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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 focal S:N501 build is now updated with data from 13 Jan!

There are a total of 247 non-UK & non-South African sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

I'll do an additional thread later on, covering S:E484 & the 'Ohio variants'.

1/18

https://t.co/3bdttjKVl4


There are 244 new sequences in 501Y.V1 (B.1.1.7) from Australia, Belgium, Denmark, Germany, India, Israel, Italy, Netherlands, New Zealand, Norway, Portugal, Singapore, Spain & USA, as well sequences as from Ecuador and Greece for the first time.

2/18


Greece has 3 new sequences in 501Y.V1 for the first time. They indicate 2 separate introductions.

Ecuador has 2 sequences for the first time. They also indicate 2 separate introductions.

3/18


The USA has 61 new sequences (orange), from Florida, Minnesota, California, Pennsylvania, & New York.

A few of these represent separate introductions. Others form distinct clusters that may indicate ongoing local transmission.

4/18


Israel has 35 new sequences (orange). Some of these show separate introductions, but many link with older sequences, indicating ongoing local transmission.

5/18
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Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
🎉Happy New Year!🎉

To kick off 2021, here's an update on:
- S:N501 variants (501Y.V1/V2) with data from 31 Dec 2020
- 69/70del variants
- 20A.EU1 variant (most prevalent variant in Europe)

(Here are some fireworks that look a bit like phylogenies! 🎆)

1/23


The latest sequences from 31 Dec show new sequences in the S:N501Y.V1 variant (originating from SE England) from Netherlands, Denmark, Australia, Italy, Canada, the USA, Germany, Switzerland, & India.

2/23

S:N501 link
https://t.co/TfHfPgBEBS

Image link
https://t.co/3aCKv1pAcI


Canada, Germany, & Switzerland all have sequences that fall in 501Y.V1 for the first time, scattered across the tree.

3/23


The USA also has its first 2 sequences that fall in 501Y.V1, from Colorado & California. India also had its first 3 sequences, also from different regions.

In both cases, the sequences are not connected, indicating separate introductions.

4/23


In countries with previous sequences:

6 new sequences from Netherlands, in orange/yellow (green are older).
1 is clearly separate - zooming in (& in divergence view, coloured by country) it is harder to determine the relationship between the others.

5/23
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Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
The focal S:N501 build has been updated with data from 15 Jan, & includes 164 non-UK, non-South African sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

The S:E484 build has also been updated. Includes 501Y.V3 & 20B/S.484K (predominantly in Brazil).

1/16

https://t.co/3bdttjKVl4


There are 161 new, non-UK sequences in 501Y.V1 (B.1.1.7) from the Netherlands, Denmark, Australia, Spain, Norway, Germany, the USA, & Switzerland, and from Turkey and Ecuador for the first time.

2/16


Turkey has 19 sequences in 501Y.V1 for the first time. These indicate many independent introductions, though a few clusters may indicate local transmission, and pairs with common exposure.

3/16


Ecuador has 4 sequences in 501Y.V1 for the first time, which represent 2 separate introductions (pic 2). 3 are identical, and may represent exposure to a common source (pic 3). The connection to the Spanish sequence may be a common source, or onward transmission.

4/16


Denmark has 66 new sequences (orange). A few are independent introductions, though many link with older sequences, showing continuing local transmission.

5/16
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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
Dr Emma Hodcroft
@firefoxx66
To add to the excitement of your Saturday evening, the focal S:N501 build is now updated with data from 8th Jan, including 48 new seqs in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

1/12

https://t.co/AbdhO1rqpw


There are 46 new non-UK sequences in 501Y.V1, from the Netherlands, Italy, Israel, Ireland, Norway, Sweden, the USA, and Luxembourg.
And 2 new non-South African sequences in 501Y.V2, from Australia for the first time.

2/12


In 501Y.V1:

Ireland has 4 new sequences (orange). 2 sit separately but are identical, indicating an additional introduction. 2 link to a previous sequence (green), 1 mutation away each. This could indicate location transmission, unsampled diversity, or a common exposure.

3/12


The Netherlands has 10 new seqs (orange). Many sit apart on the tree, indicating additional introductions. 3 cluster together separated by a few mutations. 2 are identical to an older seq. 1 falls in a cluster of older seqs. Some of these could indicate local transmission.

4/12


Israel has 22 new sequences (orange). 1 links to an older sequence, but is separated by 3 mutations, so may be separate introductions. Another is identical to an older sequence. But most new sequences cluster together (blue), clearly indicating local transmission.

5/12
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