Share this page!

Maybe Scrolly?
Dr Emma Hodcroft Profile picture
Twitter logo
24 Jun, 9 tweets, 6 min read
Another brief update: many of the latest focal builds are still baking🥖, but I've gone ahead and pushed up some finished Delta-related runs.

In particular, I wanted to look a little at what's being called 'Delta Plus' = Delta + S:417N mutation

1/9
nextstrain.org/groups/neherla…
S:417N has actually popped up multiple times in the Delta variant - it's of interest because it's thought to be related to immune escape & is also found in Beta.

But looking below, there are 2 main clusters - @PangoNetwork lineages AY.2 & AY.1

2/9
nextstrain.org/groups/neherla…
I don't have 1 build that shows these clusters perfectly yet (working on it!), so we'll use 2 - the focal builds for Delta & S:K417.

Delta: nextstrain.org/groups/neherla…
S:K417: nextstrain.org/groups/neherla…

3/9
Looking first at AY.1, it's found in Europe & Asia (a little US), with notable clusters in the UK, Switzerland, Portugal, Poland, & Japan.
(Delta build shown/linked first, then S:K417 build)

4/9
nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…
Looking at AY.2, it's predominantly in the USA, particularly in California.
(Delta build shown/linked first, then S:K417 build)

5/9
nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…
How do AY.1 & AY.2 differ?

In Spike, AY.1 has additional mutations at T95I (in Iota) & W258L, while AY.2 has additional mutations at V70F (deleted in Alpha & Eta) & A222V (in EU1).

AY.2 also has G142D, which is present in some AY.1 sequences.

6/9
Since I'm based in Switzerland, let's take a closer look at some of what we see there... 🇨🇭

7/9
Here's the Swiss AY.1 cluster - mostly in Geneva, Vaud & just over the border in France (location marked in red)
Note Geneva does a lot of sequencing, so more likely to pick up clusters!

Divergence view shows the order of transmission is unclear!

8/9
nextstrain.org/groups/neherla…
Switching to a Swiss-focused Delta build, we look at other Swiss Delta clusters.

The large Geneva cluster is the AY.1 we just looked at, but there are other clusters in Geneva, Basel Stadt & Land, & Bern.

9/9
nextstrain.org/groups/neherla…

• • •

Missing some Tweet in this thread? You can try to force a refresh
　

Keep Current with Dr Emma Hodcroft

Dr Emma Hodcroft Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @firefoxx66

Dr Emma Hodcroft Profile picture
24 Jun
🛠️CoVariants.org Update!🛠️

The latest push to CoVariants tweaks how sequences are classified as Variants in some cases, & you'll notice changes in some graphs as a result.

Overall, this change means better classification for lower-quality sequences👍🏻👏🏻

Read on...

1/6
CoVariants looks at nucleotide changes to classify sequences - a sequence must have all of a list of changes to be classified.🧬🔢✅

But sometimes during a sequencing, part of the DNA might not be 'read' ("low coverage"), so we have no information for some locations. ❓

2/6
If some of the positions CoVariants is looking for have low coverage & no information, they won't get classified as Variants. 🧬1⃣2⃣4⃣✖️

This can particularly impact places sequencing lower-quality sequences, as CoV will 'undercount' how many are variants! 📉

3/6
Read 6 tweets
Dr Emma Hodcroft Profile picture
21 Jun
🎉.@WHO and @nextstrain names come to CoVariants.org!🎉

Now it's easier than ever to identify the variant you're interested in - and with beautiful new badges! 🔍

Also, the date plotting on the Per Country page has been made clearer!📈

Let's take a look... 👀

1/4
CoVariants now uses the same clades (including WHO names) you see on Nextstrain.org, making it easy to find a variant of interest!

This comes with beautiful new variant badges - & an updated Name Table that includes Pango & WHO badges, & old CoVariants names! 🎨🌈4

2/4 Image
Of course, this carries over to the Per Country page, where the variant order is also more intuitive. 📜

Additionally, the date axes have been made clearer with more lines, & mouse-over now shows exactly what period the data comes from! 🗓️

3/4 ImageImage
Read 4 tweets
Dr Emma Hodcroft Profile picture
7 Jun
It's incredibly thrilling to have this paper out at last! 🎉

"Spread of a #SARSCoV2 variant through Europe in the summer of 2020"

(aka The Tale of Europe, Summer Travel, & EU1)

But why should we care about summer 2020 now? Let's take a look...

nature.com/articles/s4158…

1/24
Last Sept, while looking for #SARSCoV2 sequences that could help us understand transmission across #Switzerland, I noticed a cluster that was present not just across Switzerland, but also the UK & Spain. This is the cluster that eventually came to be known as 20E (EU1).

2/24
EU1 had a mutation at position 222 in spike - this caught my eye.

From mid-summer 2020, EU1 (orange) expanded across Europe - becoming the most prevalent variant in most of Western Europe, & accounting for >30% of sequences in Europe by the end of 2020.

3/24
Read 24 tweets
Dr Emma Hodcroft Profile picture
3 Jun
I am incredibly grateful to have received the 1st dose of the #COVID19 vaccine💉today!

A year ago, I never imagined we'd have multiple vaccines available & being distributed now.
At the same time, I'm saddened the privilege I've been granted is still unavailable to so many.

1/4
This is often particularly the case in countries where continuing high case numbers & outbreaks mean lives are still being lost & people being hospitalized. We must continue to ask countries to do more to realise equitable & fair vaccination access.

2/4
nature.com/articles/s4156…
This is esp true for Western countries which are starting to reach high vaccine levels.

I call on wealthy countries to propose a plan for how they are going to contribute to better & more equal vaccine distribution.📢💉

We aren't safe until all of us are safe. 🤲🏻🧑🏿‍🤝‍🧑🏻🧑🏼‍🤝‍🧑🏻🧑🏾‍🤝‍🧑🏻

3/4
Read 4 tweets
Dr Emma Hodcroft Profile picture
14 May
Transparency & open communication is *so key* in this pandemic.

At @nextstrain we don't claim to be perfect - but you know who we are, how we work, & we try incredibly hard to have open conversations with the community: building trust & better research.

#openscience #opensource
It can be easy to say things like "we are too busy to tweet" or "we don't have time to talk to everyone." I 💯 get it! Not every one of our emails is answered, not every discussion post responded to. But if you want to truly be part of a community: you have to open up to it. 👐🏻
It's painful sometimes: it means being open to change, being transparent about how everything works & how decisions are made -- it means openly crediting & celebrating others' work and contributions. 🎉 But all of that is vital in building a stronger scientific community. ⛓️
Read 4 tweets
Dr Emma Hodcroft Profile picture
2 May
🗓️CoVariants.org is updated🗓️, with some cool new additions:
- B.1.617.1/2 are added as 20A/S:154K & 20A/S:478K 🎉
- Beautiful new name table 📑🍾
- Mutation list displayed in full as a "side-sausage"🌭

Let's take a tour... 😁

1/7
I know this took a little time (thank you for your patience! 🙏🏻), but B.1.617 is now in CoVariants as the two sublineages 617.1 & 617.2, called respectively:
- 20A/S:154K (has 484Q)
- 20A/S:478K (no 484Q, has 478K)

2/7
We can see the two lineages best in the India graph of the 'Per Country' page - with S:154K in brighter green, & S:478K in darker green. (Note sequencing may not be representative)

They also show up in low numbers in some other countries.

3/7
CoVariants.org/per-country
Read 8 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!

Follow Us on Twitter!

Like this author's thread?

Get emails when @firefoxx66 has new unrolls!

Check out other threads from @firefoxx66!

Read all threads by @firefoxx66

:(