill up.

In South Africa, around 40% of adults are fully vaccinated, and the country has battled three severe COVID-19 waves since the pandemic began. De Oliveira said that the country’s health system will face pressure in the following days and weeks; and encouraged the public to avoid super spreader events.

Yesterday on Twitter, he also called on billionaires and financial organizations to “support Africa and South Africa to control and extinguish variants! By protecting its poor and oppressed population we will protect the world.”

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