Happy Tuesday! The latest focal S:N501 build is now updated with sequences from 11 Jan.
There are 101 new sequences in the 501Y.V1 (B.1.1.7 #b117) & 501Y.V2 variants.

Additionally, I'll include some updates on S:E484K in this thread.


There are 97 new non-UK sequences in 501Y.V1, including the first sequences in the cluster from Slovakia, Mexico, & Belgium, plus additional sequences from the Netherlands, Denmark, Australia, Spain, Ireland, & Sweden.

Slovakia has 10 sequences that fall in 501Y.V1 for the first time. These are closely linked, & likely indicate a single introduction and ongoing transmission (remember: vertical distance is not meaningful on the same branch - position of the 2 English samples is arbitrary).

Belgium has 5 sequences in 501Y.V1 for the 1st time, indicating 3 separate intros. 3 seqs cluster together (zoomed, divergence), indicating a single introduction. The connection to Netherlands might indicate transmission, or 2 transmissions from same diversity in the UK.

Mexico also has a sequence that falls into 501Y.V1 for the first time.

Ireland has 36 new sequences. Many represent separate introductions, but some do cluster with older sequences & may represent local transmission, or introductions from the same UK diversity.

Denmark has 29 new sequences (orange). These represent both new introductions, and further expansion of the large cluster (zoomed view).

The Netherlands have 6 new sequences. All fall within the section of the tree marked in red.
Zooming in, the new sequences are marked in red: 2 are separate introductions. Zooming in further (divergence view), cluster at the top are identical to an older sequence.

Australia has 6 new sequences, including the first from Northern Territory and Victoria. 1 pair of sequences from Victoria are identical to each other, representing one introduction.

Spain has 2 new sequences (yellow). One represents a separate introduction. The other links to older Spanish sequences, but it's unclear from sequences alone if this is local transmission or transmissions from a common source.

Sweden has 2 new sequences, marked in red. Both represent independent introductions. The second one is hard to see, but zooming in shows this more clearly.

Now turning to 501Y.V2:

There are 4 new non-South African sequences in 501Y.V2, including the first from Ireland (3) and the Netherlands (1).

Ireland has 3 sequences in 501Y.V2 for the first time. They cluster together, and may indicate either local transmission, or a common exposure (pictures 1 & 2).

The Netherlands has its first sequence in 501Y.V2 (picture 3).

As usual, the updated country graphs are also available. As always, interpret with care: countries are selectively sequencing to track 501Y.V1, so proportions of sequences are not representative for many countries.


Finally, an updated focal S:E484 build is also up.

S:E484K is found predominantly in the 501Y.V2 variant, & in a cluster of sequences primarily in Brazil, though it has appeared numerous times in the past.


S:E484K has been discussed recently as there are suggestions it may impact how well the immune system can recognise the virus, particularly if you've been infected with SARS-CoV-2 before.

Links to the studies are on CoVariants.org/#se484

Additionally, over the weekend, travellers from Brazil to Japan were found to be infected with a novel variant with many mutations, including S:E484K & S:N501Y.
Translated report linked below.


To help viewers identify these new samples from Japan, I've added a *temporarily* label to the S:E484K build: 20B/S.484K.501Y.

Additionally, I've added a *temporary* label to the Brazilian cluster with S:E484K: 20B/S.484K.

Interestingly, though the recent Japanese sequences carry S:E484K & seem to originate from Brazil, they do *not* branch from the larger 484K cluster in Brazil, but instead sit on a long branch separately within the 20B Clade.

Getting case numbers down saves #LivesAndLivelihoods, and reduces #SARSCoV2's opportunities to explore situations with unique selection pressures, potentially resulting in mutations expanding that we'd rather not see.

Help make my updates more boring: bring cases down!

More information on the Belgian sequences here:
PS - For related but slightly-different-angle updates on 501Y.V1 (B.1.1.7) & 501Y.V2 (B.1.351), you should follow @AineToole & keep an eye on her tweets about updated reports!

To learn more about the new variant that was found in sequences from Japan (484K+501Y) earlier in the thread, be sure to check out this great post from @nmrfaria & @CaddeProject.
This is a variant circulating in Manaus, Brazil



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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.


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.

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.

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
8 Jan
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.

Read 14 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

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