The focal S:N501 build is now updated with data from 13 Jan!

There are a total of 247 non-UK & non-South African sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

I'll do an additional thread later on, covering S:E484 & the 'Ohio variants'.

There are 244 new sequences in 501Y.V1 (B.1.1.7) from Australia, Belgium, Denmark, Germany, India, Israel, Italy, Netherlands, New Zealand, Norway, Portugal, Singapore, Spain & USA, as well sequences as from Ecuador and Greece for the first time.

Greece has 3 new sequences in 501Y.V1 for the first time. They indicate 2 separate introductions.

Ecuador has 2 sequences for the first time. They also indicate 2 separate introductions.

The USA has 61 new sequences (orange), from Florida, Minnesota, California, Pennsylvania, & New York.

A few of these represent separate introductions. Others form distinct clusters that may indicate ongoing local transmission.

Israel has 35 new sequences (orange). Some of these show separate introductions, but many link with older sequences, indicating ongoing local transmission.

The Netherlands has 34 new sequences (orange). A few of these represent separate introductions, but most form a large cluster with older sequences from the Netherlands, indicating ongoing local transmission.

Portugal has 31 new sequences (orange). Though hard to see in the zoomed-out view, most of these represent separate introductions. There is one case where 2 new seqs are identical to an older one, but this could be a common exposure source.

Denmark has 20 new sequences (orange). A few of these indicate separate introductions, but must cluster with older sequences in smaller groups or in the very large Danish group previously identified, indicating local transmission.

Norway has 14 new sequences (orange). Most indicate separate introductions, but a few are identical to or related to an older sequence, which may indicate local transmission.

Spain has 11 new sequences (orange). All of these indicate separate introductions, though some new sequences link together to form tight clusters. This could indicate local transmission or a common source.

New Zealand has 10 new sequences (orange). All represent separate introductions, though some new sequences are linked together.

Singapore has 6 new sequences (orange). Though hard to see in zoomed-out view, most of these indicate separate introductions.

Italy has 6 new sequences (orange). It's a bit hard to see in the zoomed-out view, but none of these link directly with older samples, indicating separate introductions - though 2 new seqs link together.

Germany has 4 new sequences (orange). Though hard to see in the zoomed-out view, these all represent separate introductions.

Australia also has 4 new sequences (orange), including the first from Western Australia. These indicate separate introductions, though 2 of the new sequences are identical (marked in red).

India has 2 new sequences (orange, one hidden behind the green - pic 1). One is a separate introduction, the other links with a previous sequence (pic 2).

Belgium has 1 new sequence, which links 1 mutation away from a previous sequence (pic 3).

There are 3 new non-South African sequences in 501Y.V2, from Germany for the first time. They are identical, which may indicate a common exposure.

The updated country plots will go up soon, and I'll add another thread later on S:E484 & the 'Ohio variants'.

The updated country plots are now up. As always, be careful interpreting plots as many countries are selectively sequencing S:N501 & S-drop outs (which often increases S:N439), so frequencies are often not representative!


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More from @firefoxx66

15 Jan
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 link🙂

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… Image
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!

3/10 ImageImage
Read 11 tweets
14 Jan
There's been a lot of news today about 'new variants in Brazil' & 'S:E484' and 'Ohio variants'. A short thread discussing what we know about each.


#SARSCoV2 #Ohio #BrazilVariant #Brazil #COVID19 Image
There are two variants circulating in Brazil: 20J/501Y.V3, recently detected in Japan & prevalent in Manaus. And temporarily-labelled '20B/S.484K', a larger clade circulating more widely in Brazil.

They both carry the spike mutation 484K, though this arise separately.

2/11 Image
S:E484K is also found in 501Y.V2 (primarily circulating in South Africa).

Why are we particularly concerned about S:E484K? You can read more at, as discussed in a tweet from earlier this week:


Read 14 tweets
12 Jan
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).

Read 23 tweets
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

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