The latest focal S:N501 build is now up! It includes data from 4 Jan 2021.

We have new sequences in 501Y.V1/B.1.1.7 from Denmark, Singapore, Australia, Italy, Spain, France, Portugal, Germany, Brazil, Jamaica, Luxembourg, Pakistan & the USA.

1/12

https://t.co/FTjvV7T7wL

Denmark has 43 new sequences (in orange). These indicate additional introductions, as well as further expansion of the existing large local transmission cluster we saw previously (shown in zoomed divergence view).

2/12
10 new sequences from Portugal (orange) indicate additional, separate introductions.

3/12
Singapore has 5 new sequences (yellow). These indicate at least 5 separate introductions for the total of 6 sequences, with two identical sequences likely being 1 introduction.

4/12
5 new sequences from the US, from Florida & California (older sequences crossed through).

Zooming in (divergence view) on the California cluster, the relationship between these samples is difficult to infer from phylogenies alone.

5/12
3 new sequences from Spain (orange) indicate 2 more introductions, with the 3rd new sequence linking to the first sequence (green).

6/12
2 new sequences in Germany & 1 new sequence in Australia indicate separate introductions

7/12
1 new sequences in Italy represents another separate introduction (little hard to see in this picture), and 1 new sequence from France (yellow) indicates an additional introduction.

8/12
Additionally, we have the first sequences that fall in 501Y.V1 from Brazil (1), Jamaica (1), Luxembourg (1), & Pakistan (2).

Though hard to see on the larger tree, the 2 Pakistan sequences sit apart on the phylogeny, & thus indicate separate introductions.

9/12
The S:N501 'reduced UK' build is also updated. *Please remember not to use this build to look at connections between countries!* Use it only alongside the larger, complete S:N501 build.

10/12

https://t.co/9md0yn9Qgp
Finally, the country plots have also been updated. As countries are preferentially sequencing 501Y.V1 samples at the moment, the 'hot pink' sections *do not* represent true frequencies of the variant in countries!

https://t.co/c7wlQOLRiq

11/12
We can see the current screening process in action in the Swiss chart - variants with the 69/70 deletion are being preferentially sampled. Sequences from the 439K cluster also have that deletion - they're being picked up in the search to find 501Y.V1! 🙃

12/12

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

Good question: what proofs has BDA provided of his authenticity?

Let's go through some of them.


- BDA predicted the Saudis would assassinate Suleimani. They did.
- He said the dog that got Badghadi's arm deserved a Medal Of Honor. The next day the President posted a joke image showing him giving the dog a MoH.

- He said one of his ops in Syria would severely disrupt a CIA drug trafficking operation. This was proved true within a few days:
https://t.co/Hranupwcxj
- He sent gold to Brazil to help pay for an anti-trafficking operation there. That op became public soon afterwards.

- On May 31 this year, he predicted the President would be giving a speech the next day. June 1, the President gives a surprise address at the Rose Garden.
- He predicted the US would be making diplomatic moves on Greenland. True.

- He said the US would be pulling all troops out of Afghanistan. This was confirmed within the month.
- He claimed earthquakes would be hitting Iran's nuclear facilities in December. Yep.
- There were FOUR facilities hit, not the three made public. Also true.
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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