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Dr Emma Hodcroft Profile picture
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5 Jan, 8 tweets, 5 min read
Following some increased interest tonight in S:E484, a new focal build is now up!

This build is created by pulling out all sequences with a mutation at nucleotide 23012 & adding background sequences.

1/8
@jbloom_lab @Tuliodna

nextstrain.org/groups/neherla…
Mutations at nucleotide 23012 causes changes in the amino-acid (AA) at position 484 in Spike. We can see here it changes from E (green) to Q (yellow), K (blue), & R (red).

2/8
Changes at position 484 are found most prominently in the 501Y.V2 variant (originating in South Africa), ID by @Tuliodna @rjlessells & team
as well as in a cluster of sequences primarily in Brazil, ID by @atrvlncc & team

3/8
nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…
You can read more about each of these variants in these preprints:

501Y.V2: medrxiv.org/content/10.110…

S:E484K in Brazil: medrxiv.org/content/10.110…

4/8
However, they're also found in many other places around the world - this mutation has arisen multiple times in many places. Everywhere with a dot that's not just green has had sequences with a change at S:E484.

5/8
Importantly, as pointed out by @jbloom_lab, mutations at S:E484 have been popping up since very early in 2020. However, many of these don't seem to have expanded into larger clusters.

6/8
Many labs around the world are hard at work looking into the impact of S:E484 mutations. You can read some just-released work by @jbloom_lab here:



7/8
This build & S:E484 aren't yet linked on my SARS-CoV-2 Variant Tracking site - but they will be up very soon! I'll be adding it to the regularly tracked & updated builds 👍🏻

8/8
github.com/hodcroftlab/co…

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
7 Jan
Each day brings new challenges, but here's an update to the dedicated S.N501 build, using data from 6 Jan 2021 to keep you going.

There are 42 new non-UK sequences in 501Y.V1 (B.1.1.7) & 7 new non-South-African sequences in 501Y.V2.

1/14

nextstrain.org/groups/neherla… Image
There are 42 new non-UK sequences in 501Y.V1 from the Netherlands, Italy, Hong Kong, Finland, Sweden, Germany, USA, Switzerland, Brazil, and the first sequence from 501Y.V1 in Oman.

nextstrain.org/groups/neherla…

2/14 Image
Oman has their first sequence which falls into 501Y.V1:

3/14 Image
Read 14 tweets
Dr Emma Hodcroft Profile picture
5 Jan
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

nextstrain.org/groups/neherla…
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
Read 12 tweets
Dr Emma Hodcroft Profile picture
4 Jan
European countries have likely bought time by stopping/restricting UK flights to reduce 501Y.V1 (B.1.1.7) import. Vaccine rollouts are progressing, & spring is around the corner.

But what do the next few months have in store? What should we be preparing for? 🗓️🤔
#SARSCoV2

1/24
First, some good news: The fact we have a vaccine 💉 is fantastic🎉, & it will make a difference - but we likely won't have enough people vaccinated to really impact transmission levels in the next few months. We must hold fast to other methods until more are vaccinated.😷

2/24
More good news: Last spring & summer brought reductions in cases: the virus does seem seasonal.
This means spring🌸& summer🌞2021 should help reduce transmission📉, giving us a great window to scale-up vaccination before autumn🍂 & hopefully a break in strict restrictions.

3/24
Read 28 tweets
Dr Emma Hodcroft Profile picture
1 Jan
🎉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
nextstrain.org/groups/neherla…

Image link
nextstrain.org/groups/neherla…
Canada, Germany, & Switzerland all have sequences that fall in 501Y.V1 for the first time, scattered across the tree.

3/23
Read 24 tweets
Dr Emma Hodcroft Profile picture
29 Dec 20
The latest focal #SARSCoV2 S:N501 build, with data from the morning of 29 Dec, is now up!

In the SE England (N501.V1 / B.1.1.7) & South African (N501.V2) variants we see new sequences from Portugal, Norway, Finland, Sweden, & South Korea.

1/8
nextstrain.org/groups/neherla…
Within N501.V1 (SE England variant):

There is 1 sequence now from Sweden, 2 from Norway, & 2 from Finland. The 2 Finnish sequences & 2 Norwegian sequences are separated on the tree, indicating 2 separate introductions in each country.

2/8
There are 3 sequences from South Korea clustering together. Zooming in (& in divergence view) we can see they are closely related, and likely indicate 1 introduction.

3/8
Read 8 tweets
Dr Emma Hodcroft Profile picture
29 Dec 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
nextstrain.org/groups/neherla…
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
Read 10 tweets

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