B.1.1.529, the ‘Omicron’ SARS-CoV-2 Variant

26th November 2021

Dr Andrew Page is Head of Informatics at the Quadram Institute and leads the genomic surveillance work which has been undertaken by the Quadram Institute and other UK centres since March 2020 for the UK’s National Health Service (NHS) and public health agencies. 

Life comes at you fast in a pandemic. It is barely a year ago that myself and colleagues at the Quadram Institute started paying close attention to a cluster of SARS-CoV-2 cases in the south Norfolk town of Wymondham (pronounced windum).

It was 20th November 2020 that we started focusing on what appeared to be a new lineage or variant of the virus circulating in Norfolk.  Informally, we called it the Wymondham variant, but it became much more widely known as the Alpha variant (which was first identified in Kent). This was the new variant that led to a pre-Christmas surge of COVID-19 cases in 2020 and then the lockdown in January 2021.

Since then, we’ve seen the emergence of the Delta variant (first identified in India) which reached the UK in April 2021 and has come to totally dominate Coronavirus cases in this country. A key part of what we do through genomic sequencing is provide early warning surveillance about potential new variants.

Preparing samples for COVID-19 sequencing in Quadram Institute

To date, at the Quadram Institute, we have sequenced 60,000 genomes and we normally sequence more than 2,000 samples every week. Now we have another new variant to hunt but you can be reassured that the UK has one of the very best scientific systems in the world for doing this.

B.1.1.529 has recently been identified in Botswana and South Africa and given the scale and nature of its mutations we do need to be vigilant for it in the UK. When B.1.1.529 was officially classed as a variant of concern the World Health Organization assigned it a letter from the Greek alphabet, Omicron. NB. For more information about the naming conventions for new variants and how they were developed please read Prof Mark Pallen’s blog.

All RNA viruses mutate. As a virus makes copies of itself, occasionally a random change happens that propagates, sometimes the change or mutation is significant but often it’s not. We can expect a virus to mutate.

With SARS-CoV-2 these mutations normally happen at a rate of around one to two mutations per month and, because of this on-going process, many thousands of mutations have already arisen in the SARS-CoV-2 genome since the virus first emerged in 2019.

The vast majority of the mutations observed in SARS-CoV-2 have no apparent effect on the virus and only a very small minority are likely to be important and change the virus in a significant way (for example, a change in the ability to infect people; cause more severe disease; or make vaccines ineffective.)

But the Omicron variant is concerning because it has a very large number of mutations in the spike protein of the virus, and they could potentially make this new variant more transmissible or reduce the effectiveness of current vaccines.

At the Quadram Institute, we will continue to hunt for new SARS-CoV-2 variants and to give the UK early warning of any emerging threats but, importantly, we can all help protect our communities by getting our vaccinations, limiting contact with other people, and wearing face masks in crowded places.