Omicron is exploding – but scientists are better prepared than for any past variant
It’s beginning to feel a lot like last Christmas. Case numbers of a new Covid variant are exploding across the UK, and the prime minister is cautioning that restrictions may be called for. But while the threat of Omicron likely surpasses that of previous variants, our tools to track and combat the virus have also advanced since last year.
The world was alerted to Omicron by the Botswanan and South African scientists who first sequenced the novel variant on 24 November, and it was designated as a variant of concern by the World Health Organization two days later. It was immediately obvious to them that they had something alarming on their hands when they saw the large number of mutations in the Omicron genome.
More than 20 mutations differentiate Omicron from Delta, the variant that has dominated the pandemic since the summer of 2021. And many of those mutations are in sites that change the way the virus interacts with our immune system or that increase transmissibility.
Those scientists realised the mutations meant the new variant would be likely to infect people who had been vaccinated and might even reinfect people who’d already had Covid-19. And Covid-19 cases were rising rapidly in the Gauteng province of South Africa.
Because of all these mutations, Omicron sits at the end of a long branch in the Covid-19 family tree– like a rather strange-looking cousin who doesn’t seem to fit in with the rest of the family. There are three possible explanations as to where this variant might have come from and how it has managed to accumulate so many mutations while remaining hidden.
It might have evolved in a part of the world that does little virus sequencing – sequencing inequity means that we are missing early opportunities to detect new variants from many places. Or it might have arisen after a human infected an animal population, allowing the virus to mutate in a new environment unmonitored, and then be transmitted back to us.
Or, most likely, the variant may have come from a chronically infected Covid-19 patient with a suppressed immune system – a person living with HIV, for example, or a patient undergoing cancer treatment. Such a situation would allow the virus to accumulate mutations without being challenged by a normal immune response. The Alpha variant that ravaged the UK last Christmas is thought to have evolved within a chronically infected patient.
The first Omicron infection in the UK was reported on 27 November, just a few days after the variant was first identified in Africa. The UK Health Security Agency (UKHSA) and the Covid-19 Genomics UK (Cog-UK) consortium have been tracking Covid-19 genomes since the beginning of the pandemic. A regular PCR test doesn’t read the entire genetic sequence of the virus, so a proportion of all Covid-19 diagnoses are fully sequenced so as to spot worrying mutations and identify variants of concern, allowing us to track how the virus is spreading and evolving, in order to inform policy.
This has served us well throughout the pandemic. As soon as Alpha was identified in December 2020, analyses comparing its spread to previous variants showed it was far more transmissible. It was clear that the restrictions already in place against other variants were insufficient to stall the spread of Alpha, and this finding led to the third national lockdown in January 2021 and a huge drop in daily case numbers.
In March 2021, when the Delta variant was detected in the UK, it had mutations in its genome that scientists suspected would make it far more transmissible than Alpha. Analysis coordinated by the UKHSA through its expert modelling group showed that although Delta was even more transmissible than Alpha, the vaccines were also working well against it. Because of this, the UK changed its vaccine policy, speeding up the delivery of second doses. By the end of June, Delta accounted for nearly all Covid-19 cases in the UK, and while the number of cases increased dramatically, deaths didn’t.
The discovery of Omicron – and the finding that it is able to evade immunity in people with two vaccine doses – also resulted in a change in policy, this time with the acceleration of the booster programme.
The current challenge is trying to determine whether the rapid spread of Omicron is due to the variant being more transmissible in general, or because it is able to infect people who have previously been vaccinated or infected. The balance of these two factors will determine how Omicron will spread in populations that do not have the immunity of South Africa and the UK.Researchers are also trying to gauge how severe Omicron infections are compared to Delta infections, but this will take time as those infected with Omicron this week will not be admitted to hospital for another week or more. These results will enable the UK and other countries to determine the scale and timing of hospital surges, so that we can be better prepared.
Even though this pre-Christmas wave may feel similar to last year, we are in a much better position than 12 months ago. Crucially, we have vaccines that significantly reduce the severity of the disease. While case numbers are unprecedented and rising, vaccinated people are so far experiencing symptoms even milder than in previous waves.
And Omicron was detected much faster than previous variants. We were able to quickly assess its risk based on our growing understanding of the virus’ mutations. Finally, we have streamlined processes to aggregate and analyse data, allowing us to make timely and realistic predictions of the impact of policies.
Previous epidemics (such as polio, measles or the 1918 influenza) have only been studied retrospectively by epidemiologists. During this pandemic we are in a live arms race against the virus, adapting our tools against it in real time as we decode its genome. Nonetheless, it is a battle that cannot be fought solely by scientists, and it remains essential that we continue to deploy all our defences: by getting vaccinated, avoiding closed and crowded spaces, reducing contacts, testing when recommended, and continuing to wear masks.
Dr Manon Ragonnet-Cronin is an MRC Fellow at Imperial College London and a member of the Imperial College Covid-19 response team