BC SOCIETY
Saved by @SteveeRogerr

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
If we look just at 20B/S.484K (top cluster), we can see there are clusters of sequences in the UK, Canada & the USA, and exports to Norway, Malaysia, & Australia.

6/10

https://t.co/D3AE3V9GOw
Importantly, the clusters in the USA & Canada are identical (though each country also has an additional imports), so they may be from a group of travellers returning, rather than local transmission (left pic). They also date from Nov - so not recent (right pic).

7/10
We can see 8 UK sequences in the 20B/S.484K cluster. There are 2 clusters, but neither are identical. They could be from a common exposure (same part of Brazil, same travel group), or possibly be local transmission. These samples are from Nov & Dec.

8/10

https://t.co/w5oISsCFYb
If we look at 20J/501Y.V3, we can see that sequences only are found in Brazil and Japan (known travel to Brazil), but no other countries.

9/10

https://t.co/4lzibcXzmW
Hopefully, this thread helps distinguish what the '2 variants' are that are circulating in Brazil, and from which there have been samples detected in the UK.

And, I hope it shows how phylogenetics can help us 'tell viruses apart' & follow them as they move & change!

10/10
To add: why are scientists concerned about these variants circulating primarily in Brazil?

@BillHanage write a fantastic thread here:

11/10

https://t.co/qvF92BV7CZ

More from Dr Emma Hodcroft

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
SOCIETY
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
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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
FOR LATER READ
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
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
FOR LATER READ

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David Neiwert
David Neiwert
@DavidNeiwert
1) “Eliminationism” is a term you need not just to become familiar with, especially in today’s American rush toward authoritarianism. This will be a long, illustrated thread explaining what it means, how it works, and why Donald Trump is now our Eliminationist in Chief.


Warning: Some images contain violence and are disturbing.

Also warning: This thread is ridiculously long. 75 tweets is insane. I apologize. But this stuff is important. I hope you find it compelling anyway. If not, I understand.

2) So, what exactly do we mean by “eliminationism”? Here’s the academic definition:


3) It was largely coined by Holocaust scholar Daniel Jonah Goldhagen in his 1996 book Hitler’s Willing Executioners, about the role ordinary Germans played in the Holocaust, which he described as fueled by “eliminationist antisemitism.”


4) The book describes how in reality the largest numbers of Jews and other victims killed by Nazi directive were rounded up and gunned down or immolated en masse and buried in mass graves by ordinary Germans and non-Jewish residents of German-occupied territories.
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Anthony B. Bradley
Anthony B. Bradley
@drantbradley
I'm teaching a class on race and after reading bell hooks we've moved on to @JohnHMcWhorter. Fact: liberals/progressives generally will never critique the poor moral choices of disadvantaged blacks and tend to blame black morality on "white racism." https://t.co/GEvSKupDox via

Meanwhile conservatives, generally, struggle to confess that Jim Crow was a (Christian) conservative movement. This is why we can't make any progress in 2020. The idea that black people *and* white people *both* have zero moral culpability on our past or present is fiction.

It's not "racist" for a white male to say black men in urban areas commit more crimes in their own neighborhoods and, therefore, are more likely to have contact with police. And it's false that men who commit violent crime & property crime are only doing so because of poverty.

Yes, evangelical Christians, in Jesus name, supported and defended Jim Crow, resisted integration, and struggle with white nationalism as an idol in 2020. Absolutely! Many of their pastors are cowards for never addressing or aiding and abetting it.

Yes, there are cultural patterns in disadvantaged black communities that are not derivative of white racism but emerge from the fact that black men & women, just like white men & women, chose, on purpose, actions that lack virtue & wisdom. Why? B/c all humans are morally flawed.
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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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BlackCalvinist
BlackCalvinist
@BlackCalvinist
LOL at the uptick in followers.

Fair Warning: I believe that Cultural American Patriotic Churchianity (CAPC for short - aka White Evangelicalism/Christian Nationalism) has caused more damage to the body of Christ and the credibility of the church than CRT ever has or will.

It's been a systemic problem since the founding of the country (indeed, before the founding of the country) and has contributed to the church being complicit in chattel slavery, Jim Crow, cointelpro, redlining and a host of other things the Bible condemns as sin.

The conflation of Christianity with Americanism since the founding of the country has left too many actual believers confusing love of country and culture with biblical Christianity (thus, in their minds, to fight against conservative political culture is also to fight against

what they think is biblical Christianity). It's part of what makes it okay to minimize the sins of men like Dabney while extolling his ability as a theologian in other areas, or minimizing it as him being 'a man of his time'. It also allows you to have an atheist speak at your

Christian conference while condemning your brother who holds different political views than you, but professes the same faith you do.

On the other side of the issue, the phrase 'black lives matter' is true because of the Imago Dei. Debate your momma about it if you disagree.
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George Monbiot
George Monbiot
@GeorgeMonbiot
I’ve just finished some research about the use of biosolids (human sewage sludge) as farm manure. The results will keep me awake at night.
¾ of biosolids in the UK are spread on farmland. The rules about what it can contain are not fit for purpose. Please read and share this 🧵

Biosolids typically contain a wide range of synthetic chemicals, including antibiotics and other pharmaceuticals, personal care products, microplastics and persistant organic pollutants, among them “forever chemicals”. Yet testing is restricted to a small number of contaminants.

Spreading them across the land means spreading them through the foodchain and the ecosystem. There’s plenty of evidence of uptake of many of these chemicals by crops, earthworms and other soil animals, and of large-scale antibiotic resistance developing among soil bacteria.

When soil is blown or washed off the land, these chemicals enter the air and water. Some seep into groundwater. We're likely to eat, drink and breathe them. It’s hard to say what the health thresholds are, or what the combined impact of this cocktail of synthetics might be.

Yet the issue has been wilfully neglected by governments. Regulation is negligible. Farmers in the UK are “responsible for knowing the levels of any potentially toxic elements” before spreading sludge. But how? With an on-farm lab that can test for 80,000 possible contaminants?
SOCIETY

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Here is why 👇

Startups fixed the problem of innovation, that corporations lack.

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Agile startups could launch, iterate fast and eventually stumble upon new growing market opportunities.

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Anu Satheesh
Anu Satheesh
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Thiruvairanikulam Mahadeva Temple
Ernakulam Kerala🚩
#temples

Temple is known as Sabarimala of Women

Thiruvairanikulam Mahadeva Temple is situated on the banks of the Periyar River. Siva Temple has a separate sannidhi for Parvathi Devi which will be open only for 12 days a year


The Nadathurappu Mahothsavam happens every year on Malayalam month of Dhanu. On opening day, a grand procession starting from Akavoor Mana carries the ornaments of Devi to the temple. Swayamvara Archana is the main pooja here to clear the obstacle in marriages.
Legend is that 👇


Vigraham existed in another place called Iranikulam. A Namboodiri of Sreemoolanagaram used to visit the Iranikulam temple regularly. Akavoor Chathan, a boatman will take him to the Iranikulam temple and back. Because of Bhakthi of Namboodiri, Shiva traveled with him to his place.


Akavoor Chathan identified Siva chaitanyam and their family built a temple here. Parvati devi herself will cook Nevidyam here for Shiva, which was witnessed by a priest. Devi was angry at this and decided to leave the place. But when the priest offered his sincere apology👇


Devi blessed him and told that she will be present here 12 days in a year. Thus the period which begins from Thiruvathirai Day in Dhanu is known as the Nadathurappu festival.
Temple Nada opens today night.
Picture credit: Google.
🙏🕉🙏
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