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Saved by @CodyyyGardner

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
Switzerland has 2 new sequences. One (marked 1st pic) is a clear separate introduction. The other (marked 2nd pic, zoomed, divergence) is from Bern & identical to an earlier sequence from Zurich ('ZH'). This could be local transmission or a common exposure.

6/14
There is 1 new sequence from Singapore (orange).

Zooming in (divergence view), we can see it is identical to 2 older sequences, which may indicate local transmission or a common exposure.

7/14
There are ~19 new non-South African sequences in 501Y.V2, including for the first time from Botswana (6), South Korea (1), & France (1), as well as additional sequences from the UK (~9).

(UK data may be affected by subsampling due to large sequence numbers.)

8/14
At least 9 new sequences from the UK are now in 501Y.V2 (UK data may be impacted by subsampling).

These are a mix of separate introductions & local transmission.

Connections to French sequences are in the next tweet...

9/14
France has 2 sequences in 501Y.V2. They cluster together, which may indicate local transmission or a common source.
They are related to seqs from England, but whether this is European transmission or exposure to common diversity in S Africa can't be distinguished clearly.

10/14
Botswana has 6 sequences in 501Y.V2. One sits apart from the others, indicating at least 2 introductions.

The other 5 cluster together, but are separated by a 1-3 mutations. This could indicate local transmission or transmission from unsampled South African diversity.

11/14
Lastly, South Korea has a sequence in 501Y.V2 for the first time.

12/14
As previously, the country plots are also updated. Lithuania is now added!

Remember: many countries are currently focusing sequencing efforts on S:N501 variants, so frequencies are often not true representations of the 501Y variants.

13/14

https://t.co/c7wlQOLRiq
Finally, we've added a new label to help identify a cluster of sequences with a S:N501*T* mutation currently circulating in Australia.

This is another independent appearance of a S:N501 (again, to T, not Y) mutation, & is not related to 20C/501Y.V2 or 20B/501Y.V1.

14/14

More from Dr Emma Hodcroft

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
FOR LATER READ
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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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
SOCIETY
Dr Emma Hodcroft
Dr Emma Hodcroft
@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
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
WORLD

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👇🏻👀

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Today's Twitter threads (a Twitter thread).

Inside: Planet Money on HP's myriad ripoffs; Strength in numbers; and more!

Archived at: https://t.co/esjoT3u5Gr

#Pluralistic

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On Feb 22, I'm delivering a keynote address for the NISO Plus conference, "The day of the comet: what trustbusting means for digital manipulation."

https://t.co/Z84xicXhGg

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Planet Money on HP's myriad ripoffs: Ink-stained wretches of the world, unite!

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