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
3 new sequences from Spain (orange) indicate 2 more introductions, with the 3rd new sequence linking to the first sequence (green).

6/12
2 new sequences in Germany & 1 new sequence in Australia indicate separate introductions

7/12
1 new sequences in Italy represents another separate introduction (little hard to see in this picture), and 1 new sequence from France (yellow) indicates an additional introduction.

8/12
Additionally, we have the first sequences that fall in 501Y.V1 from Brazil (1), Jamaica (1), Luxembourg (1), & Pakistan (2).

Though hard to see on the larger tree, the 2 Pakistan sequences sit apart on the phylogeny, & thus indicate separate introductions.

9/12
The S:N501 'reduced UK' build is also updated. *Please remember not to use this build to look at connections between countries!* Use it only alongside the larger, complete S:N501 build.

10/12

https://t.co/9md0yn9Qgp
Finally, the country plots have also been updated. As countries are preferentially sequencing 501Y.V1 samples at the moment, the 'hot pink' sections *do not* represent true frequencies of the variant in countries!

https://t.co/c7wlQOLRiq

11/12
We can see the current screening process in action in the Swiss chart - variants with the 69/70 deletion are being preferentially sampled. Sequences from the 439K cluster also have that deletion - they're being picked up in the search to find 501Y.V1! 🙃

12/12

More from Dr Emma Hodcroft

🎉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
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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प्राचीन काल में गाधि नामक एक राजा थे।उनकी सत्यवती नाम की एक पुत्री थी।राजा गाधि ने अपनी पुत्री का विवाह महर्षि भृगु के पुत्र से करवा दिया।महर्षि भृगु इस विवाह से बहुत प्रसन्न हुए और उन्होने अपनी पुत्रवधु को आशीर्वाद देकर उसे कोई भी वर मांगने को कहा।


सत्यवती ने महर्षि भृगु से अपने तथा अपनी माता के लिए पुत्र का वरदान मांगा।ये जानकर महर्षि भृगु ने यज्ञ किया और तत्पश्चात सत्यवती और उसकी माता को अलग-अलग प्रकार के दो चरू (यज्ञ के लिए पकाया हुआ अन्न) दिए और कहा कि ऋतु स्नान के बाद तुम्हारी माता पुत्र की इच्छा लेकर पीपल का आलिंगन...

...करें और तुम भी पुत्र की इच्छा लेकर गूलर वृक्ष का आलिंगन करना। आलिंगन करने के बाद चरू का सेवन करना, इससे तुम दोनो को पुत्र प्राप्ति होगी।परंतु मां बेटी के चरू आपस में बदल जाते हैं और ये महर्षि भृगु अपनी दिव्य दृष्टि से देख लेते हैं।

भृगु ऋषि सत्यवती से कहते हैं,"पुत्री तुम्हारा और तुम्हारी माता ने एक दुसरे के चरू खा लिए हैं।इस कारण तुम्हारा पुत्र ब्राह्मण होते हुए भी क्षत्रिय सा आचरण करेगा और तुम्हारी माता का पुत्र क्षत्रिय होकर भी ब्राह्मण सा आचरण करेगा।"
इस पर सत्यवती ने भृगु ऋषि से बड़ी विनती की।


सत्यवती ने कहा,"मुझे आशीर्वाद दें कि मेरा पुत्र ब्राह्मण सा ही आचरण करे।"तब महर्षि ने उसे ये आशीर्वाद दे दिया कि उसका पुत्र ब्राह्मण सा ही आचरण करेगा किन्तु उसका पौत्र क्षत्रियों सा व्यवहार करेगा। सत्यवती का एक पुत्र हुआ जिसका नाम जम्दाग्नि था जो सप्त ऋषियों में से एक हैं।