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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
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 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
SOCIETY
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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
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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X : Do you think cloud will decentralise?
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@warikoo
How I created content in 2020

A thread...

Back in Aug 2016, I started creating content to share my experiences as an entrepreneur.
Over 3 years I had put out 1,200+ hours of content - posting every week without


Little did I know that something I started almost 4 years back would give my life an entirely new direction.

At the end of 2019, my biggest platform was LinkedIn with ~700K followers.

In Jan 2020, I decided to build a team that would help me with the content.

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OK, more housekeeping ahead of putting this account up on blocks.

#BurnNotice - search for that coming from my account, you'll learn some things about troubles in late 2020.

But this is going to be pretty meta, it's about what goes a #BurnNotice and why.

We've used the #BurnNotice tag in the past to denote an entity that is in need of special attention. That practice dates back to 2011/2012 and lapsed some time ago.

This is a more traditional sort of

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1) people I dislike

2) people I think are competitors in some fashion

3) "feds", whatever you people mean by this undefined term.

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MALUME ZANO
MALUME ZANO
@ZanoUrban
The Misrepresentation of the Levites

[A Bonus Smallanyana Thread]

Disclaimer:

This thread is not part of the Angelology Threads we are focusing on this month of February but it is a response to what uNkulunkulu laid on my heart when I was finishing up Part 3 of the main threads.

This thread is also not an attack but a personal observation.

Let's Begin 📖

The Levites or the Tribe of Levi was/ is one of the original 12 tribes of Israel. Descended from Levi the son of Jacob. Descendants of Aaron, the first high priest of Israel. The Levites were designated as the priestly class, also known as the Kohanim.

Principal roles:

Singing Psalms during temple services
Teachers of the Word
Judges (Politics)
Construction and Maintenance of the Temple
Serving as Guards

The Levites were known to stand for truth, at all cost. Some considered them an army set apart by and for uNkulunkulu.

Numbers 18:6

And behold, I have taken your brothers the Levites from among the people of Israel. They are a gift to you, given to the Lord, to do the service of the tent of meeting.
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The #worldwildlifeday2021 theme is Forests and Livelihoods: Sustaining People and Planet aligning with UN Sustainable Development Goals 1, 12, 13 and 15. So, what are the UN Sustainable Development Goals (SDGs) & how can children begin to learn about them & get involved ?

https://t.co/8ICvHxE9QL is easy & fun to follow for our smallest of people #EYFS. Early childhood is the perfect stage to introduce the core concepts of what it means to be a global citizen. For our reception & KS1 children please take a look at this fabulous free resource

https://t.co/tZx8UIS58Q Storytelling is a powerful communications tool and helps children remember lessons and virtues that they will use in everyday life. The idea is to simplify the lessons of the (SDGs) so young children can relate to – and better understand – the SDGs.

For older children here’s a board game that aims to help teach children around the world about the Sustainable Development Goals in a simple and child-friendly way

This is a lovely free book for children to enjoy flicking through themselves https://t.co/ScMbQCfpjl Elyx, the United Nations’ digital ambassador, uses various expressions and actions to help demonstrate the meaning of each Sustainable Development Goal.
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All is more or less as expected....except for this bit about Native American.


The family is almost completely composed of Spanish peasants (from various regions) who emigrated, along with a massive wave in the late 19th-cent./early 20th-cent., to Cuba back when it was a booming economy (richer than Spain's) and worth emigrating to (Communism killed that).

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Did you know?

When Saudi Arabia's King visited India in 1955, PM Nehru ordered all the Hindu Temples and Idols of Hindu Deities that came in Saudi King's way to be covered up.
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But suggesting that something ignorant or divorced from reality warrants the same kind of treatment in public debate as something based in fact or at least credible is absurd and when done on behalf of a society in public media or academic settings it is self-destructive.

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"I lied about my basic beliefs in order to keep a prestigious job. Now that it will be zero-cost to me, I have a few things to say."


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