BC SOCIETY
Saved by @CodyyyGardner

🎉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
Denmark has 24 new sequences, shown in orange.
2 identical sequence at the top are separate introduction(s?) than the larger cluster below.

The other sequences form a tight cluster very indicative of onward transmission.

6/23
1 new Australian sequence (the large orange dot) is close to an older sequence (large green).

From the phylogeny alone, it's hard to say if these are connected or separate, as the sequences are identical. (Vertical order is not meaningful for identical sequences!)

7/23
Finally, there are 2 new sequences from Italy (orange).

1 (top) seems to be a separate introduction. The other (zoomed view) may be related to an earlier Italian sequence as they're separated by 1 mutation, but we cannot say for sure.

8/23
Now: 69/70del variants. Why do we care about 69/70del? Well, this deletion is found in 501Y.V1, but also in other major variants like S:Y453F & S:N439K.

Read/see more in the 69del section of my 'SARS-CoVariants' tracking page!

9/23

https://t.co/9eKGmBKKe6
In a new Virological post @bblarsen1
& @MichaelWorobey identify a novel 69/70del lineage in the USA:
https://t.co/6qUN3nlYA9

10/23
In the focal S:H69- build, we can see this cluster below.

Importantly, in this build the cluster appears to be close to 501Y.V2, but this is a focal build so this connection must be interpreted cautiously!

11/23

https://t.co/CgWL7o7W4c
We can also see the cluster in our soon-to-go-live-today @nextstrain North American build (subsampled, in grey).

(In the build live at 14.30CET 1 Jan the 'cluster' is only 1 sequence! We'll push the new one later today!)

12/23
Notably we do see 69/70del clusters pop up often (as well as individuals/pairs with the deletion) - here's just a few:

18 sequences from the UK, Denmark, Germany & France.

13/23

https://t.co/ZVJDv67PDL
A small cluster of 4 sequences from England, Germany, Australia.
https://t.co/T8xfvuaCto

A small cluster of 6 sequences from England.
https://t.co/fCUAK6mhXA

14/23
A cluster of 8 sequences from the Ivory Coast and Burkina Faso.

15/23

https://t.co/5jvtHtygx9
We can also see 69/70del popping up inside of variants other than the recognised 501Y.V1, 453, & 439:

We can see ~10 sequences in 20A.EU2 (S:477) from France with 69/70del. Gaps aren't used in the phylogeny building, so they don't cluster here.

16/23

https://t.co/OOkwr8dlyJ
Interestingly, @richardneher has queried all the 69/70 deletions in SARS-CoV-2 sequences (all across the tree), and they all occur with the same nucleotide pattern, implying this is a good way to get this deletion, for one reason or another.

17/23

https://t.co/kIu3woMnbE
Finally, a brief note on 20A.EU1.

This is the variant that expanded in Spain before spreading across Europe over the summer (you can read more in our preprint below). It is the most prevalent variant in Europe, containing ~64,000 sequences.

18/23

https://t.co/tTgE9I2Mdn
We have no evidence that the mutations in 20A.EU1 (notably S:A222V) make it more transmissible - we think its spread was mostly due to summer travel.

But long after summer travel has ended, it persists (in orange below) - & continues to spread...

19/23

https://t.co/zLZ72luHE2
In the last 2 weeks we've seen the first appearance of sequences in 20A.EU1 in the USA, Thailand, Malaysia, Peru, Finland, Israel, & South Korea - all sampled in autumn.

20/23

https://t.co/hXIPuqrCmt
This is a variant with no evidence of increased transmissibility, during a time when global travel is severely depressed.

20A.EU1's movement across Europe & the world show how effectively & efficiently #SARSCoV2 #COVID19 can spread.

21/23

https://t.co/AiPX50GRew
Our #SARSCoV2 strategies must take this into account: getting cases down in your country won't last if they are being imported from elsewhere.

And it reminds us how vital & informative it is to track the virus via phylogenetics - only possible with good sequencing.

22/23
2020 has often been a stressful, sad, lonely, desperate, scary year.

But it has also been one where we've seen what science can accomplish when resources are made available & scientists work together.

With all we leave behind in 2020, let's carry that into 2021!

23/23

More from Dr Emma Hodcroft

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
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
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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
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
SOCIETY
Dr Emma Hodcroft
Dr Emma Hodcroft
@firefoxx66
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
FOR LATER READ

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