Headlines like the one circulating about India always need to be taken cautiously: until we have sequence data, speculation about a new variant or new mutations is entirely that - speculation.

But let's dig into what's being reported right now about 40,000 breakthroughs...

1/N
Headlines are saying things like "40,000 breakthrough COVID cases". But what does breakthrough mean here? Most generally, at least in Western media, this is used to refer to infections in fully-vaccinated (commonly 2-dose) people.

2/N
However, 1 site reporting the 40,000 defines this as "people contracting the disease a second time or fully vaccinated".
Another implies this is infection after 1 or 2 doses.

3/N

indiatoday.in/coronavirus-ou…

news18.com/news/india/ker…
So lets look at all breakdowns:
According to Kerala's dashboard, 15,759,471 have 1 dose, 6,442,507 have 2 (these also seem to be included in 1 dose counts).

So, if 40,000 is out of fully vaccinated people, that would be 0.6% of vaccinated people.

4/N

dashboard.kerala.gov.in/covid/
If it's 40,000 out of everyone with 1 or more dose, that's 0.25% of vaccinated people.

If it's 40,000 out of everyone previously infected (3,415,595) or fully vaccinated (6,442,507) (assuming none of these people overlap), that's 0.4%.

5/N
Even though these numbers change a little bit depending on definition, the takeaway is that this is well within the expected efficacy of vaccines.

It's easy for big numbers to sound scary, but context matters! Here, the number of people vaccinated is much, much bigger!

6/N
Of course, ongoing genetic surveillance, including of breakthrough cases, remains critical for keeping an eye on new mutations & variants. But these numbers, in context, don't need a variant to explain them!

7/N

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More from @firefoxx66

28 Jul
Today, my best birthday present is being fully vaccinated! 🎂

But so many still aren't - & the pandemic has wrecked havoc on routine vaccinations too.

Donate to @gavi, @UNICEF or others & I'll match up to $500! Send your receipt to vaccine_donations@protonmail.com & plz RT!

1/
As well as desperately requiring stronger action towards more equitable #COVID19 vaccination, the pandemic has meant so many children weren't able to get basic vaccines.

This could add unnecessarily to the already too-large burden of the pandemic.

2/

who.int/news/item/15-0…
The pandemic has hit a lot of people hard in many ways, including financially. Please do not give if it would cause you hardship. ❤️

There are other ways you can help!
Talk to an unvaccinated friend 🗣️, or put pressure on your government to do more to help globally! 📨

3/
Read 4 tweets
19 Jul
I want to repeat what others have said:

**If you do not get vaccinated against SARS-CoV-2, you /will/ get infected one day.**

We won't eliminate SARS-CoV-2.
The choice isn't "vaccine or not" - it's "vaccine or infection". This is critical for weighing up risks/unknowns.

1/5
If the mindset is "vaccine or not", it is easy to think that waiting & watching is safer, because you stay in 'nothing happens' territory.

But this isn't accurate. As we see now: unvaccinated people are where cases are spiking & this is going to remain true for a long time.

2/5
I still hear concern from people about the 'unknown long-term effects' of vaccination.

But what I don't hear people also considering is the unknown long-term effects of COVID-19.

Or a fair comparison of the well-known shorter-term effects & risks of both.

3/5
Read 5 tweets
16 Jul
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
Read 5 tweets
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

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