Three more BA.3.2 wastewater detections this week. Rhode Island, New Hampshire, and California. Wastewater: 8 Patient detections: 0

We've been doing wastewater metagenomics for 2 years. In the first 20 months we never detected measles once. However, in the last 4 months we've detected it 10 times across numerous states. It's going endemic again; good reason to get vaccinated. health.hawaii.gov/news/newsroo...

Got the sniffles, Parainfluenzavirus 2 is having a big year. [one of many common cold viruses] Curious, it was virtually absent last year.

Three more BA.3.2 detections from US wastewater. Rhode Island (different sewershed, but near the previous one), Vermont, and Florida. All from CDC NWSS data. Looks like it might be getting a foothold in New England. @snpoehlm.bsky.social @ryanhisner.bsky.social @siamosolocani.bsky.social

Does anyone know what strain of H5N1 is responsible for the most recent poultry outbreaks, particularly in Indiana? D.1.1 I presume?

I agree. Wasn't sure before, but I think BA.3.2 is probably going to start accelerating.

Informal poll: A few years ago we tracked down a cryptic lineage through wastewater, but at the time we didn't know they were coming from people. 1/

Another US wastewater detection of BA.3.2.2 (from CDC-NWSS surveillance) This time from Austin on 11/19 The score: Wastewater 2 Patient surveillance 0

I’ve got another wastewater mystery. This one from Southern California, and it’s pretty fishy. 1/

The Nebraska cryptic lineage appeared again this week. It really puts BA.3.2.2 in perspective.

Another US BA.3.2 wastewater detection. This time from Bristol County, RI on Nov 11. It was about a third of the seqs. I wonder if it was someone who flew back from Australia through SF? @ryanhisner.bsky.social @snpoehlm.bsky.social @rajlabn.bsky.social

Flu Overview update. A month ago we detected flu in less than 10% of samples. In the most recent batch over 50% had FluA (H1N1 and/or H3N2) and 75% had FluC. Numbers were low, but flu season is starting.

What should we expect this flu season? Here’s a forecast from a wastewater perspective (because sh*t don’t lie) 1/

This is wild. Remember the NJ crytic lineage? I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out. Some colleagues took me up on it. Guess what they found? 1/

This is a very sad day for public health and evidence-based science in general.

Oh crap. There was a BA.3.2 in California last week. It's GBW and 'environmental', so presumably from plane waste. @ryanhisner.bsky.social Had you heard about it? Did they miss it? It was only 5% of the sample, but very clear.

Guess what we're hunting for.

Are prickly pears or their fruit seasonal? There are several cactus viruses that appear seasonally (Aug-Oct) just about everywhere. I can't think of any other cacti that are commonly eaten. Or maybe it's infecting something else?

Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community? That is the question we asked in our latest pre-print. Turns out you can. 1/ www.medrxiv.org/content/10.1...

Help me out, I’ve got another wastewater virus mystery. This one really blows my mind. 1/

Warning, we've had more measles detections from wastewater in the last month than in the last 2 years combined. We don't have every site on our dashboard yet, and we don't have Measles on the dashboard because we hadn't been seeing it. Things change. health.hawaii.gov/news/newsroo...

It looks like Coeur d’Alene, ID cryptic is gone for now, but it has still managed to answer a lot of lingering questions for me about SARS-CoV-2 evolution, and what to expect next. Here's a whole genome summary and interpretation. 1/

Cryptic update. GPHL just updated their July sequencing and the Georgia variant is playing peek-a-boo with me. It was only present in one of the July samples, and it was a tiny fraction of the total sequence, it but it was clearly present on July 22. 1/

I really want to know which vaccine he got. www.yahoo.com/news/article...

If XFG drives the extinction of JN.1* we will have our first reset in 2 years. While XFG isn't that different than JN.1*, the reset provides a useful tool. 1/

We added a couple more sites to our dashboard this week. We now have a weekly readout on the viruses being shed by domestic cows, pigs, chickens, turkeys, and about 10 million people. lungfish-science.github.io/wastewater-d...

Cryptic lineage update. It looks like the Coeur d’Alene cryptic is gone for now. It was a BQ.1.1, so at least a 2.5 year infection. Did the person move away? Get better? Something worse? We’ll probably never know. 1/

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...

Had a nice visit to San Francisco this week, and I actually got to meet @jbloomlab.bsky.social in person. Nothing happened while I was gone did it? gladstone.org/events/viral...

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...

Coeur d'Alene, ID continues to have by far the highest SC2 levels among the 192 wastewater SCAN sites. Guess where it is coming from? 1/

I was wondering whether D68 would surge again this year. Apparently the answer is yes. Last year it didn't peak until Early October, so it's probably still going up. I know there have been a lot of respiratory virus infections in Columbia, I'll bet that's what it is.

Some cryptic lineages like to play peak-a-boo with me. Here’s one example: One of our screens is looking for a distinct XBB signature in spike [22200A+22317T] That signature showed up in Boone, NC in Oct of 2024, and then again last week. 1/

This is overdue. XFG* is the 11th world dominant lineage, and the first to hold the title since KP.3.1.1 a year ago. Strangely, there are still a few corners of the world (particularly China) where it is almost completely absent.

I pay attention to numbers. Does X put the breaks on certain topics? I posted 3 threads this weekend, each on X & bsky. The first thread (about cryptic lineages) had 10-20 times more RTs and likes on X than here (1.1k likes total). 1/ bsky.app/profile/soli...

I was starting to believe the H5N1 outbreak from dairy cattle was winding down. I was wrong. I hadn’t detected H5N1 in CA wastewater in 6 months, and then 4 samples in a row came up positive. The sequences were all B3.13 (the dairy cattle lineage). 1/

Our wastewater dashboard was updated yesterday (we’re behind because of an equipment failure). I’d like to point out some things you can learn from the dashboard about respiratory virus [and stupid vaccine policy]. 1/ lungfish-science.github.io/wastewater-d...

I’ve found cryptic lineages from sequencing wastewater. I’ve found cryptic lineages from screening databases. This is the first time I’ve found a cryptic lineage from social media. This was an interesting story. 1/

Interested air sampling for pathogens? I'm a big wastewater surveillance proponent, but it is not the answer in every situation. Our team has a short blog about the currently available air samplers if this is something you are interested in. lungfish-science.github.io/2025/09/04/o...

Anyone notice a lot of Hand, Foot and Mouth Disease (HFMD) this summer? I've heard about a lot of anecdotal cases. Based on our wastewater surveillance, I think it's being driven by Coxsackievirus A6. 1/

I wish bsky had analytics. I would have been curious to know the differences between the two platforms when discussing vaccines. x.com/SolidEvidenc...

Cryptic update, and minor rant. The cryptic from Nebraska is back. It is a weird one. Here is it’s RBD compared to lineages that have been circulating the last 2 years. I saw the exact same sequence in 2 different samples from a few weeks ago. 1/

It’s been 2 days, lots of comments, and I’ve been called lots of bad names (mostly on the other site). Here’s what I learned about protein based Novavax (NV) vs mRNA COVID vaccines. 1/

Can someone explain to me why some feel so strongly that the Novavax vaccine is superior to mRNA? From the data I've seen they are about equivalent, and both are very safe. a priori I would think that mRNA is better because it elicits both arms of the immune system, but is there data either way?

A few have asked me about this. XFG is the main lineage in the US at the moment. If there is a choice between a JN.1 or an LP.8 vaccine, I would take LP.8.

I read @erictopol.bsky.social's Super Agers book this summer. Wow. That was the most rigorous (>1,500 refs), comprehensive, and bullshit-free book on health I’ve ever seen. Too much info for a thread, but I’ll mention some highlights. www.simonandschuster.com/books/Super-... 1/

Wastewater fun fact quiz of the day. One of the fish from the catfish order we frequently detect from wastewater is the Shark Catfish. 1. Why is this not surprising, even though it allegedly does not live in the Americas? 2. Why have most people never heard of this fish?

Time for some more wastewater mysteries. I made some updates to our wastewater species frequency dashboard and every time I make changes I find new questions. Today’s mysteries are about food, fish, and rats. 1/

HIPAA DOES NOT APPLY TO MUNICIPAL WASTEWATER TESTING. Just needed to get that off my chest.

Geez, the cryptic are starting to come out of the woodwork. This week it's a Delta (I think) from California. I don't have the full analysis yet, but the RBD is classic: 440K-441R-449R-450D-452Q-453F-456Y-460K-484A-486I-498Y-501T-504D.