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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, 2024Cardiomyopathy Caused by Coxsackievirus Strain A9wwwnc.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.

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/

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.