2/14
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
2/14
3/14
Zooming in (divergence view), we can see 2 new sequences are identical (possible local transmission), & 2 differ by 2 mutations (1 each).
4/14
5/14
6/14
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
(UK data may be affected by subsampling due to large sequence numbers.)
8/14
These are a mix of separate introductions & local transmission.
Connections to French sequences are in the next tweet...
9/14
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
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
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
More from Dr Emma Hodcroft
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
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
More from For later read
1. The death of Silicon Valley, a thread
How did Silicon Valley die? It was killed by the internet. I will explain.
Yesterday, my friend IRL asked me "Where are good old days when techies were
2. In the "good old days" Silicon Valley was about understanding technology. Silicon, to be precise. These were people who had to understand quantum mechanics, who had to build the near-miraculous devices that we now take for granted, and they had to work
3. Now, I love libertarians, and I share much of their political philosophy. But you have to be socially naive to believe that it has a chance in a real society. In those days, Silicon Valley was not a real society. It was populated by people who understood quantum mechanics
4. Then came the microcomputer revolution. It was created by people who understood how to build computers. One borderline case was Steve Jobs. People claimed that Jobs was surrounded by a "reality distortion field" - that's how good he was at understanding people, not things
5. Still, the heroes of Silicon Valley were the engineers. The people who knew how to build things. Steve Jobs, for all his understanding of people, also had quite a good understanding of technology. He had a libertarian vibe, and so did Silicon Valley
How did Silicon Valley die? It was killed by the internet. I will explain.
Yesterday, my friend IRL asked me "Where are good old days when techies were
Where are good old days when techies were libertarians.
— Cranky (@rushingdima) January 9, 2021
2. In the "good old days" Silicon Valley was about understanding technology. Silicon, to be precise. These were people who had to understand quantum mechanics, who had to build the near-miraculous devices that we now take for granted, and they had to work
3. Now, I love libertarians, and I share much of their political philosophy. But you have to be socially naive to believe that it has a chance in a real society. In those days, Silicon Valley was not a real society. It was populated by people who understood quantum mechanics
4. Then came the microcomputer revolution. It was created by people who understood how to build computers. One borderline case was Steve Jobs. People claimed that Jobs was surrounded by a "reality distortion field" - that's how good he was at understanding people, not things
5. Still, the heroes of Silicon Valley were the engineers. The people who knew how to build things. Steve Jobs, for all his understanding of people, also had quite a good understanding of technology. He had a libertarian vibe, and so did Silicon Valley
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First thread of the year because I have time during MCO. As requested, a thread on the gods and spirits of Malay folk religion. Some are indigenous, some are of Indian origin, some have Islamic
Before I begin, it might be worth explaining the Malay conception of the spirit world. At its deepest level, Malay religious belief is animist. All living beings and even certain objects are said to have a soul. Natural phenomena are either controlled by or personified as spirits
Although these beings had to be respected, not all of them were powerful enough to be considered gods. Offerings would be made to the spirits that had greater influence on human life. Spells and incantations would invoke their
Two known examples of such elemental spirits that had god-like status are Raja Angin (king of the wind) and Mambang Tali Arus (spirit of river currents). There were undoubtedly many more which have been lost to time
Contact with ancient India brought the influence of Hinduism and Buddhism to SEA. What we now call Hinduism similarly developed in India out of native animism and the more formal Vedic tradition. This can be seen in the multitude of sacred animals and location-specific Hindu gods
i wonder if you can make a thread bout witchcraft in malaysia.. or list of our own local gods/deites..
— r a y a \U0001f319 (@lcvelylilith) February 20, 2020
Before I begin, it might be worth explaining the Malay conception of the spirit world. At its deepest level, Malay religious belief is animist. All living beings and even certain objects are said to have a soul. Natural phenomena are either controlled by or personified as spirits
Although these beings had to be respected, not all of them were powerful enough to be considered gods. Offerings would be made to the spirits that had greater influence on human life. Spells and incantations would invoke their
Animist ceremonies of a religious or magical nature were normally held for the purpose of divination or making a request. This would either be done at a keramat or at a shrine similar to the Thai spirit houses or Chinese roadside shrines pic.twitter.com/I1hliyi0x3
— \u2745\u1710\u170b\u1713\u170e (@uglyluhan) June 16, 2019
Two known examples of such elemental spirits that had god-like status are Raja Angin (king of the wind) and Mambang Tali Arus (spirit of river currents). There were undoubtedly many more which have been lost to time
Contact with ancient India brought the influence of Hinduism and Buddhism to SEA. What we now call Hinduism similarly developed in India out of native animism and the more formal Vedic tradition. This can be seen in the multitude of sacred animals and location-specific Hindu gods