BC FOR LATER READ
Saved by @CodyyyGardner

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
Norway has 3 new sequences (orange). 2 cluster together but differ by 1 mutation, making their relationship hard to confidently infer. The other sits separately and indicates an independent introduction.

6/12
Italy has 2 new sequences (orange). Zooming in (divergence view) we can see they are identical (yellow), so are likely a single introduction.

7/12
The USA has 2 new sequences, from Connecticut (orange). They sit separately from each other & other USA sequences on the three, indicating independent introductions.

8/12
Luxembourg has 2 new sequences (orange). They sit apart on the tree, indicating separate introductions.

Sweden has 1 new sequence (orange). It sits separately, indicating an additional introduction

9/12
In 501Y.V2:

Australia has sequences that fall into 501Y.V2 for the first time. Zooming in (divergence), we can see they are identical, indicating one introduction.

10/12
As always, the S:N501 "reduced UK" build is updated, & the country-graphs are also updated - remember: many places are preferentially sequencing S:N501 (hot pink), so the frequencies shown may not accurately reflect the true proportion of S:N501!

11/12

https://t.co/c7wlQOLRiq
Finally, the main CoVariants SARS-CoV-2 Variant Tracking page is updated with new links & a new section for S:E484 - but as always, I welcome Pull Requests & Issues in the repository, with papers or online resources I've missed!

12/12

https://t.co/6qBdWhREtl

More from Dr Emma Hodcroft

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
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
WORLD
Advertisement
Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
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
FOR LATER READ
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
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
FOR LATER READ

More from For later read

truth_serum007
truth_serum007
@truth_serum_007
💥BOOM💥 Linn Wood!! They can't stop what is coming!
Chief Justice John Roberts must resign today. Over the past several weeks, I have met with a courageous whistleblower who has risked his life to tell you the truth. Jeffrey Epstein arranged for the...
Part 1.1
FOR LATER READ
Rob Henderson
Rob Henderson
@robkhenderson
The common understanding of propaganda is that it is intended to brainwash the masses. Supposedly, people get exposed to the same message repeatedly and over time come to believe in whatever nonsense authoritarians want them to believe /1

And yet authoritarians often broadcast silly, unpersuasive propaganda.

Political scientist Haifeng Huang writes that the purpose of propaganda is not to brainwash people, but to instill fear in them /2


When people are bombarded with propaganda everywhere they look, they are reminded of the strength of the regime.

The vast amount of resources authoritarians spend to display their message in every corner of the public square is a costly demonstration of their power /3

In fact, the overt silliness of authoritarian propaganda is part of the point. Propaganda is designed to be silly so that people can instantly recognize it when they see it


Propaganda is intended to instill fear in people, not brainwash them.

The message is: You might not believe in pro-regime values or attitudes. But we will make sure you are too frightened to do anything about it.
FOR LATER READ , ALL
Advertisement
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."
FOR LATER READ
Dr Raul Pacheco-Vega
Dr Raul Pacheco-Vega
@raulpacheco
THREAD: On the full-fledged process of responding to a Revise-And-Resubmit (R&R).

I have written pieces of the process, but I hadn't actually written a thread or a blog post showcasing how all my blog posts fit with one another. I teach this process when I give workshops.

So here's what I do (now), and let me share a lesson from my past lives:

DO NOT SIT ON R&Rs.

I know, they're painful and scary and sometimes we don't know if our paper will get rejected in the end.

But remember, an R&R means an OPPORTUNITY to get your paper published.

Sitting on R&Rs, leaving them for later, and not prioritizing them has gotten me fewer publications. I know this for a fact. I am not ashamed of admitting that I have sometimes felt that I will not be capable of responding to multiple (often conflicting) comments.

HOWEVER...

Sustained, frequent advice from professors who are senior to me (though I am senior myself now too) is always the same and on-point:

The goal is the R&R.

You're not getting a desk rejection.

You are getting your work read, reviewed carefully, thought about, responded to.

What do I do now (and have been doing for the past few years, with success)

When I get the R&R (the "decision letter"), I make sure to calm down, because I am always afraid I'm going to get nasty comments. These have been (luckily) very rarely present in my latest submissions.
FOR LATER READ
JefimVogel
JefimVogel
@JefimVogel
LEEDS LEADS CLIMATE BREAKDOWN

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”
🧵


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

2/ Also a lot of "I do have sympathy for residents suffering from planes flying over their roofs at night, BUT” - followed by more blah blah.
One councillor kindly offered his advice: “the way to less noise is more planes”. Right, Sherlock. Want to try that in your backyard?🤦‍♂️

3/ The true sympathies were revealed at the end. The Panel's priority was not the well-being of those living under the flight path, nor the lives and livelihoods of threatened by climate breakdown. Their priority was a bigger, noisier airport, with a terminal in bronze-champagne.

4/ First declaring your sympathy for people’s suffering and then supporting a development that directly aggravates their suffering, is a proper kick in the face for those suffering the consequences. Like first declaring a climate emergency and then aggravating climate breakdown.
FOR LATER READ

You May Also Like

Vibhu Vashisth \U0001f1ee\U0001f1f3
Vibhu Vashisth 🇮🇳...
@VIBHU_Tweet
VEDIC COSMOLOGY, also known as Hindu Cosmology, and cosmography are both interesting and inspiring. Today’s “modern” Vedic texts originated around 3,000 B.C.E. This is the oldest scientific and the oldest religious doctrine known to the human race.


Our current astronomy of the solar system and universe has its roots in Vedic knowledge. It only shows that man had advanced knowledge of astronomy way before our current civilization came into existence.
We are here to talk about the Vedic version of the planetary system,

starting at the top from the eternal planets to the temporary planetary system within innumerable universes in the material world.

Talking about “cosmic manifestation,” we need to incorporate both spiritual and material existence.


The spiritual realm of the planets is everlasting, and this will forever be beyond what the material universe can encapsulate. The spiritual realm belongs to the “super dimensional” or “anti-material” dimension. It means that it is beyond what we can perceive,


beyond time as a linear dimension, and the space of our vision and perception.

There are innumerable planets, all indestructible and forever lasting. That is what the Vedas say about the spiritual planets. Our concentration here is more towards the material side of things.
ALL
Anumah, Abdulraheem Okehi \U0001f468\u200d\U0001f52c\U0001f1f3\U0001f1ec \U0001f1eb\U0001f1f7 \U0001f1f5\U0001f1f9 \U0001f1ea\U0001f1f8
Anumah, Abdulraheem Ok...
@AnumahABD
Department List of UCAS-China PROFESSORs for ANSO, CSC and UCAS (fully or partial) Scholarship Acceptance
1) UCAS School of physical sciences Professor
https://t.co/9X8OheIvRw
2) UCAS School of mathematical sciences Professor

3) UCAS School of nuclear sciences and technology
https://t.co/nQH8JnewcJ
4) UCAS School of astronomy and space sciences
https://t.co/7Ikc6CuKHZ
5) UCAS School of engineering

6) Geotechnical Engineering Teaching and Research Office
https://t.co/jBCJW7UKlQ
7) Multi-scale Mechanics Teaching and Research Section
https://t.co/eqfQnX1LEQ
😎 Microgravity Science Teaching and Research

9) High temperature gas dynamics teaching and research section
https://t.co/tVIdKgTPl3
10) Department of Biomechanics and Medical Engineering
https://t.co/ubW4xhZY2R
11) Ocean Engineering Teaching and Research

12) Department of Dynamics and Advanced Manufacturing
https://t.co/42BKXEugGv
13) Refrigeration and Cryogenic Engineering Teaching and Research Office
https://t.co/pZdUXFTvw3
14) Power Machinery and Engineering Teaching and Research
EDUCATION
Advertisement
Anshul Pandey
Anshul Pandey
@Anshulspiritual
THE IMPORTANCE OF DEVI BEEJ / BIJA MANTRA.

Once Suutji in his discourse with King Janmajeya repeated the words of Vyasji regarding the pronounciation of the word ऐ. Vyasji had heard the importance of this word in a meeting of all important saints at Naimisharanya.


There this story was discussed.

In that gathering of such great sages, Rishi Jamdagni asked a question to all the eminent luminaries. He wanted to know which diety is the most revered and gets satisfied easily with our prayers. So Lomash rishi replied that Devi

Bhagwati was one such diety. She will be satisfied and is ready to grant you a boon even if you just say the first letter of her beej mantra. In this context he narrated the story of Satyavrat. The story is as follows.

There lived a Brahmin named Devdutt in Kosal.

He was childless. He arranged for an elaborate yagya for a intelligent son to be born. He invited all the eminent rishi's to conduct this Yagya. Rishi Suhotra, Pael, Brahaspati Yagyavalka were assigned different tasks. Rishi Gobhil was asked to sing the Saamved.

He sang the verses very well, but he had to take respite in order to breathe between two verses. This angered devdutt. He spoke his thoughts to Gobhil rishi.

The rishi got very angry as devdutt did not realise the practicalities of singing. He cursed devdutt that
ALL
Robin Berjon
Robin Berjon
@robinberjon
Recently, the @CNIL issued a decision regarding the GDPR compliance of an unknown French adtech company named "Vectaury". It may seem like small fry, but the decision has potential wide-ranging impacts for Google, the IAB framework, and today's adtech. It's thread time! 👇

It's all in French, but if you're up for it you can read:
• Their blog post (lacks the most interesting details): https://t.co/PHkDcOT1hy
• Their high-level legal decision: https://t.co/hwpiEvjodt
• The full notification: https://t.co/QQB7rfynha

I've read it so you needn't!

Vectaury was collecting geolocation data in order to create profiles (eg. people who often go to this or that type of shop) so as to power ad targeting. They operate through embedded SDKs and ad bidding, making them invisible to users.

The @CNIL notes that profiling based off of geolocation presents particular risks since it reveals people's movements and habits. As risky, the processing requires consent — this will be the heart of their assessment.

Interesting point: they justify the decision in part because of how many people COULD be targeted in this way (rather than how many have — though they note that too). Because it's on a phone, and many have phones, it is considered large-scale processing no matter what.
TECH
Priyanka (Astrology Guidance)
Priyanka (Astrology Gu...
@AstroAmigo
1

From today, we will memorize the names of 27 Nakshatras in Vedic Jyotish to never forget in life.

I will write 4 names. Repeat them in SAME sequence twice in morning, noon, evening. Each day, revise new names + recall all previously learnt names.

Pls RT if you are in.

2

Today's Nakshatras are:-

1. Ashwini - अश्विनी

2. Bharani - भरणी

3. Krittika - कृत्तिका

4. Rohini - रोहिणी

Ashwini - अश्विनी is the FIRST Nakshatra.

Repeat these names TWICE now, tomorrow morning, noon and evening. Like this tweet if you have revised 8 times as told.

3

Today's Nakshatras are:-

5. Mrigashira - मृगशिरा

6. Ardra - आर्द्रा

7. Punarvasu - पुनर्वसु

8. Pushya - पुष्य

First recall previously learnt Nakshatras twice. Then recite these TWICE now, tomorrow morning, noon & evening in SAME order. Like this tweet only after doing so.

4

Today's Nakshatras are:-

9. Ashlesha - अश्लेषा

10. Magha - मघा

11. Purvaphalguni - पूर्वाफाल्गुनी

12. Uttaraphalguni - उत्तराफाल्गुनी

Purva means that comes before (P se Purva, P se pehele), and Uttara comes later.

Read next tweet too.

5

Purva, Uttara prefixes come in other Nakshatras too. Purva= pehele wala. Remember.

First recall previously learnt 8 Nakshatras twice. Then recite those in Tweet #4 TWICE now, tomorrow morning, noon & evening in SAME order. Like this tweet if you have read Tweets #4 & 5, both.
VEDICNAKSHATRA