We added St Louis to our dashboards this week. The St Louis zoo clearly has Hippos. 1/

New cryptic from Little Rock, Arkansas this week. Not enough info to make the big board yet, but it's clearly an XBB.1.5 derivative (over 2 year infection) that has started picking up new mutations.

BA.3.2 is starting to show traction.

The most prominent cryptic lineage in the world right now is from Lincoln, Nebraska. It's a B.1 infection (about 5 years old) that has been detected in their wastewater every week for about the last 18 months. Sooo.... 1/

Happy to report that we submitted a new manuscript this week. The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social 1/ medrxiv.org/cgi/content/...

Pompano and other mystery fish. The reveal. About a year ago I was looking at the species distribution in wastewater from Ottumwa, Iowa and found a surprise. Parrotfish? There’s no ocean in Iowa, and you don’t keep parrotfish as pets. 1/

Mystery solved. Those who follow me know that I puzzle over species I detect in WW that don't make sense. One I've mentioned before is Pompano; we've detected 177 times to date from all over the place. Who knows where it is from? I'll post the answer tomorrow.

This is fun, made a bunch of updates to the species dashboard, both sites and outputs. Pet shop data. 1/ dholab.github.io/public_viz/0...

BA.3.2 update. We're now up to 192 wastewater detections across 31 states. 1/

I love that they didn't cut the clip at minute 5. www.youtube.com/watch?v=qE38...

This is interesting. I noticed that we detect a lot of sturgeon in Northern California. Particularly Sacramento. 1/

Our species dashboard was updated and upgraded. I learn something new on this dashboard every time I look at it. Read to the end for the fish fact of the day. 1/ dholab.github.io/public_viz/0...

BA.3.2 update. A few more patient sequences appeared, so the score is now 119 to 4. The 2 states where it has been most prevalent (Maine and Rhode Island) have had virtually no patient sequencing. #shitdon'tlie

The North Carolina variant appeared again in December, so I decided to add it to the dashboard. NC-2 1/ dholab.github.io/public_viz/0...

BA.3.2 update. We're up to 89 US wastewater detections. It's around 2% of the total now.

I assume that everyone that talks about how awful AI is for the planet rode their bike to work today. (chart generated by AI)

Small landmark. As of last week we've identified over 1,000 unique vertebrate 12s sequences from our species diversity project. 60% are fish. dholab.github.io/public_viz/0...

So far there has only been one US patient reported with BA.3.2. Meanwhile, these are the wastewater detections to date. Want to know what's really going on? Check the wastewater; we don't miss shit.

More zoo creatures. We’ve detected 3 different penguin species across our 12 sampling sites. The first site was Boise, where we detected a banded penguin (matches Humboldt, African, or Magellanic). 1/

I missed this, there is a second site (Boston) where Hippos showed up in our data, but there it was pygmy hippopotamus. Checks out, apparently they have a colony at the New England zoo in Boston.

We've made some updates to our dashboard if you want to check it out. Influenza C is having a strong year. dholab.github.io/public_viz/0...

We found a new (I think) cryptic lineage this week. I know I say this all the time, but this is really weird. Warning, this thread is for nerds only. 1/

This is cool, the KC zoo only has 1 or 2 hippos, but we've detected them in KC wastewater 9 times. Usually I get in trouble when I talk about detecting individuals from wastewater, I hope they don't feel like I've invaded their privacy.

It's a slow but persistent wave. 22 more wastewater detections of BA.3.2 (including ALL recent samples form RI). It's staring to be the dominant lineage in many cases. I think the score on wastewater vs patient surveillance is now 44-to-1

Who knew? This confused me. The second most prevalent fish in Palo Alto wastewater is Largemouth bass. I kept trying to find the lab that was using it for toxicology studies or something, but I was barking up the wrong tree. 1/ dholab.github.io/public_viz/0...

I'm behind, I didn't realize that the H5N1 in Wisconsin dairy cattle last month was actually D1.1. That means that there have been at least 3 independent spillovers into dairy cattle in the last 2+ years. 1/ www.avma.org/news/wildlif...

Seven more detections of BA.3.2 from US wastewater. It's fanning out, this week it includes detections in CA, UT, and NYC.

BA.3.2 update. It’s picking up speed. 7 new US wastewater detections in the last week, mostly from New England. 1/

We've now had 7 consecutive sequencing plates where we detected Measles somewhere, and they are all independent.

This is kind of unexpected. There's been a big December surge in enterovirus D68 in every single West coast sewershed we track (mostly CA and including a few not listed), but nowhere else in the country. Everywhere else there was a surge in Fall that has since died out.

Another BA.3.2. This time from Dulles airport on Dec 7.

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...