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Dr Emma Hodcroft Profile picture
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27 Dec, 5 tweets, 3 min read
A "Zwischen den Jahren" (between the years) update of the focal S:N501 build, with data from 25th Dec. ❄️

In 20B/501Y.V1 (SE England variant), we have new sequences from Australia, Israel, & Hong Kong:

1/5
#Newcoronavirusvariant #SARSCoV2 #COVID19

nextstrain.org/groups/neherla…
Filtering to just look at the Hong Kong & Israel samples, we can see that the 2 Hong Kong sequences sit further apart on the tree, indicating two separate introductions.

2/5
nextstrain.org/groups/neherla…
Similarly, the 3 Australian sequences also sit apart on the tree, indicating separate introductions.

3/5
nextstrain.org/groups/neherla…
Looking at the 501Y.V2 (SA variant) we can see one sequence from the UK nesting within those from South Africa, indicating an introduction to England.

4/5
nextstrain.org/groups/neherla…
We're expecting more sequences in the next few days, & I will continue to update here with their positions in the phylogeny!

Most countries are now screening sequences immediately, so we will likely hear in the media first about cases. Still, the phylogeny can inform us!

5/5

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Dr Emma Hodcroft Profile picture
29 Dec
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… Image
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 ImageImage
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 Image
Read 8 tweets
Dr Emma Hodcroft Profile picture
28 Dec
Many are interested in using the 69/70 deletion to scan for cases of the new #SARSCoV2 variants.

As it can impact some primers (seen as an 'S drop-out' in PCR), it can be a high-throughput way to check for the 'SE England' variant - but some important things to remember!

1/5
First, the 69/70 deletion has arisen multiple times independently: not everything with 69/70 is the SE England variant!

You can see that 69/70del appears many times here: notably it's associated with 501Y.V1 (English variant) AND 453 & 439.

2/5
nextstrain.org/groups/neherla… Image
In particular, S:N439K is widespread across Europe, and about 3/4 of the sequences in this cluster have the 69/70del.
So there's a fair chance a 69/70del in continental Europe is part of this cluster, not the 'new variant' from England.

3/5
nextstrain.org/groups/neherla… Image
Read 6 tweets
Dr Emma Hodcroft Profile picture
24 Dec
Merry Christmas! 🎄 The latest focal S:N501 build is now up.

Zooming in on 20B/501Y.V1 (SE England variant), we can see new sequences in Europe from the Netherlands.

1/4
#Newcoronavirusvariant #SARSCoV2 #ChristmasCovid

nextstrain.org/groups/neherla…
Zooming in on this further, and switching to divergence view (showing mutations rather than time), we can see they share 1 unique mutation & then have 1 unique mutation each, suggesting 1 introduction, possibly from the UK, & onward transmission.

2/4
nextstrain.org/groups/neherla…
We can take a similar look at the Danish sequences. They too, share one unique mutation, & some further unique mutations, suggesting a single introduction & onward transmission.

3/4
nextstrain.org/groups/neherla…
Read 4 tweets
Dr Emma Hodcroft Profile picture
24 Dec
On this Christmas Eve, I would like to spare a thought for the many scientists, researchers, & lab technicians & assistants who have been 'called up' thanks to the new #SARSCoV2 variants.
It's been a tough year & many of us had hoped this week might be a well-earned break.

1/6
Academia/science is rarely a 9-5 job, & we're a bit famous for our tendency to overwork, but it's a rare year when evolutionary biology & phylogenetics are so urgently needed that we can't slip away for a few quiet days over Christmas!

2/6
(see alt text for the ornament shop!) https://www.etsy.com/listing/883890228/plush-virus-in-face-m
I imagine many, like myself, are humbled & proud that we can contribute to the efforts against #COVID19 #SARSCoV2.
But it's been an incredibly long, hard year for many of us, compounded by the same restrictions, loss, & loneliness that so many have felt.

3/6
Read 6 tweets
Dr Emma Hodcroft Profile picture
23 Dec
A case of the '#SouthAfrica' variant has been detected in the UK. There's also talk about a 501Y mutation in Wales.
It's getting confusing!

First: all 3 of these 501Y mutations are independent. It's appeared a few times, separately.

#Newcoronavirusvariant

1/10
We can see this because the 3 variants (UK=1, Wales=2, SA=3) are not next to or inside each other in the tree below. In fact, we need to trace back to before March to find their common ancestors:

2/10

nextstrain.org/groups/neherla…
Are the UK and South Africa variants the same? No. See this thread for more info:

Critically, the SA variant does not have the 69/70 deletion we see in the UK variant.

3/10

Read 10 tweets
Dr Emma Hodcroft Profile picture
21 Dec
Switzerland has now banned flights from the UK - following on from an increasing number of other countries.

If the new UK variant may already be in more countries across Europe, why are countries stopping flights from the UK?

#SARSCoV2 #COVID19

1/10

In short: numbers matter.

The number of people with the new variant in continental Europe is likely still small: with testing, tracing, identification & restrictions, we might be able to prevent them from passing the virus on. That's easier with 10 people than 1000.

2/10
However, border closures make the most sense when coupled with fast action *inside* countries as well.

Even a few cases can become a few thousand quickly, if there's nothing to stop them. So as well as border controls, countries need to be stepping up measures within.

3/10
Read 11 tweets

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