Thread by @firefoxx66

A case of the '#SouthAfrica' variant has been detected in the UK. There's also talk about a 501Y mutation in Wales.
It's getting confusing!

First: all 3 of these 501Y mutations are independent. It's appeared a few times, separately.

#Newcoronavirusvariant

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We can see this because the 3 variants (UK=1, Wales=2, SA=3) are not next to or inside each other in the tree below. In fact, we need to trace back to before March to find their common ancestors:

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nextstrain.org/groups/neherla…

Are the UK and South Africa variants the same? No. See this thread for more info:

Critically, the SA variant does not have the 69/70 deletion we see in the UK variant.

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https://twitter.com/firefoxx66/status/1340359989395861506

For more information about the South African variant (501Y.V2), check out this preprint by @Tuliodna and his team:

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https://twitter.com/Tuliodna/status/1341673111477993473

We can see the South African variant in more detail in the Africa @nextstrain build - it's at the top in red. The % of sequences that are part of that variant are shown in the chart at the bottom - you can see how it rises.

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nextstrain.org/ncov/africa?c=…

What about the 'UK'* (southeast England - B.1.1.7) and 'Welsh'* variants?

They also both have the 501Y mutation, but the Welsh variant does not have the 69/70 deletion while the 'UK' one does. They also differ in many other positions.

*=Yes, confusing nicknames!

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Here is the UK focal build, zoomed in to the 20B clade (divergence view). The 'UK' variant is in lime green at bottom. The 'Welsh' variant is in blue. We can see they are quite separated on the tree.

(The blue dot in green group may be seq error)

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nextstrain.org/groups/neherla…

We know less about the 'Welsh variant,' but it is being monitored closely by the fantastic team in Wales including @tomrconnor & @SmallRedOne !

So far it does not seem as transmissible as the 'UK' or South African variants.

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https://twitter.com/tomrconnor/status/1341787238720557060

What does it mean when we see a mutation arising independently multiple times?

It's hard to say. Mutations arising multiple times can mean they give an advantage (that's why we keep seeing them). But it's not straightforward to show this conclusively.

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Further, it may be that 501Y does not alone cause increased transmission, but that it needs to appear alongside other mutations to see a significant change.

Scientists are hard at work piecing all this information together to learn more about these variants & mutations!

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