Understanding how Coronavirus is mutating and evolving

Update 17th February

Worrying development from the USA : Two variants of the SARS-CoV-2 coronavirus that causes covid-19 have combined their genomes to form a heavily mutated hybrid version of the virus. The “recombination” event was discovered in a virus sample in California, provoking warnings that we may be poised to enter a new phase of the pandemic. The hybrid virus is the result of recombination of the highly transmissible B.1.1.7 variant discovered in the UK and the B.1.429 variant that originated in California and which may be responsible for a recent wave of cases in Los Angeles because it carries a mutation making it resistant to some antibodies.

UK and Californian coronavirus variants have MERGED into one

Read more: https://www.newscientist.com/article/2268014-exclusive-two-variants-have-merged-into-heavily-mutated-coronavirus/#ixzz6mgOAQtyN

Since the start of the pandemic, coronavirus has been mutating, its genetic code slowly changing as it spreads from person to person around the world. Virus mutations are normal and most genetic changes have no effect on how dangerous the virus is, and some even weaken the virus.

There are now a number of mutatated variants of particular concern, although Researchers do not have the same level of evidence for each, but in each case, researchers see a seed of something concerning. The B.1.1.7 variant was first detected in Kent in September, which is more transmissible and slightly more deadly, and is set to be the world’s dominant strain. Then there’s another pair of variants —one discovered in South Africa in October, and another in Brazil in December — that are less well understood. Scientists are beginning to suspect that they might have evolved ways to evade the human immune system, at least a little bit. In addition, there were another pair of variants in Bristol and Liverpool.

Now, researchers from Edinburgh University have now identified another new variant of coronavirus (B.1.525) in the UK with some potentially troubling mutations(38 cases – 2 in Wales and 36 in England). It appears similar to the South African variant which prompted door-to-door tests in areas where it has been found. This variant has been seen in other countries, including Denmark, Nigeria and the US, but It is too soon to say if it should be added to the UK’s list of “variants of concern“, or whether mass testing for it should happen. So, for now, it is a “variant under investigation”. click full article.

coronavirus particles
Another new UK coronavirus variant

One of the variations B.1.525 has is a mutation called E484K which is also found in the Brazil and South African variants – that may help the virus evade some of the body’s immune system defences. The concern is that the virus is changing in ways that could let it easily spread and escape from the vaccines that we already have to fight Covid.

So why is this happening ? There are 4 main reasons, but it all boils down to one thing: evolution :

Coronavirus’ genetic diversity increases over time. Viruses mutate because they’re constantly making copies of themselves in enormous numbers. If you were writing a draft of something millions of times on a computer, extremely quickly, you’d probably make some typos. This has happened millions and billions of times across the globe. The longer the pandemic rages on, the more chances the virus has to evolve.

So that’s one major part of it. The virus has just had a lot of opportunities to become something slightly different. The increased diversity doesn’t quite explain why we’re seeing these particular — seemingly more concerning — variants at this particular time – evidence of adaptive evolution. These variants appear to be either getting better at infecting people or possibly evading the immune system in similar ways.

Coronavirus is probably evolving in response to increasing human immunity. genetic diversity only explains part of the story. The other part of the story: natural selection. Some of the virus’s genetic changes provide an advantage, which has led, in some cases, to these variants outperforming older strains of the virus. Some of those [genetic] substitutions are actually helping the virus replicate better.

Both the P.1 variant found in Brazil and the 501Y.V2 variant found in South Africa have a mutation called E484K, which changes the part of the virus that attaches to human cells (it’s also the part that the immune system most readily recognizes after someone is vaccinated), which might allow reinfection.

Coronavirus has spread so far that rare things are starting to happen. The longer the pandemic goes on, the more chances there are for rare — and sometimes consequential — things to happen. The B.1.1.7 variant might be one of these consequences. It appears to have acquired significant genetic changes over a short period — so many that scientists suspect the variant might have emerged in an immunocompromised person. In people that have compromised immune systems, though, there’s a very different dynamic;. the virus could be in them for months instead of weeks, giving the virus more time to evolve, to accumulate mutations that might make it easier to thwart the immune system.

Some Covid-19 treatments might have instigated some evolution. The rise of these variants may have something to do with the use of convalescent plasma. There are cases where the identical [mutations] that characterize the UK variant have also evolved in patients who are chronically infected with the virus and were then given convalescent plasma,, creating a perfect storm. The virus has built up genetic diversity in the patient, and then the convalescent plasma acts as a force of natural selection, choosing among those variants one that could evade antibodies in that plasma.

Whats next – Vaccine induced mutations ? The virus will keep changing, and there will be more variants. Not all will be variants of concern, but there also might be more variants of concern in the near future, as the virus is getting exposed by another big selection pressure: vaccines. If, due to random mutations, there’s a strain of the virus that is just a little bit better at evading the immunity provided by vaccines, it could spread. That’s why these viral evolution experts want vaccination to happen as fast as possible. Just as partial immunity in a single immunocompromised person can act as a selection pressure for evolution, partial immunity in the population at large can as well.

What we don’t want is for there to be high levels of virus circulating and spending a lot of time with a partially vaccinated population. That’s because “once you vaccinate hundreds of millions of people, the virus is going to be under really quite intense pressure to evolve [immune] escape variants. Some of these variants may already be in existence among the public but have not yet been detected — or may soon form as the pandemic continues.

Those variants could sweep up to a much higher frequency once vaccination provides this huge selective force. Evolution happens when there’s a lot of genetic diversity, which then meets a selection pressure. This is what’s happening as the pandemic continues during a vaccination campaign. click full article.

So there we have it. The good news is that, for now, it appears the existing vaccines will still be broadly effective against the variants, and that it’s possible to update the vaccines to account for future changes. But how can we stop more viral evolution from happening in the future ? The best way to avoid it is to not allow the pandemic to spin so out of control. If we had done that, and then vaccinated, which will be the position in Australia and New Zealand, then we would be in a much less dangerous situation. Time will tell.

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