Ryan Hisner

Who will be blamed when it happens? I suppose the right will blame the very agencies they've defunded and destroyed.

If you have the nuc sequence, I wouldn't mind taking a crack at it. Alignment programs can make weird decisions. The Nextclade interpretation of the S:144-147 region of a recent chronic LB.1.3.3 was an "undeletion" at 144 + four nuc substitutions. Really it's just an AAC insertion—RdRp-stutter-type.

Definitely not a BA.3. I can't tell why it would be categorized that way. Looks like a humdrum low-coverage NB.1.8.1.

On its face, this seems hard to believe. The sky is big. Contrails are small. But 3% of flights contribute to nearly 2% of radiative forcing? Might be one of those things that's totally counterintuitive I suppose.

"[Contrails] contribute roughly 2% to the world’s effective radiative forcing."

Fascinating!

An R682L that showed up yesterday, but mutations that truly erase the FCS are very rare. R682X, R685X, or FCS deletion almost always turn out to be Vero-passaged samples.

@solidevidence.bsky.social can give more detail, but FCS is often badly ablated in Cryptic WW variants.

One last note: I never include S:K679N in these searches because the vast majority are artifactual reversions to wild-type. However, there's one workaround: G23599T is the reversion to WT, but G23599C also causes K679N. It was ~nonexistent before BA.2.86 & has ramped up dramatically recently.

Oh, god, please no. I hadn't seen this at all. Most of these recombinants are between extremely similar variants. The exception is XDV/NB.1.8.1, but that one's clearly on a slow, terminal decline. Frankenstein, ugh.

Finally, CoV-Spectrum is meeting trees 🌳 – this week, we released a new feature to browse the SARS-CoV-2 UShER tree on CoV-Spectrum. With the new feature, you can see a subtree of your variant of interest. 1/4

...as Delta was the most unstable and fusogenic variant of all, so mutations increasing stability and taming its fusion activity would likely be more tolerated than in a less fusogenic spike background.

All of these mutations were virtually absent prior to BA.2.86 (without ∆S31). The only very partial exception was in the Delta era, when there was a very small but very distinct increase in these mutation. I think this makes sense...

...I think the circumstantial is very convincing. Bulky or inflexible residues (F/Y/P) in & near the FCS should inhibit cleavage (S680F/Y/P). These are also highly correlated with R683Q/W/L mutations and to K679M/N, both of which are appearing far more frequently than ever before....

It's a very recent thing, so there's nothing in the literature about it. I should also say that this weakening isn't 100% certain since no one has actually tested these mutations in the lab. However...

Pretty rich for a guy trying to ram through extremely unpopular "reforms" against the will of the population to lecture others about democracy.

I'm still not sure if this is a T cell-evasion mut pattern (like another pattern involving 8 regions) or if there's something functional going on. The presence if K1795Q in so many of these (together with the fact that 6/7 are in NSP3) suggests to me there's a functional connection of some sort.

I haven't run through all of them, but at least two of these have the 7-region pattern that I've taken to calling "6-7a" (short for 6xNSP3 + ORF7a).

Here are a few of the many conventional chronic sequences with mutations in at least 6 of the 7 regions.

I think that one disappeared. I suspect they may have died, but there's no way of knowing for sure. If they died, we can all sleep well knowing that their privacy was protected.

It doesn't happen very often. However, this is one of the many reasons that you should never trust a single data point. Recently, a very prominent Covid tweeter posted that some place in Spain had its highest Covid levels of the pandemic—got like 5000 retweets—based on a single outlier WW reading.

I just updated our cryptic lineage dashboard if anyone is interested.

Viewer warning: this site contains a ton of actual data that really long persistent COVID infections are still occurring.

1/
dholab.github.io/public_viz/0...

I couldn't find any reference to data showing rising cases. We've come to rely pretty much entirely on wastewater testing in the US. The UK still has some decent conventional testing, don't they? I haven't followed UK stuff since they stopped funding the great reports they used to release.

Teacher: "Uh, no. The word is 'ratio', and it's definitely spelled right."

Student, putting both hands in the air palms forward: "Agree to disagree."

Any time I hear that phrase I'm reminded of something that happened in a 6th-grade math class I was in. They were doing quiz review. A kid raises his hand, "You misspelled 'radio' here."

Teacher: "No, that's the word 'ratio', and it's spelled correctly."

Kid: "I'm pretty sure you misspelled it."

YouTube video by The Middle East - Topic Black Death 1349

I've never tried to make a playlist on the theme of disease, but one of my favorites is "Black Death, 1349" by The Middle East, a real stunner. Love the bit at 0:45 where the time signature seems lost for 10-15 seconds.
www.youtube.com/watch?v=7MJ-...

I love every song on Four Tet's "Pause" album... except for this one. Totally out of place on the album, and it has to have one of the most annoying choruses of all time.

Same. Streaming sucks. It's also a very inefficient way of listening to music or watching video. If you download a video or song to a computer, you can listen/watch them a million times without using up any bandwidth.

Streaming is all about corporate control. They want us to be dependent on them.

"Maths" is just too hard to say. Talking should be easy, and words like "maths" make it not so easy.

Reminds me of the mischievously named band The Sixths and their albums "Wasps Nests" and "Hyacinths and Thistles."

Lastly, a funny story. At first, @siamosolocani.bsky.social referred to BA.3.2 as "The Great Cucumber," which we all found quite confusing. Apparently, this is the Italian translation for "The Great Pumpkin" in the classic Peanuts Halloween special. 3/3

And though the BA.3.2 wastewater levels in Western Australia fluctuate widely from week to week, @mikehoney.bsky.social notes that the WW prevalence of the Great Pumpkin have reached their highest levels yet, at around 20%. 2/3
bsky.app/profile/mike...

"The Great Pumpkin"—@siamosolocani.bsky.social's apt nickname for BA.3.2—has now shown up in New South Wales, Australia, for the first time.

Together with its continued presence in clinical samples and wastewater in Western Australia, this confirms real community BA.3.2 transmission in AUS.
1/3

'Course not.

What can you tell us about the event?

However, there's a well documented connection between spike NTD deletions & spike cleavage, as documented by @enyaqing.bsky.social, @grovearmada.bsky.social, & others. I've discussed this some in recent BA.3.2 🧵's & in this older 🧵 dedicated to the subject. 4/4
threadreaderapp.com/thread/15690...