The underlying problem isn't that the UK COVID-19 app is 'too sensitive.'

With a quarter-million cases & few restrictions, even if only correct contacts were pinged, that would be a huge number of alerts & isolations!

And yes - that's going to cause a lot of disruption 🤷🏻‍♀️

1/5
We're papering over the consequences of huge case numbers with debates around sensitivity.

Yes, we can turn sensitivity down - but # of alerts will continue to grow with cases - still potentially annoying people (who uninstall) & certainly continuing to cause disruption.

2/5
This isn't to say we shouldn't try to make pings more accurate, rather, that this isn't an actual solution to high number of pings right now.

Even if 30% pings were bad & we could get perfection now, UK cases rose 33% this week - so we are still at crazy high notifications.

3/5
Yes, there are legitimate debates to be had around who should isolate at all if the govt "strategy" is not to actively limit transmissions - but even with a fairly strict isolation definition, *with large case numbers will come large numbers of isolations & further cases.*

4/5
The higher the number of cases 📈
The harder it is to bring them down 😰
The greater increase in health risk 🏥
The more disruption from those isolating & ill 🤒
The more financial hardship follows 💸
The more confidence & ability to resume normal activities stalls🙅🏻🛍️🍲

5/5

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More from @firefoxx66

15 Jul
I've run preliminary @nextstrain focal builds on 20B/S:796H (B.1.1.318) (pictured) & 20A/S:210T (B.1.619).

These aren't part of CoVariants (yet?) but they've caught a couple eyes and I thought it was worth taking a closer look.

1/8 Image
20B/S:796H (B.1.1.318) is behind most of the recent increase in 'other' variants circulating in Greece (shown in grey on the CoVariants plot, below - disregard last point, low sequence #'s).

It's very prominent in Greece, but also found worldwide.

2/8

nextstrain.org/groups/neherla… ImageImage
Taking a closer look at Europe only, we can see there's a large cluster in Greece, but also distinct clusters in Switzerland & Ireland, & many sequences from other countries scattered between.

3/8

nextstrain.org/groups/neherla… Image
Read 8 tweets
7 Jul
🎉CoVariants.org update! 🎉

4 new variants & focal builds added:
- 21G (Lambda) (C.37)
- 21H (B.1.621)
- 20B/S:732A (B.1.1.519)
- 20A/S:126A (B.1.621)

Also - we have awesome new flags on the Per Country page! 🏁🚩

Let's take a closer look...👀

1/10
21G (Lambda) was recently classified a VoI by @WHO & included in @nextstrain builds. It seems to originate in South America - we can see its prevalence in countries like Chile, Argentina, Ecuador, & Peru (purple-pink):

2/10
Looking at the focal build, we can see that 21G (Lambda) has also been found in North America, Europe, the Middle East, and Australia.

Lambda has a unique 7 AA deletion in Spike, & a mutation at S:L452Q.

3/10

nextstrain.org/groups/neherla…
Read 10 tweets
24 Jun
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
Read 9 tweets
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
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
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

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