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Dr Emma Hodcroft Profile picture
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28 Dec, 6 tweets, 3 min read
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…
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…
In the UK & particularly SE England, using the 69/70del as a proxy for the variant works because it is in many areas the most common variant.

In other places, where frequency is expected to be lower, it's very important to double-check S drop-out results!!

4/5
Finally, the South African variant (501Y.V2) does *not* have the 69/70 deletion - but we know it has also been import outside of SA.

So, if also interested in looking for 501Y.V2, don't depend on 69/70del - it won't pick this up!

5/5
For a more detailed thread on the 69/70del & "S drop-out", see here!

6/5

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Dr Emma Hodcroft Profile picture
29 Dec
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… Image
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 ImageImage
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 Image
Read 8 tweets
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 10 tweets
Dr Emma Hodcroft Profile picture
27 Dec
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…
Read 5 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

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