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Ryan Hisner @ryanhisner.bsky.social · 18h

Three PJ.2.1 just showed up in New South Wales, Australia. Collection dates Sept 8, 20, 21. PJ.2.1 makes up: 3/54 NSW sequences collected since Sept 8 2/7 NSW sequences collected since Sept 20 They look like three separate introductions. PJ.2.1's traveling well for sure.

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The Monarch Diaries @monarchdiaries.bsky.social · 19h

Great thread, why a H5N1 mink farm outbreak is a big red alert. When the 1918 flu virus genome was recovered I asked the late Bob Lamb, an eminent virologist, if this was a terrorism hazard. His answer: “Not unless they’ve got a lot of ferrets. Or a mink farm.”

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Ryan Hisner @ryanhisner.bsky.social · 29/09/2026

By far the most commonly mutated CD8 T cell-epitope site in chronic infections is ORF1a:T1638, and mutations there are now far more common in circulating lineages than they ever have been. In one case (RF.5.4.1) it's paired with another major HLA*01:01 escape mutation: ORF1b:T730I.

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Mike Honey @mikehoney.bsky.social · 26/09/2026

Globally since August, PJ.2.1 showed a growth advantage of 4.5% per day (32% per week) over XFG.*, which predicts a crossover in late October. 🧵

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Thijs Kuiken @thijskuiken.bsky.social · 28/09/2026

Regarding discussions about fur farming, see also recent opinion article in the Lancet Regional Europe: bsky.app/profile/fla-...

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Ryan Hisner @ryanhisner.bsky.social · 27/09/2026

Mink farming is a massive pandemic risk. It's insane that they are allowed to exist. Now we have an active H5N1 outbreak on a mink farm, & "state officials have no clear plan to rein it in." Imagine if uncontrolled H5N1 transmission in mink were allowed in a research lab...

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Federico Gueli @siamosolocani.bsky.social · 26/09/2026

This is a milestone paper. Read it and read the 3D that makes everyone able to access very difficult informations. Congrats to @turville.bsky.social for this giant 4-5years long work.

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Ryan Hisner @ryanhisner.bsky.social · 26/09/2026

Phenomenal 🧵 (& paper) about why Omicron is less efficient at infecting the lung than previous variants. Initial ideas on this were proven wrong, & it's been an utter mystery since. Stuart, doing work on one else is doing, has largely explained it & revealed vital aspects of the SARS-2 life cycle.

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Ryan Hisner @ryanhisner.bsky.social · 26/09/2026

Later in the day, 12 additional PJ.2.1 sequences were uploaded from New York, making a total of 21 on the day. 14/94 (14.9%) sequences from New York collected since September 10 have been PJ.2.1. No additional A475V sequences, though 4 NY sequences lack coverage at 475.

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Ryan Hisner @ryanhisner.bsky.social · 25/09/2026

Two measles cases reported in the small county I live in. No public details. We have the 5th-highest Amish population of any county & 3rd-highest by population density. I do not know their vax status, but if it was low in Lancaster, PA, it's likely low here as well. www.wane.com/news/local-n...

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Ryan Hisner @ryanhisner.bsky.social · 24/09/2026

This new one represents a second independent acquisition of A475V by PJ.2.1. I think seeing A475V twice already—in addition to the existing reasons to think it could be advantageous in PJ.2.1 (see next post)—mean it's very likely that A475V will grow faster than baseline PJ.2.1.

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Stefan Pöhlmann @snpoehlm.bsky.social · 23/09/2026

🧪Where is SARS-CoV-2 circulating? Below is a collection of useful surveillance sites from around the world - wastewater, genomic and respiratory-virus data - that may help you assess virus circulation in your area and make informed decisions about protection.

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Daniel Hurdiss @danielhurdiss.bsky.social · 21/09/2026

Excited to share that our norovirus NS3 study is now online in Nature Communications! 🎉 These enzymes, found across an entire order of RNA viruses, have long been molecular motors in search of a function. We think we’ve uncovered their role. (🧵) www.nature.com/articles/s41... #virology #cryoEM

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Ryan Hisner @ryanhisner.bsky.social · 23/09/2026

Three PJ.2.1 travel sequences (out of 21 total) in US airports showed up today as well, from Cuba, the Dominican Republic, and Chile. Collection dates Sept 6, 8, and 9. This after two travel sequences a few days ago from Germany and Cuba.

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Ryan Hisner @ryanhisner.bsky.social · 22/09/2026

Glad to see this effort. Really, really hope they consider trying remdesivir + Paxlovid combination in a placebo trial. There are dozens of case studies documenting chronic infections cleared through treatment, most w/remdesivir + Paxlovid. Crazy that we're still stuck on the idea of monotherapy.

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Ryan Hisner @ryanhisner.bsky.social · 22/09/2026

First PJ.2.1 from Australia was uploaded today from Queensland. Collected July 31. Zero mutations relative to baseline PJ.2.1. EPI_ISL_20536911 May be a one-off that was imported and died out as there were no PJ.2.1 among the 226 Queensland seqs collected since August 1.

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Solid Evidence @solidevidence.bsky.social · 21/09/2026

Every week I get a metagenomic readout of the most elevated viruses from wastewater collected the week before (44 sites). COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.

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Federico Gueli @siamosolocani.bsky.social · 21/09/2026

New update of the wonderful tool created by @solidevidence.bsky.social #lungfish team: lungfish-science.github.io/wastewater-d... Again PJ.2.1 is clearly the fastest growing. Behind it good performances for BA.3.2(!) RW.1.1 TA.1, XFZ and maybe TK.1 and SV.2.4, with SW.2.1 and RF.5 apparently slower

lungfish-science.github.io

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Indrapramit Das @indrapramitdas.bsky.social · 19/09/2026

What else could this be but genocide. Any alleged progressives denying it still have chosen the side of imperialism, colonialism, and fascism.

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Ryan Hisner @ryanhisner.bsky.social · 19/09/2026

7/19 sequences (37%) just uploaded from New Brunswick, Canada, are PJ.2.1, including 4/7 collected since Sept 1. This is the highest local percentage we've seen yet.

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Ryan Hisner @ryanhisner.bsky.social · 19/09/2026

It's a relatively good match right now. PJ.2.1 has a somewhat different mix of antibody vulnerabilities than other top variants, but I think the real story is that it has some other, more subtle advantage over them, similar to BA.2.86. When BA.2.86 emerged, it was...

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Ryan Hisner @ryanhisner.bsky.social · 19/09/2026

"Value of the US stock market is ~$80 trillion. If the AI bubble bursts, it can easily lose 20-30%... a loss of wealth of $16-$24 trillion. It is plausible the drop would be even larger.... The drop in demand w/the collapse of the AI bubble...would be 3-4% of GDP. That is a very severe recession."

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Ryan Hisner @ryanhisner.bsky.social · 19/09/2026

One PJ.2.1 from NYC today has A475V, which I expect to be the first in a series of spike mutations we see in PJ.2.1, give the great amount of ACE2 affinity it has to trade off for AB-evading mus. Unclear if A475V will make a huge difference, but at some point it will likely find something that does.

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Ryan Hisner @ryanhisner.bsky.social · 18/09/2026

New paper from phylogenetics/evolution arch-guru Richard Neher (@neher.io) and Luca Sesta! Tantalizing title ("Epistasis and the changing fitness landscapes of SARS-CoV-2") and abstract. Paywalled, unfortunately. academic.oup.com/genetics/adv...

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Stefan Pöhlmann @snpoehlm.bsky.social · 17/09/2026

The spread of PJ.2.1 in Spain 🇪🇸 raises an obvious question: What about the rest of Europe? The answer: We largely don’t know. Of 886 SARS-CoV-2 sequences collected in Europe since July 1 and submitted to GISAID, 671 are from Spain. Much of the rest of Europe has gone dark on genomic surveillance.

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Ryan Hisner @ryanhisner.bsky.social · 17/09/2026

Wow, what an effort. This kind of data, combined with mRNA technology, ought to make continual updating of flu vaccines a regular, ongoing process. There's no reason we should have to tolerate the kind of "mismatches" we've often seen in the past. Only bottleneck is regulatory/bureaucratic.

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Darren Dahly @statsepi.bsky.social · 16/09/2026

TLDR: They can't take up the scholarship they were offered because they can't produce the right paperwork because they live in a in place that is being systematically turned to rubble.

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Ryan Hisner @ryanhisner.bsky.social · 16/09/2026

Wild. I've never seen a single BA.3.2 chronic in the >1.5 years it's circulated, which I think is at least partly due to its loss of ORF7a, which seems vital for most chronic infections, probably due to its role in combating T cell responses. I think all 3 of these mutations are unprecedented.

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Kristian G. Andersen @kgandersen.bsky.social · 16/09/2026

PJ.2.1 seems a likely *parental* lineage for our winter wave this year. It's clearly got teeth, but given its very high ACE2 binding and low immune escape, I expect it'll be an off-shoot of it that'll gain traction. Maybe even a near-complete sweep, which has been a while.

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Ryan Hisner @ryanhisner.bsky.social · 15/09/2026

Here's a quick visual summary of the amino acid mutations on the branches leading from BA.2.86 to PJ.2.1.

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Ryan Hisner @ryanhisner.bsky.social · 15/09/2026

Today two US international travel sequences showed up from Cuba & Germany (Aug 31, Sept 1 collection dates), adding to the list of countries we've seen PJ.2.1 in. We've had ~zero sequences from Cuba or Germany, so this is, at the very least, an indication that PJ.2.1 is not rare there.

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Ryan Hisner @ryanhisner.bsky.social · 15/09/2026

As @siamosolocani.bsky.social points out, @solidevidence.bsky.social's wastewater variant dashboard makes it clear that PJ.2.1 is the fastest-growing lineage in the US. I've inserted arrows pointing to some of the PJ.2.1 mutations. The farther above the dotted diagonal line, the faster the growth.

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Ryan Hisner @ryanhisner.bsky.social · 14/09/2026

13 additional new PJ.2.1 sequence were just uploaded from the US, 10 from California and three from Colorado, making a total of 21 new PJ.2.1 sequences uploaded today.

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Jesus Lizard Superstar 🖤 🐀🐀🐀 @acekatana.bsky.social · 14/09/2026

If you actually want to shatter the GOP coalition you will never have a better opportunity than “Trump is pro data center and pro Flock”

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Federico Gueli @siamosolocani.bsky.social · 13/09/2026

Very brief and not exhaustive point on SC2 variants as of today: Americas are led by SW.2.1 and RW.1.1 Asia is split with eastern dominated by PQ.16.1.1 with the exception of Japan dominated by BA.3.2 and Indian subcont+middleast by RF.5 and XHA

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Ryan Hisner @ryanhisner.bsky.social · 13/09/2026

A recent study from @cellpress.bsky.social's Cell Reports convincingly traces neutrophil inflammation and NETs during SARS-CoV-2 infection to the Mac2-Mac3 domains (which they call SUD2core) of NSP3. Mac2/3 recruits HEPB2 along with an E3 ligase that ubiquitinates it, leading to its degradation...

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Ryan Hisner @ryanhisner.bsky.social · 12/09/2026

Turns out there are likely quite a few accessory genes in this new bat-CoV; the authors just decided to put most of them in the supplementary. I went ahead & gave the ones that could be real names (I think ORF3a/b are likely distantly related to the sarbeco ORF3a/b, but not sure about the others).

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Ryan Hisner @ryanhisner.bsky.social · 12/09/2026

Question for virologists: Does anyone sample bat respiratory tracts for viruses? Seemingly all the coronavirus samples from bats are intestinal/fecal/abdominal cavity, etc. Genbank search for BetaCoV bat samples > 2000 nt show only 1 respiratory sample. All others unlabeled or else feces/GI tract.

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Kristian G. Andersen @kgandersen.bsky.social · 10/09/2026

Take a look at the examples Antrophic provides for research that they blocked, and it's immediately clear almost much all of it is just basic research - but research that has gotten scary-sounding names via the media. An example, put Ebola genomes into Claude Science and ask for a TMRCA > blocked!

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Ryan Hisner @ryanhisner.bsky.social · 11/09/2026

Great thread on the PJ.2.1 variant situation, what we do & do not know, & where it stands now. Worth emphasizing that a recent Yunlong Cao preprint found PJ.2.1 has very high ACE2 affinity, meaning that, like BA.2.75 or BA.2.86, it has plenty of space to acquire new Ab-evading spike mutations.

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Ryan Hisner @ryanhisner.bsky.social · 10/09/2026

Not much in the way of accessory genes in this one. Like all BetaCoVs, it has an "internal protein" in a +1 reading frame within N, called "ORF8b". Pretty sure it's got an additional "internal" gene—ORF8c?—though. 120-AA ORFs in the same ORF8b alternative reading frame unlikely to be a coincidence.

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Ryan Hisner @ryanhisner.bsky.social · 09/09/2026

Furthermore, this 10-fold increase in S1/S2 cleavage, while it had no effect on viral reproduction or viral egress, had severely deleterious effects on subsequent entry into other cells. doi.org/10.1038/s414...

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Ryan Hisner @ryanhisner.bsky.social · 09/09/2026

...a fantastic & IMO criminally overlooked study on ORF3a discovered "3DBs", large vesicles loaded with S and M whose production requires ORF3a. And mutations in the region of ORF3a crucial to their formation had a dramatic effect on S1/S2 cleavage, increasing it 10-fold...

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Ryan Hisner @ryanhisner.bsky.social · 09/09/2026

Great spot. All the others in that alignment have an N-liked glycan in the same location as well. On occasion, SARS-2 has acquired N-linked glycans in proximity to the FCS—primarily at 678 (T678N) or 689 (S689N). Perhaps more relevant to this specific case...

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Ryan Hisner @ryanhisner.bsky.social · 08/09/2026

Awesome new feature at Gensplore, already an invaluable tool! Now you can compare any uploaded sequence with the reference genome.

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Ryan Hisner @ryanhisner.bsky.social · 08/09/2026

There are already plenty of bat BetaCoVs with FCS's. There's an alignment in the paper that shows several of them. The "no FCS in sarbecoviruses" was never the slam dunk some presumed it to be. Now all or most of 3/5 BetaCoV bat subgenera have FCS's. Furthermore...

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Ryan Hisner @ryanhisner.bsky.social · 07/09/2026

In fact, two XBB.1.5 sequences w/the deep-lung adaptation pattern showed up in an XBB.1.5. Yellow are BAL-pattern mutations and green are immunodominant A*01:01 CD8 T cell-escape muts, very common in chronics. In one key way, the mutations in these seqs is the polar opposite of typical chronics...

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the Mountain Goats @themountaingoats.bsky.social · 06/09/2026

I got the Pfizer/comirnaty at a CVS yesterday. Really recommend getting it done, because with the maniacs in charge of HHS, you never know if they’re going to find some absurd grounds to make it harder to get them.

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Ryan Hisner @ryanhisner.bsky.social · 05/09/2026

The new @bsky.app feature that automatically numbers each post is GREAT. Now I don't have to worry about numbering each post so people know how long the 🧵 is & where they're at. Thank you, @bsky.app! Please, enable posting images in chat groups/DMs next. Really frustrating that we can't do this.

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Ryan Hisner @ryanhisner.bsky.social · 05/09/2026

Someone asked about nuc composition by insertion position. Quick & dirty analysis shows some differences -1 is the last (3'-most) & +1 the first (5'-most) nuc. Basically, G's enriched toward end, A's/C's enriched toward start of insertions. Not sure if this is statistically significant.

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