Thread by @Unusual_Times, A Laymans Guide to Mutations & Variants.I think we can beat covid [...]

A Laymans Guide to Mutations & Variants.

I think we can beat covid in the UK if we really try. It's NOT endemic it's too young and it is still spreading too fast. In the words of @ArisKatzourakis chickenpox is endemic, HIV is not endemic.

We do NOT have to just live with it

We have seen today that vaccinations are working and deaths are dropping in the aged population. We know Lockdowns reduce cases. We've also seen that SARS-CoV2 mutates - basically mutations are RBD nucleotide changes on the viral spike proteins (the bits that bind to human cells)

I will briefly cover mutations. There are quite a few but only four of major concern I believe.

D614G - this occurred in China as the virus moved into Europe in Feb 2020. It made the virus more transmissible and is pretty much in everywhere

E484K - first appeared I believe in Brazil in July 2020. It was documented as enabling the virus to evade neutralising antibodies in July. It is also a mutation in the South African Variant although the variants are separate.

This is the one that is worrying the UK right now

N501Y First appeared in the UK in September 2020 as part of the Kent N501Y.V2 Variant of Concern (VoC). It's now spreading worldwide. We don't know VOC2's origin. It doesn't fit in with any viral family tree. It makes SARS 30%-70% more transmissible and 30% more lethal.

There is one more that you probably have not heard of. This is the 69/70 deletion. This was first identified in (but but) Sweden in April 2020. It is widely believed to be a fitness enhancement and a stabilising mutation. It "might" help the virus evade the bodies natural defense

So to summarize...

D614G - everywhere and made it more transmissible

E484K - "helps" the virus to evade the bodies neutralising antibodies

N501Y - is spreading and makes it 30-70% more transmissible and 30% more lethal (source Nervetag)

69/70 - Del made it "Strong and Stable"

Now these mutations ALONE do NOT make a "VARIANT" as such - we have FOUR Variants of Concern in the world (Five if you count the one that will be identified in Southern California in about a fortnight from now).

So lets cover Variants of Concern next - when I've had a fag break.

There have been thousands of mutations on the spike protein but only some of these lead to distinct advantages for the Virus (that we understand anyway).

The mutation "combinations" that give the virus an advantage lead Nervetag and the WHO to flag them as "Variants of Concern"

Below is an excellent infographic from the 8th Feb released by The ECDC in Europe this only covers the first three. The Second picture I, well, just nicked off Twitter from this guy @jusdayda

The Fourth VoC is the Bristol Variant - this is basically the addition of the E484K mutation (and some other bits & bobs

) to the UK variant.

The Liverpool variant is different and not yet categorised as a VoC but again add E484K and whatever else.

So the names of each:

VoC 1 - B.117 = Kent = D614G N501Y 69/70 Del

VoC 2 - B.1351 = http://S.Africa = D614G N501Y E484K

Voc 3 - P.1 = Brazil = D614G N501Y E484K

VoC 4 - XX = Bristol = D614G N501Y 69/70 Del E484K

So in the UK we have

VoC1 as our main variant. Home grown and our gift to the world. It is highly transmissible and is dominant and already makes up around 80% of cases.

We have "introduced" VoC2 which we are trying to limit through Border controls

We have home grown VoC4

So how has this happened.

Well D614G is just there almost from day one. As soon as it hit the human population it mutated to give itself an advantage.

N501Y was another mutation that's probably occurred naturally quite early on despite it not really being highlighted until Kent

The 69/70 Deletion is more puzzling.

Early on in its identification I noticed it was only occurring in colder climates. We DON'T see it in South Africa or Brazil. There may be a link but I just don't know.

I think we are VASTLY underestimating the effect of the 69/70 deletion

E484K is also puzzling. Up until its emergence in the UK we had only seen this in warmer climates. It was ONLY found in Brazil & South Africa nowhere else. However the consensus seems to be this is something called an "escape mutation" - maybe it just spreads more in hot weather.

The fact of the matter is the spike protein on the UK VoC1 is now mutating to include E484K which helps it evade our natural defenses and may bypass immunity.

The news coming from SAGE is that this new Voc4 probably won't become dominant because VoC1 is already so transmissible

None of this sits comfortably with me. There are two issues.

1) we know environmental temperature can cause viruses to mutate. Its well documented.

2) we know environment can affect the transmissibility of a virus.

If E484K likes it warm we are in trouble come spring.

Finally a brief note on something called "Convergent Evolution".

The virus will naturally adopt mutations that give it an advantage. We are seeing this in real time. Many of the cases of VoC's are popping up across the world now in people with NO history of travel.

If the Virus comes across a situation in just one individual where E484K gives it an advantage it CAN and WILL mutate. If that advantage makes it more transmissible and the environment is suitable to it then it WILL spread faster. Seeing E484K in Bristol and Liverpool SEPARATELY

And the more cases we have the more likely mutations are to happen. We can tweak vaccines but as I have said before I do not think we can do this quickly enough to keep up.

We HAVE to get case numbers right down and eliminate this virus NOW. It is our last chance.

Allowing it to become endemic is NOT an option. No matter how much you scream for a Unicorn for your birthday you are NOT getting one.

Disclaimer:
I'm a nobody. I've just summarised what I've read. Sorry if I nicked any of your work. If there are any mistakes feel free to blast.

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