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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
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
🎉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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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
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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
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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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Cory Doctorow #BLM
Cory Doctorow #BLM
@doctorow
Today's Twitter threads (a Twitter thread).

Inside: Planet Money on HP's myriad ripoffs; Strength in numbers; and more!

Archived at: https://t.co/esjoT3u5Gr

#Pluralistic

1/


On Feb 22, I'm delivering a keynote address for the NISO Plus conference, "The day of the comet: what trustbusting means for digital manipulation."

https://t.co/Z84xicXhGg

2/


Planet Money on HP's myriad ripoffs: Ink-stained wretches of the world, unite!

https://t.co/k5ASdVUrC2

3/


Strength in numbers: The crisis in accounting.

https://t.co/DjfAfHWpNN

4/


#15yrsago Bad Samaritan family won’t return found expensive camera https://t.co/Rn9E5R1gtV

#10yrsago What does Libyan revolution mean for https://t.co/Jz28qHVhrV? https://t.co/dN1e4MxU4r

5/
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Robbie Maakestad
Robbie Maakestad
@RobbieMaakestad
@The_Rumpus is open for essay submissions until February 28, so here’s a #RumpusEssays thread in which our amazing editors share what they would like to see in submissions. Give them a follow and send your essay our way via @submittable

Features Editor @happiestwerther is “still (forever) in love with the researched essays that teach me something about a subject while I also learn about a narrator.” #RumpusEssays

Assistant Features Editor @sarahkasbeer would like to see “essays with unexpected engines / innovative structures / emotional and intellectual depth / good ole narrative tension.” #RumpusEssays

Features Editor @kaytaybayy: “I'd love to see essays that are imbued with kinetic energy. I don't care what they're about. Just sweep me into your experiences and thoughts. Compel me to shake my dust off.” #RumpusEssays

Asst Feat Ed @DJ_theoretical: "I’d love to read about that weird, niche topic you’re obsessed with. Your Pog collection, those ribbon candies that seemingly only grandmas buy, your new obscure hobby. Distract me from the horrible big picture with your hyperfixations."
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American Hacker
American Hacker
@AmericanHacker
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

Let's put some bounds on this. Those in a #BurnNotice are NOT:

1) people I dislike

2) people I think are competitors in some fashion

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

4) informants. Got a list of those, too, it's handled differently.

The #BurnNotice is more focused on people who present as if they might be working for Erik

Or maybe they work for Tiger
FOR LATER READ
Umbereen S. Nehal, MD, MPH
Umbereen S. Nehal, MD,...
@usnehal
I am done giving this doctor or team grace. I started with "We are tremendously grateful for all you are doing." He seemed irritated to speak to us. Literally I asked, "What is the likelihood our mom will die on current support, in the next 24 hours, so we can plan travel?"

He hammered us with how severe this was and that was. Yes, that is why I am asking the question. "We are asking you to be a thought partner so we can make responsible decisions as the family." I had had pre-conversations with doctor friends to understand the numbers and prognosis

He said "It would be illegal for me to tell you that she won't die, then she dies." Yes, that is why I said LIKELIHOOD - critical care docs deal in likelihoods. It so frustrating to be on this side and not get a fraction of the standard that I have been held to and hold myself to

Then I made the error of saying, "I'm a pediatrician, I literally do this work on family-centered, compassionate care." to which the charge nurse answered, "It is not the work we do. We keep people alive." End of life care IS your job. Planning IS your job. It's not just numbers

Compassion is not only a pediatric thing while critical care/end of life can proudly lack it. I've had more end of life conversations than I want to remember. My mom is not numbers. She is a human being. I am modulating my voice, complimenting you, leveraging my network.
FOR LATER READ
Tad Strange
Tad Strange
@bread157
@DawgLaser @GravelInstitute Rush Hudson Limbaugh III (/ˈlɪmbɔː/ LIM-baw; January 12, 1951 – February 17, 2021) was an American radio personality, conservative political commentator, author, and television show host.
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It's an assault on facts and reason. It's an assault on good governance. It's an assault on the bureaucracies that are being discounted. It's an assault on science and history. But it is also an assault on one of the underpinnings of democracy.

We live in a system that is grounded on the idea of collaborative government. Leaders may have a final word but even then, there are typically checks and balances. Hopefully, in this case, such checks and balances may work. But they also are being tested.

The president's position that he is smarter than all the world's scientists, than the entire intelligence community, than experts who have studied any issue all their lives, is, of course, asinine. But his belief that government turns solely on his opinion, is monarchic.

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He's STILL in charge of the Mueller investigation.

He's STILL refusing to hand over the McCabe memos.

He's STILL holding up the declassification of the #SpyGate documents & their release to the public.

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The guy had a face-to-face with El Grande Trumpo himself on Air Force One just 2 days ago. Inside just about the most secure SCIF in the world.

And Trump came out of AF1 and gave ol' Rod a big thumbs up!

And so we're right back to 'that dirty rat Rosenstein!' 2 days later.

At this point it's clear some members of Congress are either in on this and helping the cover story or they haven't got a clue and are out in the cold.

Note the conflicting stories about 'Rosenstein cancelled meeting with Congress on Oct 11!"

First, rumors surfaced of a scheduled meeting on Oct. 11 between Rosenstein & members of Congress, and Rosenstein just cancelled it.
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Why Gain/loss ratio is important that the batting average
• More than the Win Loss ratio check the total Gain /loss ratio
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• Any trader should atleast experience 3 scenarios i.e. bull, bear & consolidation
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THE SCIENCE BEHIND YAJNA

Fire is, of course, one of the greatest discovery of mankind. Our control over the fire dramatically changed the entire human habits; earlier it was used to cook food, protection from animals and to stay warm.


Among the many applications of fire, one is Yajna (यज्ञ, yajña); also called as Havana (हवन) or Agnihotra (अग्निहोत्र).
Yajna is elaborately described in Yajurveda. In Yajurveda, Yajna is the greatest among all works (Karman). One can purify his /her soul by performing Yajna.

In Vedic culture, it is thought that the holy fire is the mediator between Gods and us; when the offerings are made to Yajna with chanting mantras, it directly reaches the Gods, who bless the people with rains, food, health, and good luck.

According to Apastamba Sutra, the definition of Yajna is Vedic sacrifice; an act by which we surrender something for gods e.g. grains (Anna), pulse, milk and milk product (ghee, butter, curd) fruits, plant juice (soma), etc.

As we said; Yajna is the contact medium for gods and

to seek their blessings.

There are many types of Yajna performed by Hindus for e.g.,

1. Rajsuya Yajna
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*Heads-up that this thread will feature some extreme examples of homophobia and transphobia.*

Hey folks, have you ever wondered why trans people face constant accusations of fetishism, sexual predation and child abuse/grooming? Well, today let's talk about stochastic terrorism.

So, first we have to talk about what stochastic terrorism actually is. Remember when there was a conspiracy that there was a pedophile ring operating out of a pizza parlour basement, and a crazed gunman showed up? It's that sort of incitement that stochastic terrorism describes.

It's the demonisation or incitement against a group of people or individuals with the intent that other, unaffiliated parties will act upon it; it's the releasing doctored footage and a shooter show up at Planned Parenthood as a direct result of what he's been led to believe.

So with that in mind, let's talk about Russia's extreme anti-LGBT laws that banned the "promotion" of LGBT lifestyles to children. A move that specifically marked LGBT people as a threat to children, and resulted in neo-nazis meting out vigilante "justice" against gay men.


Groups such as this would lure unsuspecting gay men via dating sites, and brutalise and humiliate them on camera. They did so under the guise of combating child abusers, one group calling themselves "Occupy
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