In early August Gideon Schreiber and a team of virologists at the Weizmann Institute of Science in Israel began playing around with the spike protein of the Sars-CoV-2 virus – the protein that allows the virus to enter our cells – to see if they could predict future mutations that could yield dangerous new variants of Covid-19.
At the time, Schreiber noted with concern that there were a variety of ways in which the spike protein could evolve. If all of these mutations occurred at once, it could yield a variant that was both extremely transmissible and potentially capable of evading some of the body’s immune defences, blunting the efficacy of the vaccines.
Schreiber published the findings in a paper, and thought little more of it. But three months later, his fears have been realised. A variant known as B.1.1.529 – which the World Health Organization named Omicron on Friday – has emerged in South Africa in the last two weeks possessing all of the mutations that Schreiber and his team predicted.
“New variants are the norm,” said Schreiber. “This case is unique, as the variant has many more mutations than what is usually expected. These mutations may increase immune evasion, making it even more problematic. Whether the variant will cause more severe disease is at this stage not known.”
Around the world, teams of virologists are racing to get their hands on Omicron’s genetic sequence, and try to figure out what might happen next. So far, work conducted by Tulio de Oliveira, a bioinformatician who runs gene-sequencing institutions at two South African universities, has revealed that the variant contains more than 30 mutations on its spike protein, compared with the original strain of Sars-CoV-2.
The most concerning of these are mutations that enable it to evade antibodies, either from previous infection with Covid-19, or vaccination. “I’d expect [Omicron] to cause more of a hit on vaccine- and infection-elicited antibody neutralisation than anything we’ve seen so far,” tweeted Professor Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Centre in Seattle.
According to De Oliveira, Omicron already accounts for 75% of the Sars-CoV-2 genomes being tested in South Africa, while it has also been detected in Botswana, Hong Kong and Israel. “It seems to be highly transmissible,” said genomic scientist Yatish Turakhia, an assistant professor of electrical and computer engineering at UC San Diego. “In less than two weeks, it seems to have become the dominant variant in South Africa, surpassing Delta.”
How exactly Omicron emerged remains something of a mystery. Scientists suspect that, like the Beta variant that also emerged in South Africa in 2020, the most plausible explanation is that the virus was able to grow and steadily evolve in the body of an immunocompromised person, probably an untreated HIV/Aids patient. With 8.2 million HIV-infected people, more than anywhere else in the world, South Africa’s fight against Covid-19 has been particularly complicated as these patients struggle to clear the virus, meaning it can linger in their bodies for longer.
But while many virologists were expecting the next major Covid-19 variant to be an extension of Delta, Omicron is completely unrelated. Instead it combines some of the most problematic mutations seen in the Alpha, Beta and Gamma variants, along with some newly acquired ones. For Ravi Gupta, professor of clinical microbiology at the University of Cambridge, who said earlier this month in an interview with the Observer that he was 80% sure a new super variant would emerge, the evidence so far is worrying.
“It’s not a twist on Delta as people were expecting, but a new thing based around mutations we have seen before all mixed into one virus,” he said. “That worries me. It’s had a long time to adapt and clearly has done a good job if we accept the rapid expansion in South Africa. Without concerted international action now, we are in for many more lost lives globally due to this variant.”
Scientists say that travel bans will help slow the spread of Omicron, but stopping it in its tracks is almost impossible. Instead Gupta is calling for testing of all travellers for the novel strain, as well as worldwide S-gene target failure, a form of surveillance that can identify if a new variant is rapidly increasing in prevalence in a particular region.
In the meantime, vaccine manufacturers and scientists are trying to work out just how much Omicron might be able to blunt the protection offered by the existing Covid-19 vaccines. The four cases identified so far in Israel – all individuals who had just returned from African countries – had still been infected despite being double-vaccinated. However, as William Hanage, an epidemiologist at the Harvard TH Chan School of Public Health points out, the more important question is whether it causes severe disease in those it infects.
“Delta is also found in vaccinated people,” he said. “So that’s not special. A lot of the noise about immune evasion is based on what we think we know from the mutations in the spike protein. It will be important to know what sort of disease results from the breakthrough infections and reinfections. However, for the parts of the world where high levels of vaccination are a pipe dream, this could well be serious.”
BioNTech – which released the first authorised Covid-19 vaccine with Pfizer just over a year ago – expects to have laboratory data on how its jab performs against Omicron in two weeks’ time. The company revealed that it took steps earlier this year which mean that, if necessary, it can adapt its vaccine against a new variant within six weeks and begin shipping the new version to countries in 100 days.
For high-income nations such as the UK, which has already begun giving booster jabs to vulnerable members of the population, the impact of Omicron may be less severe. Schreiber says that while the variant might be capable of evading some antibodies from the vaccines, all the available jabs still have many different ways of combating the virus – for example by stimulating T-cell immunity.
Instead, the full impact of the variant is likely to be felt in countries like South Africa, where just 24% of the population is fully vaccinated. It is data from these nations in the coming weeks and months that will reveal the real potency of Omicron.
“It seems to be quite good in immune evasion,” Schreiber said. “This may not be that surprising with the high number of mutations in the spike protein. The more important question is whether it will cause severe disease in vaccinated people. We just don’t know. Moreover, while the variant is spreading fast, it may disappear again, as happened to many other variants. One cannot know at the moment. What is clear is that we should be on alert and careful.”