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.
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.
Here, we can zoom in on the clade & get a closer look at how 22E sequences are distributed around the world, & their diversity.
4/8
On the Per Country page, 22E / BQ.1 is already clearly visible in the US & much of Europe, where it's already at 5-15%. Remember that sequencing data is always a few weeks (at least) behind - so it's likely higher today.
More information on 22E / BQ.1 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!)
As before, I've created a file for 22E / BQ.1 mapping all defining mutations (relative to ancestral), including nuc->AA. This is available on CoV github!
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!
I think it would be smart to prepare for both an increase in #COVID19 due to seasonal (behavioural) change & a new variant.
As so many others have elegantly illustrated, new lineages of SC2 are sparking interest.
Since the dominance of BA.5 (22B), most of the world hasn't seen much else move in (though in some places BA.4/22A hangs on), with the exception of India & BA.2.75 (22D).
📡CoVariants.org Update📡
This update doesn't impact the visualizations or the data, but @MoiraZuber deserves a public appreciation thread thanks to her tireless efforts & recent refactoring achievements - so here it is!
1/7
CoVariants is a labour of love - I'm always trying to squeeze it in between the million other things I 'should' be doing (which hopefully lead to publications, the hard currency of academia). Because of this, the time I can put into CoVariants is sadly limited 😞⌛️
2/7
Thus, CoVariants code is all a little bit hacked together in spare minutes. As a result, the main processing script had grown arms, legs, toes & tentacles - it took >2.5 hours to run!! 🧌⏱️
Obviously, very sub-par for development!
3/7
Note that for the moment I don't have anything but year for these sequences, so month is being inferred by the pipeline - note the wide confidence interval on the date!
However, zooming into the VP1 build, we can see some interesting connections...
2/5
All part of the B3 clade, 1 seq attaches to autumn 2021 circulation in Europe/USA (1), 1 attaches back to European circulation in autumn 2019 (2), and the rest attach back to USA+ circulation in autumn 2019 (3).
Recently I've heard from collaborators in the US & Europe that #Enterovirus#D68#EVD68 cases are on the rise.
EV-D68 is what I worked on pre-pandemic, & hope to go back to.
A significant autumn 2022 wave has been a recent concern.
So what is D68 & what might this mean?
1/17
#EVD68 is a Picornavirus - a diverse family of viruses. And Enteroviruses are pretty diverse themselves: from Poliovirus, which can cause serious neurological illness, to Rhinovirus - what's behind the common cold 🤧 (and even more in between).
2/17
One of the most notable things about #EVD68 is that in Europe & North America it's historically had biennial autumn outbreaks: in 2014, 2016, & 2018. Also predicted in 2020... but that didn't happen due to pandemic!
Following that pattern, 2022 would be an outbreak season🗓️