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

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

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

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

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

THREAD: We filed RTIs on behalf of @no2uid asking the Ministry of Health and Family Welfare questions about how your personal data will be protected while you're using CO-WIN, the COVID-19 vaccination registration platform.

We got answers... kind of. Here's the new info.

1/n

Just like with Aarogya Setu, many Indians are worried that about the potential CO-WIN has to leak your data or threaten your privacy in the name of dealing with a pandemic. So, we asked the MOHFW some questions about data protection under the Right to Information Act.
2/n

In the responses we received, MOHFW said that it cannot provide us with a privacy policy on CO-WIN (?!).

Thankfully it was clarified that Aadhaar is not mandatory for registration on Aarogya Setu or CO-WIN, and that physical vaccine certificates will be provided to everyone.
3/n

The data it says it will collect will be your name, gender, date of birth, photo ID, and number.

National, State, and District level admins will have access to use the app, but there is not much further clarity on this point.

But most importantly...
4/n

The responses (or rather lack of them) related to your data privacy and protection are completely vague. We received no clear answers on which Ministries/Depts will have access to your personal data, the permissions provided, etc. This is a failure in terms of transparency.
5/n

1/ The “I Have a Dream" speech is one of the most extraordinary speeches in American history. You should read it again. First, a few thoughts about the common American heritage Dr. King relied upon in calling Americans to rededicate themselves to the unfinished work of freedom.

2/ Dr. King delivered his speech in what he called the “hallowed spot” of the Lincoln memorial. More than a picturesque backdrop, King relied on America’s reverence for Lincoln and the common celebration of Lincoln’s words and acts, especially the Emancipation Proclamation.

3/ “Five score years ago…” King echoes the words of the Gettysburg Address. Like Lincoln, King invokes the Declaration of Independence and the fundamental principles of American freedom, “life, liberty and the pursuit of happiness.” Every person in that crowd knew these words.

4/ The Declaration, Constitution and Emancipation Proclamation declared and established the fundamental American principles of freedom that all Americans knew and believed in. But these principles and promises remained unfulfilled for black Americans.

5/ Lincoln’s audience knew the history of slavery and many had suffered personal loss in the ongoing war. Dr. King’s audience knew the history of violent racism, segregation, and unequal economic opportunity. The Proclamation freed the slaves, “but the Negro still is not free.”

In the 90s I was a host on a talk radio station in LA, the same that aired Rush. I was president of LA NOW, & the liberal wkend host when he visited the station. He was so vilified by my then-crowd, I expected a monster. Instead, I met a remarkable, kind and encouraging man... 1/

He was gregarious & generous when we met. He shook my hand & I was shocked that he was nice & genuinely curious about my radio work and activism. I realized I was going to have a fascinating conversation 2/

There were many events during this time as a radio talk show host that changed me. It was my first job in the medium starting in 1993. My meeting Rush & our conversations made me realize the left had been lying to me about many things... 3/

Rush was not a monster, he wasn’t evil, he did not mean people harm, he wasn’t a bigot, or any of the other smears lobbed against him by my leftist associates. I liked him very much, and while we disagreed on many things (then) he was nothing has he had been painted 4/

In my conversations with him, we talked about the issues and despite the disagreements, he also took time to give me advice about hosting, style, connecting w the audience, etc. He encouraged me and gave me advice that made a huge difference in my career… 5/