The world was caught by surprise Friday and raced to contain a new coronavirus variant discovered by South African health authorities.
A World Health Organization panel named the newly identified coronavirus variant, B.1.1.529, as Omicron and classified it as a highly transmissible virus of concern, the same category that includes the predominant delta variant.
The B.1.1.529 variant has 32 mutations in the spike protein, the part of the virus that most vaccines use to prime the immune system against Covid. Mutations in the spike protein can affect the virus’s ability to infect cells and spread, but also make it harder for immune cells to attack the pathogen.
Prof Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation in South Africa, said there was an “unusual constellation of mutations” and that it was “very different” to other variants that have circulated.
“This variant did surprise us, it has a big jump on evolution [and] many more mutations that we expected,” he said.
There was no immediate indication whether the variant causes more severe disease. But early evidence suggests it carries an increased risk of reinfection compared with other highly transmissible variants, the WHO said. Meaning people who contracted COVID-19 and recovered could be subject to catching it again. It could take weeks to know if current vaccines are less effective against it.
This level of mutation has most likely come from a single patient who was unable to beat the virus.
Dr Tom Peacock, a virologist at Imperial College London, posted details of the new variant on a genome-sharing website, noting that the “incredibly high amount of spike mutations suggest this could be of real concern”.
In a thread on twitter, Peacock said it “very, very much should be monitored due to that horrific spike profile”, but added that it may turn out to be an “odd cluster” that is not very transmissible. “I hope that’s the case,” he wrote.
The first cases of the variant were collected in Botswana on 11 November, and the earliest in South Africa was recorded three days later. The case found in Hong Kong was a 36-year-old man who had a negative PCR test before flying from Hong Kong to South Africa, where he stayed from 22 October to 11 November. He tested negative on his return to Hong Kong, but tested positive on 13 November while in quarantine. Israel and Belgium have also reported cases.
There have been many examples of variants that have seemed scary on paper, but came to nothing. The Beta variant was at the top of people’s concerns at the beginning of the year because it was the best at escaping the immune system. But in the end it was the faster-spreading Delta that took over the world.
Ravi Gupta, a professor of clinical microbiology at Cambridge University, said: “Beta was all immune escape and nothing else, Delta had infectivity and modest immune escape, this potentially has both to high degrees.”
He added that work in his lab found that two of the mutations on B.1.1.529 increased infectivity and reduced antibody recognition. “It does certainly look a significant concern based on the mutations present. However, a key property of the virus that is unknown is its infectiousness, as that is what appears to have primarily driven the Delta variant. Immune escape is only part of the picture of what may happen.”
Prof Francois Balloux, the director of the UCL Genetics Institute, said the large number of mutations in the variant apparently accumulated in a “single burst”, suggesting it may have evolved during a chronic infection in a person with a weakened immune system, possibly an untreated HIV/Aids patient.
“I would definitely expect it to be poorly recognised by neutralising antibodies relative to Alpha or Delta,” he said. “It is difficult to predict how transmissible it may be at this stage. For the time being it should be closely monitored and analysed, but there is no reason to get overly concerned unless it starts going up in frequency in the near future.”
Britain, EU countries and some others introduced their travel restrictions Friday, some within hours of learning of the variant.
Some experts said the variant’s emergence illustrated how rich countries’ hoarding of vaccines threatens to prolong the pandemic.
As reported by The Associated press, fewer than 6% of people in Africa have been fully immunized against COVID-19, and millions of health workers and vulnerable populations have yet to receive a single dose. Those conditions can speed up spread of the virus, offering more opportunities for it to evolve into a dangerous variant.
“This is one of the consequences of the inequity in vaccine rollouts and why the grabbing of surplus vaccines by richer countries will inevitably rebound on us all at some point,” said Michael Head, a senior research fellow in global health at Britain’s University of Southampton. He urged Group of 20 leaders “to go beyond vague promises and actually deliver on their commitments to share doses.”