Tackling new variants of coronavirus

A female commuter on her way to work by underground wearing a face mask

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On 20 December 2020, the UK government announced that a new variant of SARS-CoV-2 had been found in the UK.

The new variant, B.1.1.7, transmits more easily than the previous one, and unfortunately early evidence indicates that it may also be linked to increased risk of death.

It came to light in late November 2020 when Public Health England (PHE) was investigating why infection rates in Kent weren’t falling despite lockdown and other restrictions. Backwards tracing using the genetic evidence suggested the variant emerged in September 2020 and circulated at low levels until mid-November.

After PHE’s Kent investigations, a cluster of infections linked to the new variant was found spreading rapidly into London and Essex.

South Africa, Brazil and Japan also have new variants of SARS-CoV-2.

Researchers funded by UK Research and Innovation (UKRI) explain how this is typical virus behaviour, and why we must be vigilant about the new variants.

Is the new variant different?

When a virus infects a cell it begins making copies of itself, and replicates its genetic information.

The COVID-19 virus is encoded in an RNA molecule and, while it does have some ‘proof reading’ enzymes to help it copy correctly, it is prone to error. That’s when mutations and new variants happen.

New variants can behave differently. The UK variant is more transmissible than the original and is affecting a greater proportion of under 20s, according to a report from a collaborative team from:

  • Imperial College London
  • University of Edinburgh
  • PHE
  • Wellcome Sanger Institute
  • University of Birmingham
  • COVID-19 Genomics UK (COG-UK) Consortium.

Dr Erik Volz of Imperial College London, said:

All viruses evolve, and very rarely a virus will change in a way that requires us to re-evaluate public health policy.

We find overwhelming evidence of a change in transmissibility of the B.1.1.7 variant that should be taken into account when planning our COVID-19 response.

Will the virus continue to create new variants?

Yes. Mutations in the virus’s genome occur naturally and some of these will be inconsequential, while others will change how it functions.

The COG-UK Consortium, which was formed in response to the pandemic and co-funded by UKRI, is tracking how the virus mutates.

COG-UK is undertaking random genomic sequencing of positive COVID-19 samples from across the UK, and publishing the data online. It has developed software to automatically analyse genomes for the presence of mutations, to track them over time and how they spread.

Explore the software on the CoV-GLUE website.

This massive sequencing effort has put the UK at the forefront of sequencing the virus, generating more than 165,000 sequences. Pathogen surveillance through genome sequencing is vitally important, particularly so during a global pandemic.

Professor Sharon Peacock, Chair of COG-UK, previously led a similar effort to develop an open-access database of bacterial genome sequence data for tracking MRSA infections. This resource was invaluable for researchers in the field as a tool for future surveillance and outbreak investigations.

Read about the database on The National Archives.

The biggest concern is any change that could lead to an increase in reinfections or vaccine failure. You can read COG-UK’s comments.

The G2P-UK National Virology Consortium

G2P-UK launched in early January 2021 with £2.5 million funding from UKRI. The national research project will study the effects of emerging SARS-CoV-2 mutations and flag the riskiest strains as they arise.

It will study how mutations in the virus affect key outcomes such as:

  • how transmissible it is
  • the severity of COVID-19 it causes
  • the effectiveness of vaccines and treatments.

Find out more about the G2P-UK launch.

New variants and vaccines

The UK variant identified in late 2020 is much more infectious than the original virus, making rapid mass vaccination critical.

Professor Axel Gandy of Imperial College London, said:

Until a very high proportion of the population has been vaccinated, strong social distancing measures are needed to control this more transmissible variant of COVID-19. Everybody that can be vaccinated should be vaccinated.

Dr Meera Chand, Incident Director for COVID-19 at PHE, said:

These new analyses provide further evidence of the increased transmissibility of the novel variant of COVID-19.

We now have two licensed vaccines, but this research underlines the importance of doing everything we can to reduce the spread of the virus while the vaccines are being rolled out. The basics remain very important: comply with social distancing and abide by the restrictions in place.

Will new variants resist the vaccine?

Andrew Pollard from Oxford Vaccine Group, which is partly funded by UKRI, told the British Medical Journal (BMJ) that the virus would have to mutate “quite a lot” for it to render the vaccine ineffective, which is an advantage in the short term.

Pollard told the BMJ:

Mutants can arise that escape from the vaccine when there’s a lot of pressure on the virus to change. At this moment hardly anyone in the world has been vaccinated and hardly anyone in the world has had disease, even though it feels like a huge impact. Most people have not had an infection yet. And so, the virus is not under huge immune selection.

When lots of people have had disease or been vaccinated, the virus is going to come under a lot of pressure, and when that happens some viruses just can’t compete against that immunity.

Will it mutate instead? With this coronavirus we don’t know the answer to that question yet, and that’s why surveillance is going to be critical in the year ahead, to make sure that we’re not in a position where, at the point of population immunity, the virus escapes. And if it does, we need to know that, so that we can redesign the vaccines.

This critical research, funded by the taxpayer through UKRI, builds on decades of investment into genomics research and will inform government decision making on a daily basis.

Listen to the BMJ’s interview with Andrew Pollard.

Last updated: 8 June 2021

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