11 more PJ.2.1 patient sequences from NYC (shocking, I know). It's like the opposite of BA.3.2; 6 of them are over 75 years old. I wonder if it was an outbreak in nursing home.

Coxsackievirus A9 is currently the most highly elevated virus in the US right now. It's elevated in almost every one of our 43 sites. wwwnc.cdc.gov/eid/article/...

Cardiomyopathy Caused by Coxsackievirus Strain A9 in Previously Healthy Child, Northeastern France, 2024

Cardiomyopathy Caused by Coxsackievirus Strain A9

wwwnc.cdc.gov

Speaking of gain of function, the Nebraska lineage appeared 3 more times in the last month. The SARS-CoV-2 Spike RBD looks more like a bat Sarbecovirus (RaTG13) than the Nebraska lineage. Think our immune systems would recognize it?

Maybe I should call cryptic lineages by a more descriptive name. They are 'Gain of Function lineages', and they are far more dangerous than anything going on in any lab. Do you hear any of these disingenuous blow hards worry about them? I don't think so.

COVID lineages are kind of chaos right now. 5 different groups that diverged from each other 1-4 years ago are still in circulation, but nothing shows signs of dominating. This hasn't happened before. XFG* NB.1.8.1* LF.7* BA.3.2* PJ.2.1*

Fourteen more PJ.2.1 wastewater detections. It is dominant in many sites. NYC (8), Maui (2). Maine, Virginia, Florida and DC. No obvious uptick in cases in any of these places that I could find though.

National Wastewater summary from last week. COVID is low and steady. Rhinoviruses and Parainfluenza 3 are fading. coxsackievirus A9 is most elevated (HFMD?) Paraechovirus 6 is still elevated.

Where things stand with COVID. If you look at the normalized numbers for all of our metagenomic sites, the highs were Dec-Jan. Numbers reached all time lows this Spring. Currently the 3-week average is 79% below the all-time average and 96% below winter highs.

I just realized something. This week I flew from Missouri to Texas to California to Chicago and now back to Missouri, and every single bathroom along the way was part of our wastewater metagenomics network. I'll have to check in a few days what all I was exposed to.

Hah, I thought we just couldn't detect the Cyclospora cayetanensis very well because we hadn't really seen it. But then it showed up in 10 of our metagenomic sites last week. I guess we can detect it. My bad. Keep pooping.

10 more PJ.2.1 wastewater detections. Mostly NYC, but also single detections in VT, CT, and FL.

Nationwide, COVID wastewater levels are near all-time lows, but the numbers are rising. Does not seem to be driven by any particular lineage. Just FYI.

Time for a new episode of wastewater surveillance, Animal edition. We added some sites and made some needed updates to our species dashboard. There are now more than 800 vertebrate species detected. 1/ dholab.github.io/public_viz/0...

New cryptic. I don't see a lot of s2m fixes these days, but one just popped up in Colorado. A very obvious BA.1-derivative, so a 4 year old infection.

We passed 3,000 metagenomic samples this week. I need a few hundred more hard drives.

6 more sightings this week. 4 from NYC, 1 from Florida and 1 from Alabama. Not explosive, but it has legs. Needs a name.

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.

Three more detections of the MC.10.1.7 outlier in NYC sewersheds. Does this have a designation yet? @ryanhisner.bsky.social

@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 · last mo.

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 · last mo.

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/

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 · last mo.

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/

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.

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.

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?

We released our latest metagenomics preprint. I’m really excited about this study. The unofficial title is ‘conquer the dark matter, volume 1’ 1/ www.medrxiv.org/content/10.6...

A genome-resolved view of the wastewater RNA virome

Sequencing-based wastewater surveillance is emerging as an important tool in pathogen-agnostic threat detection, potentially enabling early identification before capture through clinical surveillance ...

medrxiv.org

A new preprint was released this week that helps explain why there seems to be more BA.3.2 infections of children. 1/ www.biorxiv.org/content/10.6...

SARS-CoV-2 BA.3.2.2 is more evasive of neutralization by sera from young children

Dominant SARS-CoV-2 variants have most prominently displayed greater evasion of serum neutralizing antibodies than predecessor strains. BA.3.2, a descendant of Omicron BA.3, carrying 43 additional spi...

biorxiv.org

Let the games begin. First World Cup wastewater metagenomic plate will be done tomorrow. 43 samples (23 from WC host cities).

The good news going into the games is that COVID levels are the lowest they've been since the shutdown in 2020 (at least in Missouri).