Thread by @ewanbirney

Deep breath, my views on the SARS CoV2 Mutation story in London/South East. It's a fast moving story (at least for phylogeography); I'm a one step-away from experts, aiming here to provide some light.

Some background - like all viruses SARS-CoV-2 encodes its information in a nucleic acid, in SARS's case, RNA. This is simply a very long polymer made from 4 chemical subunits; the "long form" of these chemicals are too tedious to write down, so we give the 4 letters - A,C, U* + G

(the * is because in RNA one of the bases is Uracil - U - whereas as in DNA it is Thymine - T - basically for these purposes it doesn't matter and because one often does read outs in DNA not RNA letters, one uses T not U. One of these little "this is how it works, its a detail")

This chemical polymer - ~30,000 letters, just 1.3 million atoms - is remarkable in that if it gets into a human cell it can usurp the human cell's machinery to make more copies of itself (the polymer) and the virus coat, thus making more virus. This is... the way viruses roll.

Occasionally when it makes copies of the polymer it makes a copying error; one of the letters flips to another letter. We call this mutation, but unlike superhero movies, most of these mutations are as important as typos ... there, dectable, but don't change anything important.

Just some perspective on this error process - SARS-CoV-2 is a pretty faithful replicating virus - we know of far more error prone ones (eg HIV) or full-on let's keep shuffling the deck whenever we can ones - influenza - not SARS-CoV-2.

We can read out SARS-CoV-2 genomes (determining the precise polymer for a specific isolate) and a number of countries are doing this alot, in particular the UK. This is both a "know your enemy" sort of thing and because these errors allow us to make family trees of the virus.

From the family trees (they go back to Wuhan isolates) we can tell roughly how much mixing there is, and in a outbreak (eg, a hospital) we can tell whether a group of infected people all come from the same origin or different - this can change what one does.

More ominously, monitoring this is good to check for new strains that might infected faster, or be more virulent, or perhaps evade vaccines, though the rather pedestrian rate for the SARS-CoV-2 mutations means this is unlikely.

Today there was announcement from @CovidGenomicsUK that it was tracking a new virus variant which has grown in prevelance in London and South East England. cogconsortium.uk/news_item/upda…

You might think that "growing" is a prime facie case for "concerning" but by definition if the outbreak is growing in London and the South East (which it is) probably some viruses 'by chance' are the ones which are growing, and some will be shrinking;

So - although this is *definitely* worth more study (this is precisely why @CovidGenomicsUK is sequencing these things) do not get too concerned. There are over 4,000 similar mutations in the key Spike protein around the world for example.

I think the reason why this is slightly more of interest is that this mutation impacts parts of the RT-PCR read out at least from some reports (@The_Soup_Dragon). Again, this needs more study and should not overly concern you. I promise to freak out if it looks freaky.

Thankfully the people who design the RT PCR have a complete belt-and-braces approach with 3 independent sites to get a read out of the virus. In fact, it's going to be cool (and lucky) if we can get a read out of the strain spread from RT-PCR processing.

Viruses becoming more infectious is common; they may become more virulent or less (less is at least as common as more) and thankfully our immune system also has a belt and braces approach on detecting the virus >>

<< the key T-cell immunity happens via fragments of the virus proteins processed inside of cells - mutations might effect one fragment, but it is hard to impact all. Vaccines stimulate this (T cells) as much as B cells we hope.

So - take homes - there is a mutation in SARS-CoV-2 - this is to be expected; in London and Thames Estuary more virus is being founded; we should expect some strains to go up in prevalence. This strain is by chance spottable at the "testing" level but just by sheer chance.

We need to keep an eye on this (hence... @CovidGenomicsUK - rock on COG UK) - it might be that it is more infectious though the actual key reported mutation is also found in France and Denmark so ... we can probably get an idea (there might be a substrain issue).

We should also keep an eye on these things for vaccination, but remember all the clinical trials happened with a fair number of different "mutant" spike proteins over the summer and autumn. Never say never - we should know every moving part of this, but don't get concerned.

And stay tuned to @CovidGenomicsUK