Here's the latest variant picture for the United States, to late August. The XFG.* "Stratus" variant continued it’s dominance, finishing at 77% frequency. NB.1.8.1 "Nimbus" was flat, finishing at 12%. #COVID19 #SARSCoV2 #USA #XFG #Stratus #NB_1_8_1 #Nimbus 🧵

Here's the latest variant picture for the United Kingdom, to late August. The XFG.* "Stratus" variant remained dominant, growing strongly to 80%. NB.1.8.1 "Nimbus" fell back to 11%. #COVID19 #SARSCoV2 #UK #XFG #Stratus #NB_1_8_1 #Nimbus 🧵

Here are the leading European countries reporting XFG.* "Stratus". Ireland hit 93%, the highest I’ve seen so far in Western Europe. 🧵

My ACIP recap: 🧵 1) MMRV combo vaccine no longer recommended for children <4y. That means vaccine will not be covered by insurance, so not an option for patients. The 2 shot MMR and chickenpox vaccines are still available. This removes access. Let’s see which vaccine they will go for next!

I stand by my justification for my resignation. Sending strength to the scientists being held hostage at CDC.

FINAL THOUGHT: When scientific process is not followed, the science that make the foundation for decisions is suspect and the decisions are therefore not valid. The ACIP is no longer a scientific committee. It is an ideology machine.

There is a regular (presumably nasopharyngeal) sequence for one of these Cryptics. Maybe you already know about it. If not, it might be worth contacting the lab to see if they can provide some info.

Now that I’ve got a framework, I’ll try to clean it up and keep it updated as more cryptics appear. 9/9

The most common non-Spike change was Orf1a:K1795Q (shocking), which was in 17/37 lineages. This was an underestimate because 12 of the lineages only had coverage in Spike. 8/

The spike mutations are a bit of a mess, but the data is all there. The higher the line, the more frequent the change. The most frequence cryptic change is S:K417T, which was in 26/37 lineages. 7/

Changes are broken into 2 images: one with Spike, one with the rest of the genome. 5/

If you view the detailed visualization, it will show you all of the changes associated with each lineage. These are determined finding the changes that were present in the cryptic sewershed, but not any neighboring sewersheds during the same time period. 4/

Each lineage has some basic information about the lineage, and a timeline of when the parent lineage circulated, and when the cryptic was detected. Georgia and Nebraska are currently tied as the oldest; both are more than 4 years old. 3/

The dashboard has data on 37 cryptic lineages. This isn’t even close to all of them, but I hesitate to include lineages that I’ve only seen once, even if they are clear as day. 2/

We finally launched our cryptic lineage dashboard. It isn’t perfect, but ya gotta start somewhere. Here’s a brief tutorial. 1/ lungfish-science.github.io/wastewater-d...

The climate conversation is stuck in a loop, but out in the world things are changing. "We don't have to wait for moonshot technologies to be invested in. Most of the solutions to the climate crisis are already around us." www.abc.net.au/news/2025-09...

Many countries have reduced deaths from heart disease, cancer, lung disease & diabetes over the past decade. However, in 60% of countries, progress is slowing & in some, the number of deaths is actually rising. The global 2030 target is at risk unless govts ACT NOW! 👉 bit.ly/4pBAcKL #BeatNCDs #UNGA

🍞 What you eat affects your future children's health New study by @chassainglab.bsky.social shows maternal consumption of food emulsifiers (found in processed foods & baby formula) alters offspring's gut microbiota - even if kids never consume them directly. #Microbiome

Say "anti-vaxxers" when you mean anti-vaxxers. There is no fact-based scepticism about them or this www.theguardian.com/us-news/2025...

#Breaking: Federal vaccine adviser says former CDC officials can’t be trusted unless they agree to ‘public debate’ www.statnews.com/2025/09/18/c...

Apparently the freedom of speech no longer applies in the US while the freedom to bear arms does.

LiveAI demo fails on the first prompt at Meta Connect 2025. #Meta #AI #LiveAI

Major advance for refractory lupus by engineering the T cells in the patient's body (in vivo) and achieving success in 5 patients @nejm.org (uses mRNA/nanoparticle package) www.nejm.org/doi/full/10....

Low dose aspirin (160mg/d) reduced recurrence in people with colon cancer and PI3K mutations. Emblematic of precision, individualized medicine since the data for aspirin across all colon cancer has been mixed. www.nejm.org/doi/full/10....

Get ready for late October! Comet "Lemmon" is forecasted to reach an apparent magnitude of 5 to 2, which suggests it could be brighter than last year's comet! And it's green! This is due to the presence of a molecule you'll never find on earth: C2 (diatomic carbon)

Annual totals. 2025 is highlighted with a pink dot indicating its total is still being updated. 🥇2025🥇 is now the biggest year on record, in terms of lab detections of # flu -infected people (without defining severity). Having said that, these *are* sick people getting tested.

An expanded version of the last graph, both in the number of years included & in its horizontal stretching. #AusFlu2025 peaked in July. August was not a big drop. Sept is also declining slowly, meaning still *lots* of #flu around. Sept-2025 is now the 2nd biggest Sept on record since 2017

It’s not offshore wind that’s killing whales.

Is everyone aware that whales and dolphins are lung breathers? They don’t have gills like fish. That means if they get entangled in fishing gear and can’t reach the ocean surface, they drown.

La migliore canzone italiana degli anni 20: www.youtube.com/watch?v=3QIY...

La Commissione independente dell'Onu stabilisce che Israele ha commesso Genocidio a Gaza. Ancora piu' sconvolgenti le tre prove a supporto: Assedio e starvation senza possibilita' di fuga Distruzione del sistema sanitario e di cura Uccisione volontaria dei bambini x.com/JaninaDill/s...

"Countries should have become aware of the risk that Israel is perpetrating a genocide in Gaza months ago." Prof @janinadill.bsky.social comments as the UN commission inquiry finds Israel has committed genocide in Gaza. ⬇️

The moment at the end when @crywankband.bsky.social gets that thing That thing touches everyone of us the good and the bad the friend and the enemy there is no hide from that thing, we are helpless at the end youtu.be/8-pvLPpNtxU?... Crywank - I Am in Great Pain, Please Help Me (Original)

#COVID19 #VariantDashboard - #USA| 09/14/25 #SARSCoV2 #Lineages #30DAYTRENDS XFG (35.9%) XFG.3 (24.8%) XFG.2 (14.2%) NB.1.8.1 (6.3%) PQ.2 (3.4%) XFG.3.1 (2.2%) LP.8.1.1 (1.4%) NW.1.2 (1.4%) NW.1 (1.1%) XFC (1.1%) PY.1 (0.8%) Tracker: tinyurl.com/mryj4uu7 1/n

Chikungunya outbreak in northern Italy (Modena, Carpi, San Prospero, Concordia sulla Secchia, and Soliera) with over 104 detected and confirmed autochthonous transmissions: www.ausl.mo.it/chikungunya-...

Mosquitoes are the messengers that bring the news of climate change to your door via their infectious diseases.

Termite genomes shed light on the enigmatic deltaviruses, their ancient origins, and an intriguing example of co-option of viral genes by a host. www.cell.com/cell-reports...

climate change - it's a thing. and it affects more than just the climate and weather www.science.org/content/arti...

In. Sane.

Iberian harvester ants are the only known organism that propagates two species by itself, according to new research. Learn more: https://scim.ag/47sVFyS

Mi han detto di averti visto drogata in Brasile, sulle strade coi nomi dei presidenti di li'... ..cosa mi sarebbe costato prendermi piu' cura di te? portarti alle giostre che insistevi sempre per andarci..

Interactive genomic sequencing dataviz, code, acknowledgements and more info here: github.com/Mike-Honey/c... 🧵 ends

Preternatural insight on show here after 3 years of evolving defence of Ukraine, by Ukrainians, from Russia's use of the first Iranian Shahed drones. Often feels like many just haven't been watching or taking notes.

Variant curiosity PQ.2.6 is the frst ever designated lineage with S:G>S446T ! we had S, N, V, D, R (plus G WT) in that position in previously designated lineages but fot T is a first. anyway nothing worrying is just evolution at a hypermutable residue in the RBD

You remember a while back I got a new job, but I was too shy to say where it was… because it was a fairly big change in direction and I wasn’t sure if I would nose-dive… Well, I’m happy to say that I have settled in at the Kirby Institute and am doing things bugs and biosecurity.

To see just how good the orientations from ab initio can get, we applied the same approach to stomatin, which (like other highly symmetric proteins) often falls apart in C1 ab initio. In this case we used a resolution range of 2.5-2 Å, single class, followed directly by local refinement: 11/x

Kookjoo Kim in the lab collected some data on calmodulin (16kDa) a while ago, so we decided to have a go at that too - in that we were unsuccessful, but the fact that 2Ds have recognizable features makes me wonder whether sub-20kDa proteins might be doable in the future: 10/x

Remarkably, using a single round of 3-class HR-HAIR followed by local refinement, starting from the blob-picked stack, we were able to obtain a 3Å map. By starting after a single round of 2D, a single-class HS-HAIR gave a 2.8Å map (starting from ~1/10 the original number of micrographs): 9/x

But from 588 movies, after two rounds of high resolution heterogeneous ab initio reconstruction (HS-HAIR), we are able to find 14k particles that refine to ~4Å in C1: 6/x

To show that this same approach can work in other cases, we applied it to something even smaller - the Hb-dimer (29kDa) from EMPIAR-10250. This is a challenge - not only is it small, but it is a small fraction of the total particles, which are mostly tetramer: 5/x