Home / Politics / News /  How Omicron variant rattled the world in one week

JOHANNESBURG : Over coffee at his office on Tuesday, Tulio 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 Sigal, 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 [its] 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. Sigal, 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 Vineet Menachery, 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 to be the threat many experts worry about, its arrival portends a dismal and potentially yearslong 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. Sigal.

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. Sigal 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.

On Nov. 11, the first known samples of what is now Omicron were collected: one in South Africa’s Gauteng province, home to Johannesburg and Pretoria, and four others from a group of foreign diplomats visiting neighboring Botswana.

That same day, a 36-year-old man left South Africa for Hong Kong, a city with some of the strictest quarantine rules on earth. On Nov. 13, while staying in a designated quarantine hotel, he took a test that confirmed him as one of the earliest cases of Omicron.

Five days later, a 62-year old man staying in the room across the corridor also tested positive. He, too, had the variant, and the genomes of the two samples were so close that one had clearly caught the virus from the other, said Yuen Kwok-yung, an infectious diseases professor at the University of Hong Kong who advises the city’s government on their pandemic response.

CCTV monitors, however, showed that the two men had never met, nor opened their doors at the same time, nor shared any items, and had only contacted hotel personnel in full protective gear, said Prof. Yuen. Most likely, air from one of their hotel rooms spread into the hallway and through a door opening, where the other breathed it in, said Prof. Yuen, who inspected the site using a smoke test.

The tentative conclusion for Prof. Yuen, who has inspected several other suspected instances of quarantine-hotel transmission in Hong Kong, was that Omicron is highly transmissible, potentially more than the Delta variant.

Back in South Africa, officials noticed the speed at which infections in Gauteng province were rising. On Nov. 11, the date of the first known Omicron case in South Africa, 120 new infections were detected in Gauteng. Infections were at their lowest since the start of the pandemic. By Sunday, daily new cases in the province had spiked to 2,308. A type of polymerase-chain-reaction, or PCR, test used on those cases showed the same anomaly for nearly all of them: The signal for the S-gene present in the prevalent Delta variant was missing.

And instead of fewer than one in 100 tests coming back positive, now one in five shows a new infection, suggesting that the actual number of people with Covid-19 is much higher.

Tens of thousands in the country likely have been infected with the new variant in the last couple of weeks, according to Prof. de Oliveira, who based that estimate on the high percentage of tests coming back positive and the number showing the same S-gene oddity he relayed to Dr. Sigal.

Prof. de Oliveira said both he and South Africa’s president, Cyril Ramaphosa, knew the likely response to making the new variant public when they concluded their meeting on Thursday: Countries would slam the doors on travelers from South Africa, battering its already bruised economy, especially its tourism. South African families hoping to reunite with loved ones abroad over Christmas would be stuck.

“That’s the risk of being a scientist," Prof. de Oliveira said. “You may be accused of overreacting in the beginning….The pandemic showed us quick action is normally better than delayed action, even if you risk not to be 100% accurate."

The following day, the WHO’s working group for tracking new variants picked up on another cause for concern. An early analysis of cases from the province’s surge of infections showed an unusually high number of people who already had Covid-19 during South Africa’s third wave, said Jinal Bhiman, a principal medical scientist at the National Institute for Communicable Diseases in Johannesburg, and a member of the group. That wave peaked in July and was driven almost exclusively by the Delta variant.

Reinfection risk?

The suggestion—still uncertain—was that recently recovered people might be at risk of a reinfection, she said. “That’s why the WHO really took it seriously," she said.

Later that day, the WHO declared Omicron a “variant of concern." By then, European governments were closing the door to travelers from swaths of Africa. An unvaccinated woman leaving Egypt via Turkey had brought the variant to Belgium and two Cape Town passengers had brought it to Munich. As the hours ticked by, more cases rolled in. Thirteen people aboard two KLM flights arriving in Amsterdam from South Africa turned out to carry Omicron, and results are pending on 48 others who tested positive for Covid-19.

It will take maybe two weeks, scientists say, before they know whether the alarm was warranted.

The first significant clues about what Omicron does to the human body are set to come from where it is now spreading most widely—South Africa’s Gauteng province. Its path there will test how it performs in a mostly unvaccinated country whose case numbers were at their lowest since the start of the pandemic. Just a quarter of the country’s 60 million people are fully vaccinated.

Europe, where 67% are vaccinated, will provide a different test. There, Omicron is landing in the middle of another surge in infections, almost all of them from the Delta variant. A turf war between variants is under way.

“That fantasy that this virus is completely going to be exterminated by vaccines…it was never in the cards," said Jeremy Kamil, a virologist at Louisiana State University Health Shreveport. But “the variants aren’t going to make the pandemic go on forever…It’s just a race to get people vaccinated and lower the number of deaths." he said.



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