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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
Ireland has 36 new sequences. Many represent separate introductions, but some do cluster with older sequences & may represent local transmission, or introductions from the same UK diversity.

6/20
Denmark has 29 new sequences (orange). These represent both new introductions, and further expansion of the large cluster (zoomed view).

7/20
The Netherlands have 6 new sequences. All fall within the section of the tree marked in red.
Zooming in, the new sequences are marked in red: 2 are separate introductions. Zooming in further (divergence view), cluster at the top are identical to an older sequence.

8/20
Australia has 6 new sequences, including the first from Northern Territory and Victoria. 1 pair of sequences from Victoria are identical to each other, representing one introduction.

9/20
Spain has 2 new sequences (yellow). One represents a separate introduction. The other links to older Spanish sequences, but it's unclear from sequences alone if this is local transmission or transmissions from a common source.

10/20
Sweden has 2 new sequences, marked in red. Both represent independent introductions. The second one is hard to see, but zooming in shows this more clearly.

11/20
Now turning to 501Y.V2:

There are 4 new non-South African sequences in 501Y.V2, including the first from Ireland (3) and the Netherlands (1).

12/20
Ireland has 3 sequences in 501Y.V2 for the first time. They cluster together, and may indicate either local transmission, or a common exposure (pictures 1 & 2).

The Netherlands has its first sequence in 501Y.V2 (picture 3).

13/20
As usual, the updated country graphs are also available. As always, interpret with care: countries are selectively sequencing to track 501Y.V1, so proportions of sequences are not representative for many countries.

14/20

https://t.co/c7wlQOLRiq
Finally, an updated focal S:E484 build is also up.

S:E484K is found predominantly in the 501Y.V2 variant, & in a cluster of sequences primarily in Brazil, though it has appeared numerous times in the past.

15/20

https://t.co/Od95D6DL74
S:E484K has been discussed recently as there are suggestions it may impact how well the immune system can recognise the virus, particularly if you've been infected with SARS-CoV-2 before.

Links to the studies are on https://t.co/SmanZBHpse

16/20
Additionally, over the weekend, travellers from Brazil to Japan were found to be infected with a novel variant with many mutations, including S:E484K & S:N501Y.
Translated report linked below.

17/20

https://t.co/G1ITeT3MoV
To help viewers identify these new samples from Japan, I've added a *temporarily* label to the S:E484K build: 20B/S.484K.501Y.

Additionally, I've added a *temporary* label to the Brazilian cluster with S:E484K: 20B/S.484K.

18/20
Interestingly, though the recent Japanese sequences carry S:E484K & seem to originate from Brazil, they do *not* branch from the larger 484K cluster in Brazil, but instead sit on a long branch separately within the 20B Clade.

19/20
Getting case numbers down saves #LivesAndLivelihoods, and reduces #SARSCoV2's opportunities to explore situations with unique selection pressures, potentially resulting in mutations expanding that we'd rather not see.

Help make my updates more boring: bring cases down!

20/20
PS - For related but slightly-different-angle updates on 501Y.V1 (B.1.1.7) & 501Y.V2 (B.1.351), you should follow @AineToole & keep an eye on her tweets about updated reports!

https://t.co/fZDQqwvJmr

21/20

More from Dr Emma Hodcroft

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
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
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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
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
🎉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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1/

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but also may include

“non-disparagement” - don’t say anything negative about us EVEN IF IT IS TRUE
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Smoking gun.


https://t.co/r5xm608OD9


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https://t.co/c9lCbvv4NF
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8 hours and 1000 flawed arguments and biased procedures later, Leeds City Plans Panel voted 9-5 for airport expansion and the false promises of economic growth.
For “what Leeds needs is a premier-league football club and a premier-league airport”
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1/ There was a lot of "I do care about climate change, BUT" – followed by a lot of blah blah. Blah blah economic growth. Blah blah connectivity. Blah blah competitiveness. Blah blah Manchester. Blah blah Westminster. Blah blah offsetting. Blah blah electric planes. Blah blah blah

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@snip96581187 @Daoyu15 @lab_leak @walkaboutrick @ydeigin @Ayjchan @franciscodeasis @TheSeeker268 @angie_rasmussen Clearly, because as I have been saying for 8 months now, DTRA and DARPA have been using Ecohealth and UC Davis to collect novel pathogens for gain of function work back in the USA. I have documented this in many threads which I will post here just to annoy everyone.

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@Daoyu15 @lab_leak @walkaboutrick @ydeigin @Ayjchan @franciscodeasis @TheSeeker268 @angie_rasmussen


@Daoyu15 @lab_leak @walkaboutrick @ydeigin @Ayjchan @franciscodeasis @TheSeeker268 @angie_rasmussen


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