JOHANNESBURG—Over coffee at his office on Tuesday, Tulip de Oliveira, director of South Africa’s Center for Epidemic Response and Innovation, let a colleague in on a secret.
“There’s something going on,” he told Alex, a virologist growing coronaviruses at a South African laboratory. “They’ve found a variant they’ve never seen before.”
For days, case numbers in the nation had been rising rapidly. Puzzled lab technicians had been getting back Covid-19 tests that were positive, but showing an element was missing on the virus’s telltale spike protein, potentially signaling that the virus had undergone another change. Scientists sequenced the virus’s genome and found more than 50 modifications from the original coronavirus.
On Thursday, Prof. de Oliveira delivered the news to South Africa’s president: A new variant with potentially worrying characteristics was driving infections in the country. That same day, South Africa’s health minister and scientists announced the findings.
One day later, the World Health Organization named the new virus configuration Omicron and declared it a variant of concern. Never before had a variant moved so quickly from first detection to a WHO declaration.
The speedy detection and the rapid response of global health authorities shows how the world’s fight against Covid-19 has evolved. Scientists are now focused on finding new variants. In the case of Omicron, one was beginning to spread in a nation with the resources to identify it—and the political will to announce it to the world.
The ramifications of South Africa’s openness also became apparent. Even though the danger posed by the new variant isn’t yet fully understood, governments in Europe, Asia, the Middle East and the Americas immediately restricted travel from Southern Africa.
Uncertainties aside, investors recognized that Omicron could upend expectations that most of the world is gradually returning to normalcy, sending stocks, oil prices and government-bond yields lower.
The latest turmoil stems from a variant that was unknown to the world last Tuesday, and whose origins and abilities remain a mystery to the scientists studying it. Of particular concern: Omicron has 32 modifications on the part of the virus that the main Covid-19 vaccines target—the spike protein that the virus uses to latch onto human cells.
The next phase of the global coronavirus pandemic now hinges on what those 32 mutations mean. It will take weeks to be sure. The WHO said there was preliminary evidence that Omicron might have advantages over existing variants, pointing to rising case numbers in South Africa. Some of the mutations it has are associated with faster spread.
Mutation questions
Its mutations also might mean Omicron is better at evading the body’s immune defenses, including from vaccines. Some lab experiments conducted by researchers in the U.S. before Omicron was identified cataloged mutations that rendered antibodies less effective. Omicron has some of those, and some unfamiliar ones. But understanding the extent of that antibody resistance will take time.
“What is extremely worrisome is the accumulation of so many mutations,” said Theodora Hatziioannou, a Rockefeller University virologist studying how variants evade antibody protection. “The other worrying thing is that [it's] mutations overlap with the mutations we identified in our system. I don’t know how this thing is going to be anything but resistant.”
Dr. Si gal, working out of a high-security lab in the South African coastal city of Durban, is one of hundreds of scientists around the globe growing the Omicron variant to test how it contends against blood samples from vaccinated and recovered people.
The availability of blood samples from former patients and vaccinated people is fast-tracking some of that work. Experiments using infectious virus or that tease out the effect of individual mutations on its behavior will take more time, but research that looks at the interactions between Omicron’s mutant spike and antibodies should yield some answers on the immune evasion question in as little as a week, said Vineeth, a virologist at the University of Texas Medical Branch.
It is too early to know whether Omicron causes the people who catch it to fall more seriously ill, or whether it leads to milder symptoms. Patients currently infected with the variant will need days or weeks to see how bad their disease becomes.
BioNTech SE, which developed one of the most commonly used Covid-19 vaccines together with Pfizer Inc., and Moderna Inc. have said they are ready to adapt their shots to the new variant if necessary.
Even if Omicron turns out to not be the threat many experts worry about, its arrival portends a dismal and potentially years long challenge. Airlines, investors, hospitals, and heads of government will be forced to keep peering over their shoulder for the next variant in the global health agency’s Greek alphabet-based system. “There’ll be more Greek letters we’ll have to learn,” predicted Dr. Si gal.
So far, the WHO has declared five variants of concern, including Omicron. Alpha, which was first detected in the U.K. and drove surges of infections in Europe and the U.S. this winter, and Delta have proved to be more transmissible. Beta, whose first known case is also from South Africa, weakened the impact of vaccines. Most other variants haven’t caused greater harm or dominated other strains.
In all likelihood, Omicron was developing for more than a year before it cropped up, said Dr. Si gal and others who have studied the genome. Omicron evolved from an older, and now nearly vanished, strain of the coronavirus, known as B.1.1. It probably spent many months lurking in an immunocompromised person—maybe an HIV/AIDS patient—slowly racking up evolutionary advantages.
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