RFK Jr said these words today on national television "There were ICUs that were empty all over the country including in New York at the height (of the pandemic)" hahahahahahahahahahahahahahahahahahahahahahahahahahahahaha You are a fucking idiot hahahahahahahahahahahahahahahahaha <sobs silently>

3/ The increase in BA.3.2 frequency also appears to have coincided with increased morbidity and more hospital visits among children aged 0–4 and 5–11 years.

Seems inevitable H5N1 will reach every corner of the globe. Only question is how long until some kind of reassortment or set of mutations makes it adaptable to infect and transmit between humans. Feels like waiting for a single radioactive atom to decay. Only question is: What's its half-life?

Thijs Kuiken@thijskuiken.bsky.social · 3d ago

2 August 2026: 62 confirmed detections of H5 bird flu (highly pathogenic avian influenza) in wild birds in Australia 10 in Western Australia 42 in South Australia 2 in New South Wales 1 in Queensland 7 in Victoria www.agriculture.gov.au/campaigns/bi...

👇👇👇 It also made clear that the people essential for a functioning society are overwhelmingly low-paid workers, while hedge fund managers, corporate execs, & private equity goons could disappear from the face of the Earth & no one would notice—except for the more stable economy. That's dangerous.

Dave Andress@davidandress.bsky.social · 3d ago

Covid lockdowns demonstrated, in a deeply imperfect way, the possibility of large-scale social solidarity for a higher cause. That is a prime reason why so many powerful people want us to run screaming away from them into the comforting arms of selfish individualist competition.

Given the serology data from Yunlong Cao, David Ho, & @snpoehlm.bsky.social, it's surprising BA.3.2 hasn't grown much in China. Another mystery: BA.3.2 now appears easily dominant in both Japan & South Africa, 2 countries w/extremely different immune histories & population age structures 1/4

Stefan Pöhlmann@snpoehlm.bsky.social · 2w ago

20 new sequences from Japan 🇯🇵, collected June - July 2026. 100% BA.3.2, which apparently continues to dominate. #BA32

Update on PJ.2.1, the saltation variant originating in Ontario & found in wastewater in ~10 US states. 11/75 sequences today from New York are PJ.2.1. Eight of 11 sequences are identical, with the three others differing by 1 nuc mut. Such limited diversity typically indicates rapid spread. 1/5

If/when we have an H5N1 pandemic, there will very likely be a lot of preventable child deaths because people have been deluded by these revisionist right-wing lunatics and will insist schools must be open no matter what.

Prof Christina Pagel@chrischirp.bsky.social · 5d ago

Keeping schools open is a goal not a policy. A blanket "never close schools" is a bad lesson. I suggest these: 1. Do not prejudge next pandemic which will be a different virus and could have very different age profile of who it attacks 9/12

🧵On @thenewsagents.co.uk yesterday, school closures and the lab leak theory were offered as two examples of legitimate questions that were hard to ask. Both have in fact been asked constantly since 2020. But here's a thread on why I think they were wrong and dangerous on school closures 1/12

Haven't seen this shared, but it's a great one by a giant in the field, Trevor Bedford. Finds that fastest SARS-2 fitness growth was 2021 to mid-2022. Since then there's been a steady rate of evolution ("fitness flux") >4x faster than H3N2 flu A, a benchmark for rapidly evolving RNA viruses. 1/2

Visual summary of PJ.2.1'sAA muts on top of BA.2.86. As @solidevidence.bsky.social shows, it's spread quite far geographically, from its origin in Ontario, Canada, to (at least) Alabama, Connecticut, Florida, Hawaii, Maine, New York, Utah, Vermont, Virginia, & DC. I may be missing some. 1/2

Solid Evidence@solidevidence.bsky.social · 7d ago

Fourteen more PJ.2.1 wastewater detections. It is dominant in many sites. NYC (8), Maui (2). Maine, Virginia, Florida and DC. No obvious uptick in cases in any of these places that I could find though.

This is excellent. "The 'rogue AI' narrative helps obscure some pretty ugly truths.... Like the fact that OpenAI lost $38.5 billion last year, will likely never make a profit, & is facing total collapse or acquisition as an AI bubble looms." Also, a vision of an even dumber near future: 1/2

Karl Bode@karlbode.com · last wk.

do not anthropomorphize software, episode 7,000

RIP Glen Hansard. Such a great singer & artist. Generally, I think it's impossible to cover Neutral Milk Hotel and do the songs any justice, but Glen, with the Swell Season, did this unreal cover of "Two-Headed Boy" 15 years ago. It still gives me chills. www.youtube.com/watch?v=-EPZ...

The Swell Season covers Neutral Milk Hotel

YouTube video by The A.V. Club

youtube.com

The ongoing uptick in cases in Mexico is driven by SW.2.1. A variant that emerged in Ecuador from XFG.6.3.3 backbone and features four mutations over XFG backbone: 441I 446N 529T 641K. 23 out of recent samples from MEX are SW.2.1 @mikehoney.bsky.social @ryanhisner.bsky.social @snpoehlm.bsky.social

Questions for @ukhsa.bsky.social virus-sequencers. There are usually ~9 names for UK SARS-CoV-2 seqs. 1— GISAID #, e.g. EPI_ISL_6977941 2— CLIMB-CM7YF5GAl, PHEC-YYGZ36I, etc 3— OZ010082.1, OY997992.1, etc 4— ENA sample: ERS17830189 5— ENA biosample: SAMEA115128779 6— ENA run: ERR5706158 etc.

In new study led by @bdadonaite.bsky.social, we show many influenza HAs (H5, H7, H9, H1, H2, H3) can use avian or human MHC-II to enter cells. We then use novel combo of deep mutational scanning & cryoEM to define how H5 HA binds to avian MHC-II. Preprint: doi.org/10.64898/202...

Trump's proposal for increasing military spending dwarfs the cost of everything else in sight substack.com/home/post/p-...

Trump and Hegseth Are Demanding Big Bucks for Their Wars

Trump's military spending request dwarfs everything else in sight, even his big tax bill last summer

substack.com

1/ 🛠️ Our July update is here - and it's a technical one! New features for citations, search, submission, and more. Here's what's new in #Pathoplexus 👇 🔗 Full post: pathoplexus.org/news/2026-07...

Fantastic. @pathoplexus.org paving the way for rapid, open sharing of genomic data that properly credits sequencing labs—& which, unlike GISAID, is run openly & transparently by scientists, free from arbitrary dictates of a megalomaniacal con-artist determined to monopolize data & hinder science.

Theo Sanderson@theo.io · 2w ago

I'm really excited about SeqSets reaching fruition. Sequencing pathogen genomes is impactful: this data enables us to design vaccines, to predict future evolution, and more. But at the moment, getting scientific credit mostly requires writing a paper, not just sequencing a genome. [1/n]

Apart from P812R, a few other things catch my eye in your Vero + HNEC passage study, @connorggbamford.bsky.social. The major one is E:L37F/E:L37R in the VeroP4 virus. First, it's notable that E:L37R is the only transversion mut. E mutations show up in a specific type of chronic infection. 1/8

A JN.1.51 with 38 spike mutations (and likely ≥10 more at S:407-471, where there is no coverage) showed up in this Queensland upload as well. Wild one. Closest related sequence was collected over 2 years ago, in early April 2024.

Stefan Pöhlmann@snpoehlm.bsky.social · 2w ago

1/n 169 new sequences from Queensland, Australia 🇦🇺, collected June - July 2026.

BTW, Lungfish is an awesome organization on the forefront of environmental surveillance. Definitely check out their very cool website here. It includes most of @solidevidence.bsky.social's projects (Cryptic dashboard, plant/animal virus WW levels, etc) & has lots of exciting future plans. lung.fish

Ryan Hisner@ryanhisner.bsky.social · 2w ago

Too soon to know what PJ.2.1's growth is like. Overall Covid levels still very low, though with some recent growth. New variant TA.1, w/a bevy of spike mutations, seems to be the fastest currently according to @solidevidence.bsky.social's invaluable dashboard. 3/3 lung.fish/wastewater-d...

Here's an interesting one: S:P812R in a BA.3.2 from Western Australia—creates a furin cleavage site (FCS) in the S2' cleavage position S:685. The classic SARS-2 FCS is at S:682-685. Spike gets cleaved by furin there before it leaves the cell (usually). The S2' cleavage site is different... 1/4

This chronic-infection variant now has a name: PJ.2.1. You can see how divergent it is from other current lineages in the @neher.io/Roemer BA.2.86 tree below. It originated in Ontario but has been detected in wastewater by @solidevidence.bsky.social in New York, Florida, Alabama, & Utah I think. 1/3

Ryan Hisner@ryanhisner.bsky.social · last mo.

A mysterious, unusually diverse saltation lineage descended from KP.3.1.1 (last seen early 2025) has circulated at a low level for ~8 months in Ontario (see 🧵 on next post). Seemed a local anomaly, but @solidevidence.bsky.social just spied a weird spike in NYC wastewater—& it's the same one! 1/14

I've altered my lineage tool to include LF.7 as the XFG predecessor (XFG is ~99% LF.7). Below are pictured TA.1's muts relative to BA.2.86. In spike: TA.1 = BA.2.86 + T22N, S31P, K182R, R190S, R346T, K444R, H445R, S446N, L455S, F456L, N487D, Q493E, K529T, N532S, Q613H, V642G, K679R, V1264L 1/2

Federico Gueli@siamosolocani.bsky.social · 3w ago

Hence we have a bit of time to assign the mutations of the wonderful WW dashboard by @solidevidence.bsky.social : 532S+613H growing fast on extreme left are TA.1 the most mutated XFG

Just look at how far we went from WT with PJ.2.1:

Federico Gueli@siamosolocani.bsky.social · 2w ago

Now designated PJ.2.1

The full paragraph this quote comes from is gold, like the rest of the book. "Who was the first man to look at a house full of objects and immediately assess them only in terms of what he could get for them in the market? Surely, he can only have been a thief." - David Graeber

David Graeber Institute @davidgraeberinst.bsky.social · 3w ago

“Who was the first man to look at a house full of objects and immediately assess them only in terms of what he could get for them in the market? Surely, he can only have been a thief.” - David Graeber (from Debt, The First 5,000 Years)

Quick question, @solidevidence.bsky.social, on Cryptics that isn't visible on the dashboard. How many have the 5' UTR reversion T241C? In Cryptic-like conventional seqs, this reversion is universal. Similarly, do we know how many have ORF1:L314P reversion? dholab.github.io/public_viz/0...

Solid Evidence@solidevidence.bsky.social · 3w ago

New cryptic. I don't see a lot of s2m fixes these days, but one just popped up in Colorado. A very obvious BA.1-derivative, so a 4 year old infection.

Thx supercool 3d! I have searched a bit back on Pango repo: -Among circulating variants Orf6:P57L was in BF.15 -Muts in Orf6:61 should be in BA.2.9.7 ( to P) and in XEH ( to I)

ORF6 is a SARS-2 protein that shuts down traffic between the nucleus & cytoplasm in host cells, inhibiting host mRNA export & immune responses. But in all variants since early 2023, ORF6's abilities are hampered by the ORF6:D61L mutation. Two newish ORF6 observations.... 1/15

Great thread here. Really looking forward to digging into this paper by @mghafari.bsky.social, @spyroslytras.bsky.social, and Sanni Översti.

Mahan Ghafari@mghafari.bsky.social · 3w ago

1/ Excited to share our JVI review article with Sanni Översti, @shusukekawakubo.bsky.social, Jumpei Ito, and @antigenevo.bsky.social! From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses journals.asm.org/doi/10.1128/...