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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
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
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
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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
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Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
The S:N501 build is now updated with data from 25th Jan.

Remember, you can always check on any country by just typing that country name in the 'Filter' box on the left menu!

1/18

https://t.co/FTjvV7T7wL


In the 501Y.V1 (B.1.1.7) variant, here are a few of the non-UK countries with new sequences in this variant, including Denmark, Italy, Spain, France, Portugal, Norway, Germany, the USA, South Kora, & Switzerland, & the UAE, Austria, & Czech Republic for the 1st time

2/18


Denmark has 52 new samples (some yellow), showing both separate introductions and further spread of existing local clusters.

3/18


Spain has 62 new sequences (orange & yellow). Many of these are separate introductions, and a few new sequences form distinct clusters. Some new sequences also cluster closely with older sequences (green).

4/18


France has 72 new sequences (orange & yellow). These show both separate introductions and clustering with older sequences.

5/18
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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
SOCIETY

More from For later read

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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Emily\u2661
Emily♡
@ItsEmilyKaty
To the person who thinks that they might be autistic. - a thread. /1

I imagine you have gone your entire life wondering why you are different, why you can't seem to understand things the way that others can and why everything just seems so hard. I'm proud of you for getting this far. /2

Part of you might be thinking:
"But if I was autistic, surely it would've been noticed when I was a kid? So maybe I'm making this up."
So many autistic people aren't diagnosed until they are adults, if diagnosed at all. You would not be the first and you won't be the last. /3

"My family and friends don't think that I could be autistic."
People's understandings of autism tend to be based off of the media, which doesn't show every possible presentation of autism, or based off of someone they know, and all autistic people present differently. /4

People's perceptions of autism can also be based off stereotypes, for example, "autistic people can't make eye contact, so you can't be autistic." While this is true for some, it isn't for all, so you can begin to see how one presentation of autism can't possibly fit everyone. /5
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Roland Baker
Roland Baker
@RolandBakerIII
Moderna's mRNA-1273 & Pfizer's BNT162b2 consist of mRNA 3821 nucleotides long encoding *all* 1273 amino acids of the Spike including a 2 Proline-stabilized RBD. This is a plain English Description of the code:
https://t.co/w7koHyMJjL

The article mentions a “10 nucleotide linker” (GCAUAUGACU) in the poly-A tail. This is described in the patent link below (Modification of RNA, producing an increased transcript stability and translation

Here is a link to the full mRNA code if you wish to download it, blast it or make up a batch in your garage


An overview of the encoded spike


Initial mouse
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Angus Johnston
Angus Johnston
@studentactivism
I’ve asked Byers to clarify, but as I read this tweet, it seems that Bret Stephens included an unredacted use of the n-word in his column this week to make a point, and the column got spiked—maybe as a result?


Four times. The column used the n-word (in the context of a quote) four times. https://t.co/14vPhQZktB


For context: In 2019, a Times reporter was reprimanded for several incidents of racial insensitivity on a trip with high school students, including one in which he used the n-word in a discussion of racial slurs.

That incident became public late last month, and late last week, after 150 Times employees complained about how it had been handled, the reporter in question resigned.

In the course of all that, the Times' executive editor said that the paper does not "tolerate racist language regardless of intent.” This was the quote that Bret Stephens was pushing back against in his column. (Which, again, was deep-sixed by the paper.)
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Daniel Finn
Daniel Finn
@DanFinn95
Some familiar figures are pushing the absurd and defamatory claim that Ken Loach supports Holocaust denial. The story of this bogus talking-point, which relies upon multiple layers of falsehood and guilt-by-association, makes for a revealing case-study. 1/

It dates back to the 2017 Labour conference. In a NYT op-ed, Howard Jacobson claimed that “a motion to question the truth of the Holocaust was proposed” from the conference floor—a crude fabrication, which the NYT sanctioned in its pages. 2/


If you follow the link supplied by Jacobson or his editors, you’ll see that he was wrong on 3 counts: it wasn’t a motion, it wasn’t at the conference, and it wasn’t in favour of Holocaust denial. Quite the hat-trick! 3/

At a fringe meeting, granted no official status by Labour, an Israeli-Jewish speaker, Miko Peled, had said that he didn’t think Holocaust denial should be a criminal offense (which it is in some European countries). 4/

This is a perfectly reasonable position to hold—that opinions, no matter how wrong-headed or morally objectionable, should not be a matter for the criminal law—and of course it does not mean that Peled himself questions the truth of the Holocaust. 5/
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Vibhu Vashisth
Vibhu Vashisth
@VIBHU_Tweet
शमशान में जब महर्षि दधीचि के मांसपिंड का दाह संस्कार हो रहा था तो उनकी पत्नी अपने पति का वियोग सहन नहीं कर पायी और पास में ही स्थित विशाल पीपल वृक्ष के कोटर में अपने तीन वर्ष के बालक को रख के स्वयं चिता पे बैठ कर सती हो गयी ।इस प्रकार ऋषी दधीचि और उनकी पत्नी की मुक्ति हो गयी।


परन्तु पीपल के कोटर में रखा बालक भूख प्यास से तड़पने लगा। जब कुछ नहीं मिला तो वो कोटर में पड़े पीपल के गोदों (फल) को खाकर बड़ा होने लगा। कालान्तर में पीपल के फलों और पत्तों को खाकर बालक का जीवन किसी प्रकार सुरक्षित रहा।

एक दिन देवर्षि नारद वहां से गुजर रहे थे ।नारद ने पीपल के कोटर में बालक को देख कर उसका परिचय मांगा -
नारद बोले - बालक तुम कौन हो?
बालक - यही तो मैं भी जानना चहता हूँ ।
नारद - तुम्हारे जनक कौन हैं?
बालक - यही तो मैं भी जानना चाहता हूँ ।

तब नारद ने आँखें बन्द कर ध्यान लगाया ।


तत्पश्चात आश्चर्यचकित हो कर बालक को बताया कि 'हे बालक! तुम महान दानी महर्षि दधीचि के पुत्र हो । तुम्हारे पिता की अस्थियों का वज्रास्त्र बनाकर ही देवताओं ने असुरों पर विजय पायी थी।तुम्हारे पिता की मृत्यु मात्र 31 वर्ष की वय में ही हो गयी थी'।

बालक - मेरे पिता की अकाल मृत्यु का क्या कारण था?
नारद - तुम्हारे पिता पर शनिदेव की महादशा थी।
बालक - मेरे उपर आयी विपत्ति का कारण क्या था?
नारद - शनिदेव की महादशा।
इतना बताकर देवर्षि नारद ने पीपल के पत्तों और गोदों को खाकर बड़े हुए उस बालक का नाम पिप्पलाद रखा और उसे दीक्षित किया।
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Anu Satheesh \U0001f1ee\U0001f1f3
Anu Satheesh 🇮🇳...
@AnuSatheesh5
Eri Katha Ramar Temple
Maduranthakam

Eri Katha Ramar temple is located at Maduranthakam near Chengalpattu of Tamil Nadu. Beautiful Kodanda Ramar of about 8ft holding Ma Sita's hand & with Lakshmana. This temple story is connected with Sri Ramanujar.
@LostTemple7


It was here Periya Nambigal performed Pancha Samskaaram to Ramanujar under Magizham tree.
Sri Ramanujar was on his way from Kanchipuram to meet Sri Periya Nambigal at Sri Rangam to become his disciple. Sri Periya Nambigal also started towards Kanchipuram to meet Ramanujar.


They both met here at Madurantakam.
Small Mandapam where Ramanujar undertook Pancha Samskaaram is seen in the temple. Separate sannidhi is for Periya Nambigal & Ramanujar & this is the only temple where Ramanujar is seen as a Grahastha (married person) and not in Sanyasa kolam.


Story says about an incident which occurred during British rule. The Madurantakam lake bund was about to breach, due to heavy rain & village will be flooded if it happened. Dt collector was Cl. Lionel Blaze who took efforts to protect the bund & asked for the piles of stones


in the temple to protect it. But it was meant for Janakavalli ( sita) Thayar sannidhi which faced shortage of fund. Lionel Blaze prayed Sri Ramar to save the bund and if so he will provide fund to construct.
That night he saw in the lightning, Sri Rama & Lakshmana walked along
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Bartosz Ziembinski
Bartosz Ziembinski
@zmbnski
Still wondering about this 🤔


save as q
Q
Respectable Lawyer
Respectable Lawyer
@RespectableLaw
There's been a lot of talk about the missionary killed by the natives of North Sentinel Island. They're probably so aggressive because of this weirdo, Maurice Vidal Portman. So here's a big thread about this creep and some facts from my decade-long obsession with the island.


The Sentinelese are often described as “uncontacted,” but this not strictly true. They had a very significant contact in 1880 with Commander Portman.

Portman, the black sheep third son of some minor noble, was assigned by the English Royal Navy to administer and pacify the Andaman Islands, a job he pursued from 1880-1900 with the full measure of his own perversity.


Portman was erotically obsessed with the Andamanese, and he indulged his passion for photography by kidnapping members of various tribes and posing them in mock-Greek homoerotic compositions.


During his 20 years in a sexualized heart of darkness, Portman measured and cataloged every inch of his prisoner’s bodies, with an obsessive focus on genitals.
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Noah Smith
Noah Smith
@Noahpinion
1/Politics thread time.

To me, the most important aspect of the 2018 midterms wasn't even about partisan control, but about democracy and voting rights. That's the real battle.

2/The good news: It's now an issue that everyone's talking about, and that everyone cares about.

3/More good news: Florida's proposition to give felons voting rights won. But it didn't just win - it won with substantial support from Republican voters.

That suggests there is still SOME grassroots support for democracy that transcends

4/Yet more good news: Michigan made it easier to vote. Again, by plebiscite, showing broad support for voting rights as an

5/OK, now the bad news.

We seem to have accepted electoral dysfunction in Florida as a permanent thing. The 2000 election has never really
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