The latest S:N501 focal build is now up, with data from 28th Dec:

We can see new sequences from Italy, Israel, Spain, France, & Ireland in the SE England variant (501Y.V1) & Switzerland in the South African variant (501Y.V2).

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https://t.co/PEU7dhptO6

In 501Y.V1 (SE England variant), we can see 1 new sequence from France & Spain, each. The French sample has a travel history to the UK.

3 new sequences are from Israel (marked 1 & 2). Zooming in on '2' (divergence view) shows they are identical, indicating 1 introduction.

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There are 7 new sequences from Ireland, found roughly in 5 places on the tree (4 are singletons, 3 cluster together - 2nd 'group' from the top).

These indicate at least 5 introductions, but we need to zoom in on the 3 that cluster to see more clearly.

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Zooming in to the 3 that cluster together (divergence view), shows it can be difficult to distinguish introductions sometimes, especially as we expect strong travel links between the UK & Ireland, & may only be sampling the total diversity present in Ireland.

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14 new sequences from Italy are scattered across the tree - some alone & some clustering.

Zooming in on a few clusters shows some seem to be linked, while others are harder to determine.
4 seem to be clearly linked as 1 introduction.

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In 501Y.V2 (SA variant), there are 2 new sequences from Switzerland. As they sit quite separately within this cluster, this indicates two separate introductions to Switzerland.

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https://t.co/6Cux2E3Y6y
Additionally, a new graph showing the proportion of different variants in selected countries is also up.

Note the sharp in increase of N501 (bright pink) at the end of many graphs: this indicates increased interest in sequencing N501 samples.

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https://t.co/AUkR60o0GO
While more sequencing is great, you can see how switching to preferentially sequencing N501 samples will distort our ability to track other variants, both current & emerging.

Long-term, we need coordinated & regular sequencing of many samples to track #SARSCoV2 variants!

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For those for whom it's helpful, there's also a new 'N501-noUK' build up which reduces the number of UK sequences.
*Importantly* one /should not/ use this tree to discern connections between sequences - use in conjunction with the full N501 tree!

https://t.co/9md0yn9Qgp

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Notably, in the '501-noUK' build, an Israeli sequence seems to 'stick out' from the main 501Y.V1 cluster - we've already been in touch with Israeli scientists & there issues with this sequence (mixed base frequencies at some sites) - do not read much into its position!

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More from Dr Emma Hodcroft

Lots of tweets about this today!
Let's see what we can see in the focal S:E484 build!

Phylogenetics (what I do - making 'family trees' from virus genetics) can be very informative to see how different variants are spreading, and how cases

There are two variants circulating predominantly in Brazil:
- 20B/S.484K seems to be older & more widespread. It has (among others) a mutation at position 484
- 20J/501Y.V3 is smaller & detected recently. It has mutations at 501 *and* 484.

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https://t.co/Cw5u2kuATa


The variant predominantly in the UK (501Y.V1 / B.1.1.7) and the variant predominantly in South Africa (501Y.V2) also both have 501. 501Y.V2 *also* has the 484K mutation.

Why are there concerns about these mutations? You can read more at https://t.co/wVE7ubYBoy!

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The view below is from an analysis focusing on sequences with a mutation at 484. It shows all the samples in the 2 variants (20B/S.484K & 20J/501Y.V3) & how they're related. More closely related = closer together (very, very roughly).

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We can colour these samples by region to see where they're from. As we expect - most are in Brazil! A few are in Argentina (also red).

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https://t.co/Cw5u2kuATa
Each day brings new challenges, but here's an update to the dedicated S.N501 build, using data from 6 Jan 2021 to keep you going.

There are 42 new non-UK sequences in 501Y.V1 (B.1.1.7) & 7 new non-South-African sequences in 501Y.V2.

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https://t.co/kT1gFsSZn0


There are 42 new non-UK sequences in 501Y.V1 from the Netherlands, Italy, Hong Kong, Finland, Sweden, Germany, USA, Switzerland, Brazil, and the first sequence from 501Y.V1 in Oman.

https://t.co/XA8VR8HiEq

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Oman has their first sequence which falls into 501Y.V1:

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Finland has 12 new sequences (orange), which mostly represent separate introductions. Zooming in (divergence view), we can see 3 of the new sequences are identical (red), which may indicate the cases are connected.

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Sweden has 8 new sequences (orange), which indicate separate introductions.

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