Thread by @firefoxx66

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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nextstrain.org/groups/neherla…

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.

nextstrain.org/groups/neherla…

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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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Italy has 6 new sequences (orange), which indicate additional independent introductions.

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Netherlands has 4 new sequences (orange), indicating 1 clear additional introduction. The other new sequences cluster with older sequences, possibly indicating local transmission.

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Switzerland has 3 new sequences (orange). 1 is clearly a separate introduction.
Zooming (divergence view), we can see 2 of the new sequences differ by 1 mutation, & connect to a UK sequence. More info would be needed to conclusively determine if this is local transmission.

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Brazil has 2 new sequences, 1 (marked) shows a new introduction. The other connects to a previous sequence. Zooming in (divergence view) we can see this more clearly - they are identical, and this may indicate local transmission.

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Hong Kong, Germany and the USA (from New York), each have 1 new sequence (orange), indicating additional introductions.

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Moving on to 501Y.V2, there are 7 new non-South-African sequences in 501Y.V2, from the United Kingdom (6) and Sweden (1).

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nextstrain.org/groups/neherla…

Sweden has a sequence in 501Y.V2 for the first time.

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UK has 6 new sequences in 501Y.V2 (orange), including 1 from Scotland. Most indicate separate introductions, but 1 new seq links to the older 1 (blue). Zooming (divergence view), they are separated by 1 mutation. This could indicate local transmission or the same exposure.

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As always, the graph of variants per country is updated (remember: as people are preferentially sequencing S:N501 samples, the proportions shown are not accurate outside of UK & Denmark!)

Additionally, the 'reduced UK' S:N501 build is updated!

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github.com/hodcroftlab/co…