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.

@ryanhisner.bsky.social complained he couldn't see all of the Atlanta variant mutations. Here is an updated version of Spike. This lineage is about 2-times more divergent than Omicron was in 2021. If it were to start circulating it would be big trouble. 1/

This is a preview of our new Cryptic lineage dashboard. I added the Atlanta variant (GA-1), which recently reappeared. We added a timeline to highlight the lag between virus circulation and cryptic detection. GA-1 was below the RADAR for years before it appeared as a cryptic. 1/

You might think the animals contributing to wastewater are about the same everywhere. If so, you would be wrong. Check out our updated Wastewater Species dashboard. 1/ dholab.github.io/public_viz/0...

Update on the Atlanta variant. It is unquestionably the same lineage we detected about at year ago. The lineage is a B.1.1-derivative. Probably B.1.1.29. That means it infected the person 4.5 years ago, and is currently the dominant signal in a sewershed with 190k people. More to come.

New cryptic from Georgia, not sure yet if it's the same one from last summer. Looks like a pre-Omicron derivative. I'm working on a live cryptic dashboard, hopefully will have a Beta version ready this.

Data junkies, you are going to love this. Give this a spin, I’m beta testing a new output for our wastewater dashboard. I call this the ‘wastewater fishing report’. 1/ dholab.github.io/public_viz/0...

I've always found this frustrating. You or your child has a respiratory infection. It's not flu or COVID. Your doctor can only tell you, 'you have a virus'. Could it be a little bit more specific? We hope to help answer this question, non-invasively, and for free. 1/

Where am I?

This is cool. I was poking around at the Rhinovirus (common cold) data and realized that my perception about these viruses was completely wrong. 1/

I’m thrilled to announce the update of our water surveillance dashboard. Many improvements, and our first substantial move into ‘OneHealth’. Read to the end to find the Easter Egg. 1/ dholab.github.io/public_viz/0...

Rhinovirus A47 seems to be having a moment. I think this is just one of your common colds (unless someone knows more than me).

The cardinals sequestered my bike. Caption please. pbs.twimg.com/media/GuDO4Q...

Here's another wastewater virus mystery. Who knows something about poultry virues? The virus is Avian Nephritis virus. 1/

I've got another wastewater virus mystery (one of many). This one is about a particular picornavirus we've been detecting. 1/

Why is Enterovirus B about 100-times more prevalent in the summer than the Winter? Do people maybe get it from going swimming? lungfish-science.github.io/wastewater-d...

Based on wastewater it looks like XFG has already overtaken NB.1.8.1 in the US. lungfish-science.github.io/wastewater-d...

I'm taking votes. Our wastewater dashboard currently has 2 components: 1 - SARS-CoV-2 lineage tracking 2- Metagenomics of all human viruses. 1/ lungfish-science.github.io/wastewater-d...

New cryptic lineage popped up in the database this week. This time it is from Hillsborough, New Hampshire. The lineage is BA.1-derived, so from a 3+ year infection. This one is a classic. 1/

New cryptic lineage popped up this week. This time from Galveston, TX (I think) collected June 1. This is a weird one. 1/

Our latest cryptic lineage paper was accepted in PLoS Pathogens. This paper has some nuanced implications about the origins of SARS-CoV-2. 1/ journals.plos.org/plospathogen...

Our wastewater metagenomic dashboard updated overnight. We're getting faster, this update included samples collected less than 2 weeks ago. 1/ lungfish-science.github.io/wastewater-d...

This is so cool. I’m pleased to share version 1 of our new dashboard for displaying data from our wastewater metagenomic project. This is a collaborative projected between MU, U. Wisc, and SecureBio; funded by Inkfish and Open Philanthropy. 1/ lungfish-science.github.io/wastewater-d...

Fun fact. The first time NB.1.8.1 was detected in US wastewater was 2/26/25 from Sacramento, CA (reported 3/6/25). The first time it was found in a person was 3/18/25 from Alameda County, CA (reported 5/12/25). One of these techniques is faster (and cheaper) than the other.

We are recruiting sewersheds for an expanding project. Basically, we want to learn everything that can be learned from wastewater. Read on if you are interested. 1/

This battle between Harvard and the administration is so befuddling. The latest plot twist just doesn’t make any sense. Let me give a very quick summary for those not following along. 1/

Hey sequencing gurus, can any of you explain the basis for ONT's rapid adapter attachment. What exactly are those brown circles?

So what's happening with medical research in the US? This is the cumulative award count from the NIH for the year. Doesn't look so good. But it gets worse. 1/

There something new on the SARS-CoV-2 landscape, and I’m not sure what it is. 1/

Hey Cornhuskers, you’ve got one heck of a cryptic lineage. This one matches the longest COVID infection that I’ve seen (~4 years). 1/