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

6/14
Netherlands has 4 new sequences (orange), indicating 1 clear additional introduction. The other new sequences cluster with older sequences, possibly indicating local transmission.

7/14
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.

8/14
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.

9/14
Hong Kong, Germany and the USA (from New York), each have 1 new sequence (orange), indicating additional introductions.

10/14
Moving on to 501Y.V2, there are 7 new non-South-African sequences in 501Y.V2, from the United Kingdom (6) and Sweden (1).

11/14

https://t.co/fOPgetG9S8
Sweden has a sequence in 501Y.V2 for the first time.

12/14
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.

13/14
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!

14/14

https://t.co/c7wlQOLRiq

More from Dr Emma Hodcroft

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
FOR LATER READ
Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
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.

2/10

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!

3/10


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).

4/10


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).

5/10

https://t.co/Cw5u2kuATa
SOCIETY
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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
FOR LATER READ
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
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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Fuck Africa. I'm American. Any African mad at dem words, kick rocks. Don't like it, jump ship. Back 2 Africa. Need receipts. How much yall made off us? U think we didn't know? Mafucka, we the vibranium that made Africa pop. We werent stole. We were sold.

Yall sold us. Then yall hv the audacity 2 come here, pass as American niggas, lecture us about racism & white supremacy, police our emotion, critique our anger & then U have the bravado 2 lecture us about fighting when yall let Europeans come & take yall shit? Fuck out of here.

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Tweeting Historians
@Tweetistorian
How do you explain the Trinity in Chinese? If you're a Christian in Tang China, there's a few ways!

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There are two main writers/translators credited in the extant documents of the Christian (called 'Jingjiao' 景教 in Chinese) corpus of Tang China: Aluoben and Jingjing. ~ahc #jingjiao /2

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