I can finally reveal the rest of our World Cup surveillance. While we were working away on wastewater metagenomics, the other side of lung.fish was on the ground doing air sampling with team Canada. Preprint just out. www.medrxiv.org/content/10.6...

The truth: getting Covid early in pregnancy can cause fetal brain hemorrhaging, w/direct detection of virus in the hemorrhages. This decreased when the UK approved vaccines for pregnant women—& increased when they removed the vax recommendation for pregnant women. Hugely overlooked finding. 1/3

Aaron Rupar@atrupar.com · 2w ago

WHAT -- Rep. Lisa McClain totally makes shit up, claims "82% of women who got the vaccine in their first or second trimester had a miscarriage"

FYI, the most elevated viruses in the US last week were once again Parechovirus 6 and Coxsackievirus A9. Both are elevated nationwide.

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 · 4w ago

do not anthropomorphize software, episode 7,000

Good grief, this hits home.

Our review covering the major Neuroinflammatory events in Long Covid is finally online and open access here! www.nature.com/articles/s41... #NeuroCovid #LongCovid 🤓🧠

Witnessing phenomena like this is why I can never stop capturing landscapes.

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 · 2mo ago

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

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 · last mo.

“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)

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 · last mo.

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/...

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

We performed a metagenomic sprint this week. Samples that arrived on Tues were prepped overnight, loaded on a 10B plate Wed (25 h run), and output today. The same summer viruses continue to surge: Parechovirus 6, Rhinovirus A54, Parainfluenzavirus 3 and Coxsackievirus A9.

@ryanhisner.bsky.social I did some scavenging to see if it was in any other sewersheds in the last month. Found 3 more, 2 more from NYC (different sewersheds) and 1 from Utah. I can't say it's taking off, but it moving around pretty quickly.

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

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

World Cup virus wastewater update. While I wait ‘patiently’ for the sequences from this week (which was supposed to be done already), here is a summary of the 4 lineages that have been on the rise since the games began across our 43 sampling sites. 1/

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

Solid Evidence@solidevidence.bsky.social · 2mo ago

This is kind of weird. A new cryptic showed up in two different NYC sewersheds this month. Low coverage. RBD piece is: 403K-405N-408S-417N-435S-439N-445P-446T-450D-452K-455S-456L. Also a deletion at 621-622. 1/

“.. Members of the group Patriot Front ride the metro on the 250th anniversary of U.S. independence in Washington, D.C.” @reuters.com

“Those who profess to favor freedom, and yet depreciate agitation,are men who want..the ocean without the awful roar..This struggle may be a moral one; or it may be a physical one; or it may be both..but it must be a struggle. Power concedes nothing without a demand” Frederick Douglass America 250

I was wrong. What I thought was a cryptic lineage from NYC was actually a new highly divergent JN.1 (branched off about a year ago). Probably derived from a persistent infection. BTW, it was in 2 different sewersheds, and the most recent one was 40% of the signal.

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

It's the MC.10.1.7 saltation lineage from Ontario! This is wild. bsky.app/profile/ryan...

This is kind of weird. A new cryptic showed up in two different NYC sewersheds this month. Low coverage. RBD piece is: 403K-405N-408S-417N-435S-439N-445P-446T-450D-452K-455S-456L. Also a deletion at 621-622. 1/

Successfully appealed the biorxiv rejection and today our paper (co-authors @darrenmartin.bsky.social & Ravi Gupta) is posted. The paper's too long to do a single summary thread, but I'll do a cursory overview here, then more detailed subsection threads later. 1/16 www.biorxiv.org/content/10.6...

Coevolving Mutations in Chronic SARS-CoV-2 Infections

The SARS-CoV-2 pandemic has been marked by two outstanding features that have had major impacts on global public health: the repeated emergence and growth of highly divergent saltation variants with n...

biorxiv.org

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

Spend 3+ years painstakingly working on a paper, doing original analysis, writing 10,000s of lines of custom code, etc, only to be rejected by a preprint server, which derides it as "automated/computational analyses of public data, facile database searches, sequence alignments"...

This is so awesome. Here's a different view of the last 6 months of wastewater metagenomics from 41 sites (color coded by site). We were able to predict the sewershed each sample came from based solely on the virome present with 99% accuracy.

Cheat sheet for those wondering what the various new lineages @siamosolocani.bsky.social refers to are, or who (like me) often forget or get them mixed up. My ability to make this is utterly dependent on @angieshinrichs.bsky.social's invaluable Usher tree work. TA.1 still too new to be included.

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

RF.5 is 5/13 (India, Indonesia Djibouti) RW.1.1 is 4/13 (Dominican Republic, France) Hypermutated TA.1 is 2/13 both from Nigeria SV.1 is 1/13 with further 446N from Nepal XFG.14.1.1 from Guatemala

First World Cup wastewater metagenomics had nothing out of the ordinary. Parainfluenzavirus 3 and a couple enteric viruses are high (typical for early summer). The most exotic virus we saw was a Largemouth Bass Bunyavirus. Waiting 'patiently' for data from the second plate.

55 of the last 75 outbreaks of H5N1/HPAI/avian bird flu in the US affecting at least 1000 birds have occurred in counties in Northeast Indiana with large Amish populations: Lagrange, Elkhart, Adams, and Jay. I do not know if there is a connection here, but it seems worth looking into. 1/4

An interesting thread from a month ago that predicted exactly what we’re seeing in the reflecting pool now (peeling up, prolific microbial activity)

The Monarch Diaries@monarchdiaries.bsky.social · 3mo ago

HAHAHAhaha! they're making the world's biggest synthetic scum pond!!! The coating is a polyurea used inside pipes. It gels in about 3 seconds, making it non self-leveling. The texture is like an orange peel, the perfect substrate for biofilms. www.nytimes.com/2026/05/19/u...

Reagan forced everyone out of the psych wards and on to the streets so I guess this is some kind of demonic 1980s full circle moment.

Julia Métraux@juliametraux.bsky.social · 2mo ago

Trump's DOJ released a dubious legal memo this morning that signals the Trump admin wants to force more people into psychiatric institutions via bad faith and incorrect interpretations of ADA, Section 504, and Olmstead. New from me at @motherjones.com. www.motherjones.com/politics/202...

Probably the most spectacular rainbow I've ever seen showed up earlier today outside my house. Crazy how much brighter it is beneath the rainbow than above it.

Here is the first round of games by host city. Which match will have the most exotic viral pathogen? And what viral family will it be from?

BA.1/NB.1.8.1 recombinant uploaded today from Portugal, collection date January 2026. There were two BA.1 collected in Dec 2025 in Michigan uploaded last month as well. BA.1 not entirely finished with us yet, over 4 years after it disappeared from circulation.