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Nov 6 • 9 tweets • 7 min read
🎉CoVariants.org Update!🎉

22F (XBB) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/9
#XBB #22F
This is in line with the recent addition of 22F (XBB) as a @nextstrain clade - read more on that below! 👇🏻

2/9
As I tweeted earlier, 22F (XBB) is a recombinant variant - the first officially elevated using the Nextstrain clade designations. You can read more about what that means in the thread below!

3/9
On the 22F page, you can read about some initial 22F / XBB work on neutralizing titres, see a list of defining mutations, a plot of the variant growth, link to Aquaria protein viz, & see a list of other mutations present in the variant.

4/9
covariants.org/variants/22E.O…
There's also a link to the 22F / XXB @nextstrain focal build: nextstrain.org/groups/neherla…

Here, we can zoom in on the clade & get a closer look at how 22F sequences are distributed around the world, & their diversity.

5/9
On the Per Country page, 22F / XBB is already clearly visible in India & Singapore, & starting to appear in smaller numbers in other countries, like Austria & Australia. Remember that sequencing data is always a few weeks (at least) behind.

6/9
covariants.org/per-country
Finally, on the Shared Mutations page, you can see how 22F's / XBB's Spike mutations compare to other VoC, including its Omicron family.

7/9
covariants.org/shared-mutatio…
More information on 22F / XBB will become available in due course.
As always, CoVariants.org is open-source & we welcome your PRs & suggestions to add more studies & information to variant pages! (Or any error-catching!)

github.com/hodcroftlab/co…

8/9
As before, I've created a file for 22F / XBB mapping all defining mutations (relative to ancestral), including nuc->AA. This is available on CoV github!

Huge 🙏🏻 to all who helped check it! (Esp @DoktorYak @CorneliusRoemer & @ChaoranChen_ !)

github.com/hodcroftlab/co…

9/9

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
Nov 6
I got verified when the option arose, to try to make it harder for others to impersonate me & spread pandemic misinformation under the guise of being me. That's all.
I think for that purpose, it's really useful. But I won't pay for it.

1/5
As others have said, I put a lot of work into my tweet threads - sometimes hours. That's time that is already taken away from my 'real' work. Though I consider it privilege to be able to do this public service work, I won't pay to do it.



2/5
I have no plans to stop tweeting for now. Though it will be a lot less rewarding if nobody gets to see those tweets. If that seems to be the case, I will probably stop, because I'm not doing this for myself. I love the connections I make on twitter!

3/5
Read 5 tweets
Dr Emma Hodcroft Profile picture
Nov 2
You might be seeing a lot about XBB these days, & we're in the process of adding it to @nextstrain, Nextclade, & CoVariants.org (as 22F).

You might also be hearing it's a 'recombinant' - but what does that mean? Let's take a look.

1/9 A diagram showing two SARS-...
We've been hearing of recombinants for a while now (remember 'Deltacron'?). They can sound scarier than they are!
The process itself is likely common, but we only 'see' recombinants when someone is infected with two distinct lineages, with different mutation patterns.

2/9
When a virus copies itself, it can 'template switch' between different genomes floating around. If those are all the same, the end product isn't different!

But if distinct lineages are there at the same time, we can spot these 'chimera' children - recombinants!

3/9 Schema showing genomes as c...
Read 9 tweets
Dr Emma Hodcroft Profile picture
Nov 1
I'm pleased that case numbers & hospitalizations in many European countries have a downward trend - but hesitant to overinterpret this.

#SARSCoV2 is seasonal & while that isn't entirely due to temperature, some of it is - & this season in Europe has been... quite warm!

1/4
Here are the daily temperatures in Basel, & how they compare to average (black line) from @meteoschweiz. As you can see, we've almost been having 'August temperatures' in October! Much of Europe has enjoyed a similarly mild autumn 🌞🍂🍁

2/4
While this is great news for autumn walks & cutting #COVID19 transmission (eating outside, continuing outside activities, keeping windows open), it probably won't last - as temperatures do start to dip 🥶, we should be aware that transmission may be impacted!

3/4
Read 4 tweets
Dr Emma Hodcroft Profile picture
Nov 1
🗓️CoVariants.org Update🗓️

In preparation for more flexibility in adding variants, CoVariants.org now processes & colours recombinant sequences separately - you can spot them in brown in the Per Country graphs. 🔀🔀

1/5
Previously recombinants weren't included in CoVariants as they presented some unique problems - but now they're included and shown separately. (If any recombinants are designated as variants, they'll show up as their designated variant instead!)

2/5
For most countries these numbers are quite small (see UK above) & aren't really visible in the graphs - but for a few countries we can see recombinants that spread well in a country for a short time, like XAM in Panama in spring 2022.

3/5
Read 5 tweets
Dr Emma Hodcroft Profile picture
Oct 21
🎉CoVariants.org Update!🎉

22E (BQ.1*) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/8
#BQ1 #22E

covariants.org/variants/22E.O… Image
This is in line with the recent addition of 22E (BQ.1*) as a @nextstrain clade - read more on that below! 👇🏻

2/8
On the 22E page, you can read about some initial 22E / BQ.1 work on neutralizing titres, see a list of defining mutations, a plot of the variant growth, link to Aquaria protein viz, & see a list of other mutations present in the variant.

3/8
covariants.org/variants/22E.O… ImageImage
Read 8 tweets
Dr Emma Hodcroft Profile picture
Oct 8
I've scheduled my #SARSCoV2 COVID-19 bivalent booster! 🗓️💉How about you?

Even with immune-evasive variants, vaccinations can still help boost your protection, especially from bad outcomes! Every little bit might make the difference this autumn - you can help! 😁✊🏻
If, like me, you live somewhere where only the BA.1 bivalent is currently available, I would still recommend it. We don't know what variant may dominate, (but it's likely Omicron, like BA.1), & given how things are looking, I wouldn't wait for 2023 to get boosted.
Finally, if you recently (~3 months) had SARS-CoV-2 (in most places, likely BA.5), you likely still are still benefiting from the immunity from infection & so most advice is to wait a bit to get boosted!
Read 4 tweets

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