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The S:N501 build is now updated with data from 25th Jan.

Remember, you can always check on any country by just typing that country name in the 'Filter' box on the left menu!

1/18

https://t.co/FTjvV7T7wL

 In the 501Y.V1 (B.1.1.7) variant, here are a few of the non-UK countries with new sequences in this variant, including Denmark, Italy, Spain, France, Portugal, Norway, Germany, the USA, South Kora, & Switzerland, & the UAE, Austria, & Czech Republic for the 1st time

2/18
Denmark has 52 new samples (some yellow), showing both separate introductions and further spread of existing local clusters.

3/18
Spain has 62 new sequences (orange & yellow). Many of these are separate introductions, and a few new sequences form distinct clusters. Some new sequences also cluster closely with older sequences (green).

4/18
France has 72 new sequences (orange & yellow). These show both separate introductions and clustering with older sequences.

5/18
Portugal has 30 new sequences (orange), most of which are separate introductions, but some do connect with previous sequences.

Norway has 10 new sequences (yellow). Most of these seem to be separate introductions.

6/18
There are 10 new sequences from South Korea (yellow). These are separate introductions, but some of the new seqs cluster, which could indicate local transmission or a common exposure source.

7/18
Germany has 9 new sequences (orange & yellow), which indicate separate introductions.

8/18
The USA has 123 new sequences (orange & yellow). Many of these do cluster with older sequences and seem to indicate ongoing local transmission.

9/18
Switzerland has 30 new sequences (yellow & orange), many of which indicate separate introductions.

10/18
India has 3 new sequences (yellow). These connect to older sequences, which may indicate local transmission or a common exposure source.

11/18
United Arab Emirates has 21 sequences for the first time. Many show independent introductions, but some form a large cluster that is likely local transmission.

12/18
The Czech Republic has 10 sequences for the 1st time and Austria has 41 sequences for the 1st time.

All the Czech & many of the Austrian seqs fall in 1 cluster each, likely indicating local transmission. These clusters are near each other & connected to Slovakian seqs.

13/18
In 501Y.V2, there are new sequences from Germany, Denmark, Spain, the United Arab Emirates, and Belgium.

14/18
Germany has 4 new sequences (yellow & orange). Some indicate a new introduction, others link to an older sequence.

15/18
United Arab Emirates has 5 sequences for the first time, showing multiple introductions.

16/18
Belgium has 6 sequences for the first time, showing multiple introductions.

Denmark and Spain also have sequences for the first time.

17/18
As always, the country plot table is now updated - as usual, be careful interpreting, as sequencing is often still biased toward "S-drop-out" & S:N501 samples, meaning frequencies are not representative.

18/18

https://t.co/c7wlQOLRiq

More from Dr Emma Hodcroft

Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
The latest focal S:N501 build is now up! It includes data from 4 Jan 2021.

We have new sequences in 501Y.V1/B.1.1.7 from Denmark, Singapore, Australia, Italy, Spain, France, Portugal, Germany, Brazil, Jamaica, Luxembourg, Pakistan & the USA.

1/12

https://t.co/FTjvV7T7wL


Denmark has 43 new sequences (in orange). These indicate additional introductions, as well as further expansion of the existing large local transmission cluster we saw previously (shown in zoomed divergence view).

2/12


10 new sequences from Portugal (orange) indicate additional, separate introductions.

3/12


Singapore has 5 new sequences (yellow). These indicate at least 5 separate introductions for the total of 6 sequences, with two identical sequences likely being 1 introduction.

4/12


5 new sequences from the US, from Florida & California (older sequences crossed through).

Zooming in (divergence view) on the California cluster, the relationship between these samples is difficult to infer from phylogenies alone.

5/12
WORLD
Dr Emma Hodcroft
Dr Emma Hodcroft
@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.

1/14

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

2/14


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

3/14


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.

4/14


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

5/14
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Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
A brief update to the focal S:N501 builds to start your Friday off right! This one includes data from 7 Jan 21.

We have about 20 new sequences each in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

Let's take a look at the new sequences, starting with 501Y.V1

1/14

https://t.co/kT1gFsSZn0


There are 22 new non-UK sequences in 501Y.V1, including for the first time from Luxembourg (3), & additional seqs from Singapore (1), Australia (4), France (12), & Switzerland (2).

2/14


First, Luxembourg has 3 sequences in 501Y.V1 for the first time. Each represents a separate introduction.

3/14


France has 12 new sequences (orange). Many of these represent independent introductions.

Zooming in (divergence view), we can see 2 new sequences are identical (possible local transmission), & 2 differ by 2 mutations (1 each).

4/14


Australia has 4 new sequences (red and orange) which are spread across the tree, representing separate additional introductions.

5/14
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Dr Emma Hodcroft
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@firefoxx66
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).

1/8

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.

2/8


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.

3/8


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.

4/8


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.

5/8
WORLD
Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
Happy Tuesday! The latest focal S:N501 build is now updated with sequences from 11 Jan.
There are 101 new sequences in the 501Y.V1 (B.1.1.7 #b117) & 501Y.V2 variants.

Additionally, I'll include some updates on S:E484K in this thread.

1/20

https://t.co/dXx6nk6Llz


There are 97 new non-UK sequences in 501Y.V1, including the first sequences in the cluster from Slovakia, Mexico, & Belgium, plus additional sequences from the Netherlands, Denmark, Australia, Spain, Ireland, & Sweden.

2/20


Slovakia has 10 sequences that fall in 501Y.V1 for the first time. These are closely linked, & likely indicate a single introduction and ongoing transmission (remember: vertical distance is not meaningful on the same branch - position of the 2 English samples is arbitrary).

3/20


Belgium has 5 sequences in 501Y.V1 for the 1st time, indicating 3 separate intros. 3 seqs cluster together (zoomed, divergence), indicating a single introduction. The connection to Netherlands might indicate transmission, or 2 transmissions from same diversity in the UK.

4/20


Mexico also has a sequence that falls into 501Y.V1 for the first time.

5/20
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