England’s health secretary, Matt Hancock, has told parliament that a new variant of covid-19 has been identified and may be driving infections in the south east, leading to headlines about “mutant covid.” Jacqui Wise answers some common questions.
What do we know about this new SARS-CoV-2 variant?
It’s been snappily named VUI-202012/01 (the first “Variant Under Investigation” in December 2020) and is defined by a set of 17 changes or mutations. One of the most significant is an N501Y mutation in the spike protein that the virus uses to bind to the human ACE2 receptor. Changes in this part of spike protein may, in theory, result in the virus becoming more
infectious and spreading more easily between people.
How was the variant detected?
It was picked up by the Covid-19 Genomics UK (COG-UK) consortium, which undertakes random genetic sequencing of positive covid-19 samples around the UK. The consortium is a partnership of the UK’s four public health agencies, as well as the Wellcome Sanger Institute and 12 academic institutions.
Since being set up in April 2020 the consortium has sequenced 140 000 virus genomes from people infected with covid-19. It uses the data to track outbreaks, identify variant viruses, and publish a weekly report.
Why is this variant causing concern?
Three things are coming together that mean it is attracting attention:
- It is rapidly replacing other versions of the virus
- It has mutations that affect part of the virus likely to be important
- Some of those mutations have already been shown in the lab to increase the ability of the virus to infect cells
All of these come together to build a case for a virus that can spread more easily.
However, we do not have absolute certainty. New strains can become more common simply by being in the right place at the right time – such as London, which had only tier two restrictions until recently.
But already the justification for tier four restrictions is in part to reduce the spread of the variant.
“Laboratory experiments are required, but do you want to wait weeks or months [to see the results and take action to limit the spread]? Probably not in these circumstances,” Prof Nick Loman, from the Covid-19 Genomics UK Consortium, told me.
Is the new COVID-19 variant more dangerous?
We don’t know yet. Mutations that make viruses more infectious don’t necessarily make them more dangerous. A number of variants have already been detected in the UK. For example, the D614G variant is believed to have increased the ability of the virus to be transmitted and is now the most common type circulating in the UK, although it doesn’t seem to result in more severe disease.
Public Health England’s laboratory at Porton Down is currently working to find any evidence that the new variant increases or decreases the severity of disease. Susan Hopkins, joint medical adviser for NHS Test and Trace and Public Health England, said, “There is currently no evidence that this strain causes more severe illness, although it is being detected in a wide geography, especially where there are increased cases being detected.”
How much faster is it spreading?
It was first detected in September. In November around a quarter of cases in London were the new variant. This reached nearly two-thirds of cases in mid-December.
You can see how the variant has come to dominate the results of testing in some centres such as the Milton Keynes Lighthouse Laboratory.
MK LHL testing data showing increasing prevalence of H69/V70 variant in positive test data – which is detected incidentally by the commonly used 3-gene PCR test. pic.twitter.com/1U0pVR9Bhs
— Tony Cox (@The_Soup_Dragon) December 19, 2020
For the UK variant:
Outside of the UK, we see very small numbers of sequences in Denmark (a bit hard to see – hidden behind UK circle) & Australia. Their position on the tree indicates that they’re likely exports from the UK.
— Dr Emma Hodcroft (@firefoxx66) December 19, 2020
Switzerland has now banned flights from the UK – following on from an increasing number of other countries.
— Dr Emma Hodcroft (@firefoxx66) December 21, 2020
How far has it spread?
It is thought the variant either emerged in a patient in the UK or has been imported from a country with a lower ability to monitor coronavirus mutations.
The variant can be found across the UK, except Northern Ireland, but it is heavily concentrated in London, the South East and eastern England. Cases elsewhere in the country do not seem to have taken off.
Data from Nextstrain, which has been monitoring the genetic codes of the viral samples around the world, suggest cases in Denmark and Australia have come from the UK. The Netherlands has also reported cases.
Will the vaccine still work?
The new variant has mutations to the spike protein that the three leading vaccines are targeting. However, vaccines produce antibodies against many regions in the spike protein, so it’s unlikely that a single change would make the vaccine less effective.
Over time, as more mutations occur, the vaccine may need to be altered. This happens with seasonal flu, which mutates every year, and the vaccine is adjusted accordingly. The SARS-CoV-2 virus doesn’t mutate as quickly as the flu virus, and the vaccines that have so far proved effective in trials are types that can easily be tweaked if necessary.
Peacock said, “With this variant there is no evidence that it will evade the vaccination or a human immune response. But if there is an instance of vaccine failure or reinfection then that case should be treated as high priority for genetic sequencing.”
What Experts are saying?
Additionally, single mutations will generally have small impacts on polyclonal immune responses and the strong immune response to the mRNA vaccines would suggest that a large antigenic change would be needed to significantly reduce efficacy. 16/18https://t.co/nkDdB0ClEI
— Trevor Bedford (@trvrb) December 19, 2020