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
In 501Y.V2 (SA variant), there are 2 new sequences from Switzerland. As they sit quite separately within this cluster, this indicates two separate introductions to Switzerland.

6/8

https://t.co/6Cux2E3Y6y
Additionally, a new graph showing the proportion of different variants in selected countries is also up.

Note the sharp in increase of N501 (bright pink) at the end of many graphs: this indicates increased interest in sequencing N501 samples.

7/8

https://t.co/AUkR60o0GO
While more sequencing is great, you can see how switching to preferentially sequencing N501 samples will distort our ability to track other variants, both current & emerging.

Long-term, we need coordinated & regular sequencing of many samples to track #SARSCoV2 variants!

8/8
For those for whom it's helpful, there's also a new 'N501-noUK' build up which reduces the number of UK sequences.
*Importantly* one /should not/ use this tree to discern connections between sequences - use in conjunction with the full N501 tree!

https://t.co/9md0yn9Qgp

9/8
Notably, in the '501-noUK' build, an Israeli sequence seems to 'stick out' from the main 501Y.V1 cluster - we've already been in touch with Israeli scientists & there issues with this sequence (mixed base frequencies at some sites) - do not read much into its position!

10/8

More from Dr Emma Hodcroft

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
🎉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

More from World

Niger state shares borders with Zamfara, kebbi, Kaduna & Benin Republic. Terrorists from Niger republic and Burkina faso easily move money and arms across the borders of Kebbi, Zamfara and Benin R into Niger state. According to UN over 900,000 people have been displaced in B'Faso https://t.co/65YEMJhqDp


Niger, Mali and Burkina faso are weak countries populated by Shell terrorists who have now found a safe haven in the forests in Kaduna and Niger state. Birin Gwari, Mokwa forest, Nanati forests, Kanji lake areas.

No decent human resides permanently in forests.

We are facing both external and internal threats from these weak and failed countries we are surrounded with. As a senator you know that a FG police system with less than 300k officers can't actively police the landmass and borders in the North.
Form your state police now!

You and other senators should scrap the FG police system and devote the unaudited security votes and constituency allowance to policing your corridors and forests. Let the airforce bomb them and put your rangers in the forests. Issue an ultimatum for those in the forests to leave

You are all living in a dream if you think the current police structure will become efficient overnight.
Budget, Personnel, Technology, Equipment, Surveillance..It's impossible.
Form your state and community police and flush out the terrorists.
Watch the entire discussion if you have the time to do so. But if not, please make sure to watch Edhem Eldem summarizing ~150 years of democracy in Turkey in 6 minutes (starting on 57'). And if you can't watch it, fear not; I've transcribed it for you (as public service). Thread:


"Let me start by saying that I am a historian, I see dead people. But more seriously, I am constantly torn between the temptation to see patterns developing over time, and the fear of hasty generalizations and anachronistic comparisons. 1/n

"Nevertheless, the present situation forces me to explore the possible historical dimensions of the problem we're facing today. 2/n

"(...)I intend to go further back in time and widen the angle in order to focus on the confusion I  believe exists between the notions of 'state', 'government', and 'public institutions' in Turkey. 3/n

"In the summer of 1876, that's a historical quote, as Midhat Pasa was trying to draft a constitution, Edhem Pasa wrote to Saffet Pasa, and I quote in Turkish, 'Bize Konstitusyon degil enstitusyon lazim' ('It is not a constitution we need but institutions'). 4/n

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