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


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).

First, Luxembourg has 3 sequences in 501Y.V1 for the first time. Each represents a separate introduction.

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).

Australia has 4 new sequences (red and orange) which are spread across the tree, representing separate additional introductions.

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.

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.

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.)

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...

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.

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.

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

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.


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.


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More from @firefoxx66

9 Jan
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.


nextstrain.org/groups/neherla… Image
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 ImageImage
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 ImageImageImage
Read 12 tweets
9 Jan
I'm getting some questions about this, so here you go: We do not have sequence evidence of a new, more transmissible "US variant" - it seems to be a misinterpretation.

Still, more sequencing in the US (& globally) will help us better track existing & emerging #SARSCoV2 variants!
Importantly: you can have spikes & rises in #SARSCoV2 infections without needing a new variant. We can see this clearly in Europe in autumn: we have a good idea of the variants circulating & no new (or old) variant is responsible. It was likely weather-related.
Similarly, season & holiday related changes in travel & behaviour, changing restrictions/mandates, school & university terms, & 'restriction fatigue' - just to name a few - can play a role in #SARSCoV2 case numbers. We can't & shouldn't blame every rise on a new variant.
Read 4 tweets
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.


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.


Oman has their first sequence which falls into 501Y.V1:

Read 14 tweets
5 Jan
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.


@jbloom_lab @Tuliodna

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).

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



Read 8 tweets
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.


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).

10 new sequences from Portugal (orange) indicate additional, separate introductions.

Read 12 tweets
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? 🗓️🤔

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.😷

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.

Read 28 tweets

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