A new variant of the coronavirus has been blamed for the rapid spread, with strict level four mixing rules introduced for millions of people, tighter restrictions on mixing in England, Scotland and Wales at Christmas, and other countries banning travel to the UK.
In other words, within a few months, how did the virus go from being nonexistent to being the most common form of the virus in parts of England?
New infection advisers to the government are “moderately” confident that it is more transmissible than other variants.
The whole work is at an early stage, includes large uncertainties and a long list of unanswered questions.
But as I’ve written before, variants of viruses mutate all the time, and it is important to have a laser focus on whether the behavior of the virus is changing.
So why is this variant of concern?
Three things come together that mean it gets attention:
-It is rapidly displacing other versions of the virus
-It has mutations that affect parts of the virus that are likely to be important.
-Some of these mutations have already been shown in the lab to increase the virus’ ability to infect cells.
All of this, taken together, argues for a virus that can spread more easily.
We do not have absolute certainty, however. New strains can spread simply by being in the right place at the right time – such as in London, where until recently there were only tier two restrictions.
However, the very rationale for tier four restrictions is in part to reduce the spread of the variant.
“Laboratory experiments are necessary, but do you want to wait weeks or months [to see the results and take action to limit the spread]? Probably not under these circumstances,” Professor Nick Loman of the Covid-19 Genomics UK Consortium told me.
How fast is it spreading?
Disease was first detected in September. In November, approximately one-quarter of cases in London had the new variant. By mid-December, nearly two-thirds of cases had it.
At some centers, like the Milton Keynes Lighthouse Laboratory, it is possible to see how the variant dominates test results.
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
Using the spread of different variants, mathematicians have calculated how big a head start this variant might have.
However, it is hard to distinguish between what is attributable to human behavior and what is attributable to the virus.
The number Prime Minister Boris Johnson mentioned was that the variant could be up to 70% more transmissible. What he said was that this could increase the R-number – which indicates whether an epidemic is growing or shrinking – by 0.4.
About that 70% figure surfaced in a presentation Friday by Dr. Erik Volz of Imperial College London.
During the presentation, he said, “It’s really too early to tell…. but from what we see so far, it’s growing very fast, growing faster than [a previous variant]ever grew, but it’s important to keep that in mind.”
He said there is no “nailed down” number for how much more contagious the variant may be. Scientists whose work is not yet public have given me numbers that are both much higher and much lower than 70%.
Yet questions remain as to whether it is more infectious at all.
“The amount of evidence in the public domain is totally insufficient to draw strong or firm opinions about whether the virus has really increased transmission,” Professor Jonathan Ball, a virologist at the University of Nottingham, told.
How far has it spread?
It’ s thought that the variant either emerged in a patient in the U.K. or was imported from a country that is less able to monitor mutations in coronavirus.
While the variant occurs throughout the United Kingdom, with the exception of Northern Ireland, it is highly concentrated in London, the southeast, and the east of England. Cases in other parts of the country do not appear to be emerging.
However, data from Nextstrain, which monitors the genetic codes of virus samples around the world, suggest that cases in Denmark and Australia originated in the United Kingdom. The Netherlands has also reported cases.
Is the new UK variant the same as the new South African variant (501Y.V2)?
They both share the same mutation in spike: N501Y (N->Y at position 501). However, the 2 variants have arisen separately.
— Dr Emma Hodcroft (@firefoxx66) December 19, 2020
Another similar variant that has appeared in South Africa has some of the same mutations, but seems to be unrelated to this variant.
Has this ever occurred before?
In fact, the virus that was first discovered in Wuhan, China, is not the same one you will find in most corners of the world.
Mutation D614G showed up in Europe in February and became the dominant form of the virus worldwide.
While another, called A222V, spread in Europe and has been linked to people’s summer vacations in Spain.
What do we know about the new mutations?
A preliminary analysis of the new variant has been published and identifies 17 potentially important changes.
There have been changes to the spike protein – this is the key that the virus uses to unlock the door to our body’s cells.
One mutation, called N501Y, alters the most important part of the spike protein, called the “receptor binding domain.
It is the area where the spike makes initial contact with the surface of our body’s cells. Any change that makes it easier for the virus to get inside is likely to give it an advantage.
“It looks and smells like an important adaptation,” says Prof. Loman.
Meanwhile, the other mutation – an H69/V70 deletion that removes a small part of the spike – has been seen several times, including in infected mink.
Work by Professor Ravi Gupta at the University of Cambridge has shown that this mutation increases infectivity twofold in laboratory experiments.
Research by the same group suggests that the deletion causes antibodies from the blood of survivors to fight the virus less effectively.
Prof. Gupta commented, “It’s increasing rapidly, that’s what’s worrying the government, we’re worried, most scientists are worried.”
Where does it come from?
The variant has mutated at an unusually high rate.
The most likely explanation is that the variant emerged in a patient with a weakened immune system that was unable to defeat the virus.
Instead, their body became a breeding ground for the virus to mutate.
Does this make the infection more deadly?
There is no evidence that it is, although this needs to be monitored.
However, the increase in transmission alone would be enough to cause problems for hospitals.
If the new variant leads to more people being infected more quickly, that in turn would lead to more people needing hospital treatment.
Will the vaccines work against the new variant?
Almost certainly yes, at least for now.
All three leading vaccines develop an immune response against the existing spike, so the question is.
Vaccines train the immune system to attack several different parts of the virus. So even though one part of the spike is mutated, the vaccines should still work.
“But if we let it add more mutations, then you start to worry,” Prof. Gupta said.
“This virus is potentially on a path to vaccine escape; it has taken the first steps in that direction.”
A vaccine escape happens when the virus changes in such a way that it bypasses the full effect of the vaccine and continues to infect people.
This is perhaps the most troubling element of what is happening with the virus.
This variant is just the latest evidence that the virus continues to adapt as it infects more and more of us.
A presentation Friday by Prof. David Robertson of the University of Glasgow concluded, “The virus is likely to be able to create vaccine escape mutants.”
That would put us in a situation similar to the flu, where vaccines need to be updated regularly. Fortunately, the vaccines we have are very easy to tweak.