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Dr Emma Hodcroft Profile picture
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5 Feb, 5 tweets, 4 min read
New focal builds for S:N501 & S:E484 are now live!

nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…

1/5
As well as the major variants of concern, we can spot a couple of other clusters stemming from an 'old' #SARSCoV2 clade, 19B (originating in late 2019).

19A & 19B haven't been around much since early 2020, as they were overtaken by 20A, B & C (which carry D614G).

2/5
However, a few branches of 19B seem to be popping back up again recently.

In the UK, we can see a recent cluster that's acquired S:E484K (along with other mutations in S).

@theosanderson illustrated this one a few days ago!

3/5
nextstrain.org/groups/neherla…
Another 2 branches of 19B have mutations at S:N501Y (yellow) and S:N501T (blue).

The S:N501Y also have (among others) L452R & H655Y. Many also have Q677H
The S:N501T also have H655Y & 69 del.

4/5
nextstrain.org/groups/neherla…
Should we be worried? 😱

I'm not sure there's enough evidence yet to panic about these 2 clusters. However, they are another piece showing that we're seeing these 501 & 484 mutations repeatedly. 🤔

Certainly, it's something scientists are keeping a close eye on! 🔍

5/5

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
4 Feb
I'm still getting a *lot* of media enquiries - more than I can even respond to! So here's some of my best tips for how to reach out to me to maximise your chances of success (though I imagine they're true of other scientists too!)

1/7
(Just as a disclaimer - even if you use all of these, I can't promise I write back, or that I can say yes. If emails slip off the 'front page' of my inbox they basically fall into a black hole 😬. And sometimes I just cannot take any more interviews, even great ones.)

2/7
1. Please tell me what time zone you're in!

If I want to say 'yes' that means a pencilled-in appointment goes into the calendar immediately - so I need to know when you're likely to be awake. If I have to email you to find out... it might not happen.

3/7
Read 7 tweets
Dr Emma Hodcroft Profile picture
3 Feb
The new focal builds are now up, with data up to 2nd Feb.

Updated S:N501 build:
nextstrain.org/groups/neherla…

Updated S:E484 build:
nextstrain.org/groups/neherla…

1/15
Unfortunately it takes too long for me to do the detailed tweet threads I did originally. However, I'll try to hit a few highlights...

In 20I/501Y.V1 (B.1.1.7):

2/15
The Netherlands now has over 300 sequences in 501Y.V1, with clear signs of community transmission.

3/15
Read 16 tweets
Dr Emma Hodcroft Profile picture
28 Jan
🎉The new and improved CoVariants.org is here! 🎉

We're hoping to make this a one-stop location to track not only the 'headline' variants, but many different #SARSCoV2 mutations & variants that scientists are keeping an eye on.

Let's take a tour of the site!

1/12
The buttons on the left will take you to pages focused on key variants & mutations, while the menu at the top will help you jump between info pages (FAQ) & pages compiling together information about many variants (ex: Per country).

Let's take a look at the 20A.EU1 page

2/12
Here, we can
- Click through to a dedicated @Nextstrain build for the variant (1)
- See a list of the defining mutations (2)
- Learn a bit about the variant & see links to papers (3)
- See a distribution of 20A.EU1 per country (4)
- See a protein model! (pic 2)

3/12
Read 13 tweets
Dr Emma Hodcroft Profile picture
27 Jan
The S:N501 build is now updated with data from 25th Jan.

Remember, you can always check on any country by just typing that country name in the 'Filter' box on the left menu!

1/18

nextstrain.org/groups/neherla…
In the 501Y.V1 (B.1.1.7) variant, here are a few of the non-UK countries with new sequences in this variant, including Denmark, Italy, Spain, France, Portugal, Norway, Germany, the USA, South Kora, & Switzerland, & the UAE, Austria, & Czech Republic for the 1st time

2/18
Denmark has 52 new samples (some yellow), showing both separate introductions and further spread of existing local clusters.

3/18
Read 18 tweets
Dr Emma Hodcroft Profile picture
25 Jan
As we head deeper into 2021, a gentle reminder to double-check your #SARSCoV2 sequencing scripts for hardcoded '2020's! 😬

We've seen a real uptick recently in sequences with sampling dates in Jan 2020, with divergence that clearly indicates they meant 2021! 📅🤦🏻‍♀️
"How can we tell?" you might wonder. Actually, these cases are pretty easy to spot!
Let's take a look at two sequences reported as being from Jan 2020 - 1 in green, 2 in blue. (Spoiler, green is the imposter.)
This view is 'date view' where sequences are plotted on the X-axis by the date they were sampled. Then, we try and infer how they're connected using their genetic information - specifically, what mutations they share & don't share.
Read 10 tweets
Dr Emma Hodcroft Profile picture
22 Jan
I got a lot of messages last week about a 'new variant' in Bavaria, Germany.

Notably, scientists at @ChariteBerlin have announced this is *not* a new variant. Link may stop working so screenshot attached.

Read on to see the sequences...

1/4
spiegel.de/wissenschaft/c…
3 seqs indicated in red are apparently from the hospital. They're coloured by deletion at position 69, which likely caused them to be flagged (501Y.V1 has it too). However, they're related to other sequences in Germany & Turkey, also w the deletion.

2/4
nextstrain.org/groups/neherla…
We do see the 69/70 deletion has appeared independently previously. While this is interesting, I don't think it increases concern significantly about this group of sequences, which are part of a larger cluster that's been circulating in Germany since spring 2020.

3/4
Read 4 tweets

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