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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
Switzerland has 2 new sequences. One (marked 1st pic) is a clear separate introduction. The other (marked 2nd pic, zoomed, divergence) is from Bern & identical to an earlier sequence from Zurich ('ZH'). This could be local transmission or a common exposure.

6/14
There is 1 new sequence from Singapore (orange).

Zooming in (divergence view), we can see it is identical to 2 older sequences, which may indicate local transmission or a common exposure.

7/14
There are ~19 new non-South African sequences in 501Y.V2, including for the first time from Botswana (6), South Korea (1), & France (1), as well as additional sequences from the UK (~9).

(UK data may be affected by subsampling due to large sequence numbers.)

8/14
At least 9 new sequences from the UK are now in 501Y.V2 (UK data may be impacted by subsampling).

These are a mix of separate introductions & local transmission.

Connections to French sequences are in the next tweet...

9/14
France has 2 sequences in 501Y.V2. They cluster together, which may indicate local transmission or a common source.
They are related to seqs from England, but whether this is European transmission or exposure to common diversity in S Africa can't be distinguished clearly.

10/14
Botswana has 6 sequences in 501Y.V2. One sits apart from the others, indicating at least 2 introductions.

The other 5 cluster together, but are separated by a 1-3 mutations. This could indicate local transmission or transmission from unsampled South African diversity.

11/14
Lastly, South Korea has a sequence in 501Y.V2 for the first time.

12/14
As previously, the country plots are also updated. Lithuania is now added!

Remember: many countries are currently focusing sequencing efforts on S:N501 variants, so frequencies are often not true representations of the 501Y variants.

13/14

https://t.co/c7wlQOLRiq
Finally, we've added a new label to help identify a cluster of sequences with a S:N501*T* mutation currently circulating in Australia.

This is another independent appearance of a S:N501 (again, to T, not Y) mutation, & is not related to 20C/501Y.V2 or 20B/501Y.V1.

14/14

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
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
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Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
The focal S:N501 build has been updated with data from 15 Jan, & includes 164 non-UK, non-South African sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

The S:E484 build has also been updated. Includes 501Y.V3 & 20B/S.484K (predominantly in Brazil).

1/16

https://t.co/3bdttjKVl4


There are 161 new, non-UK sequences in 501Y.V1 (B.1.1.7) from the Netherlands, Denmark, Australia, Spain, Norway, Germany, the USA, & Switzerland, and from Turkey and Ecuador for the first time.

2/16


Turkey has 19 sequences in 501Y.V1 for the first time. These indicate many independent introductions, though a few clusters may indicate local transmission, and pairs with common exposure.

3/16


Ecuador has 4 sequences in 501Y.V1 for the first time, which represent 2 separate introductions (pic 2). 3 are identical, and may represent exposure to a common source (pic 3). The connection to the Spanish sequence may be a common source, or onward transmission.

4/16


Denmark has 66 new sequences (orange). A few are independent introductions, though many link with older sequences, showing continuing local transmission.

5/16
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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
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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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

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#Suven – Journey of my first 50 bagger…

I bought #Suven first in Apr 2013 around Rs 20…today after almost 7.5 years, its Rs 1000 (Suven pharma 920 adjusted for bonus + Suven Life 80)..CAGR of almost 68% for 7.5 years. I am fortunate to hold it throughout the journey and

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add on multiple occasions on way up. Like to share my experience in this thread for everyone’s benefit..

First time I bought because I like the management focus on R&D. It had chosen the most difficult therapeutic area in pharma which is CNS and it was investing the cash

2/n

flow it used to earn from CRAMS. It also used to write off all the R&D expenses in the P&L instead of capitalizing it in BS. That gave me lot of comfort about management quality.

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I loaded around 250-300 knowing the value of CRAMS business itself is more than 300.

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A Brian For All Four Seasons
A Brian For All Four S...
@bguthrie
So, here's my contrarian take on Why Trunk-Based Development Is Great But Probably Won't Work For You. Buckle up, it's a long one.

From time to time I talk about, or boost someone else's discussion of, "classical" continuous integration/trunk-based development/push-to-master/whatever. I do this because I've personally worked like this and I genuinely think it's a marvelous way to write software.

I've also, at this point in my career, failed—a bunch of times!—to bring this technique into practical use on the teams and organizations I've worked with. As a result, while I still do it myself, I don't focus as much on encouraging it in others.

The technoculture that's presently in vogue is what I think of as async/individual—optimize for the individual, performance-manage the individual, decouple the individual from others so they can be their best, most productive, most heroic selves.

This is in contrast to what I think of as sync/team—a culture that leans into interdependence and collaboration. If you've never worked on a team that collaborates very closely every day for months or years on end (and likes it) you've likely not experienced a team like this.
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MALUME ZANO
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The Misrepresentation of the Levites

[A Bonus Smallanyana Thread]

Disclaimer:

This thread is not part of the Angelology Threads we are focusing on this month of February but it is a response to what uNkulunkulu laid on my heart when I was finishing up Part 3 of the main threads.

This thread is also not an attack but a personal observation.

Let's Begin 📖

The Levites or the Tribe of Levi was/ is one of the original 12 tribes of Israel. Descended from Levi the son of Jacob. Descendants of Aaron, the first high priest of Israel. The Levites were designated as the priestly class, also known as the Kohanim.

Principal roles:

Singing Psalms during temple services
Teachers of the Word
Judges (Politics)
Construction and Maintenance of the Temple
Serving as Guards

The Levites were known to stand for truth, at all cost. Some considered them an army set apart by and for uNkulunkulu.

Numbers 18:6

And behold, I have taken your brothers the Levites from among the people of Israel. They are a gift to you, given to the Lord, to do the service of the tent of meeting.
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GAVNet
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Daily Bookmarks to GAVNet 02/14/2021

Study identifies significance of atmospheric rivers for New Zealand

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