iiinova — where your digital self keeps evolving

Solid Evidence @solidevidence.bsky.social · 24/09/2026

13 states, ~30 million people. East to West.

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Solid Evidence @solidevidence.bsky.social · 21/09/2026

I stopped counting because the number kept going up.

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Solid Evidence @solidevidence.bsky.social · 21/09/2026

Every week I get a metagenomic readout of the most elevated viruses from wastewater collected the week before (44 sites). COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.

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Solid Evidence @solidevidence.bsky.social · 17/09/2026

The good news is that I have not noted its spread correlating with increases in total COVID signal.

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Solid Evidence @solidevidence.bsky.social · 17/09/2026

All I can say is that the sequences were all homogeneous. Most of the time there are several lineages present, but this sample had only BA.3.2, and the RBD reads all had those 3 extra changes.

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Solid Evidence @solidevidence.bsky.social · 16/09/2026

Even more from the G24077A+T24079A screen.

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Solid Evidence @solidevidence.bsky.social · 16/09/2026

PJ.3.2 seems to be hitting the accelerator. These are the wastewater samples deposited in just the last week where it was present (based on 439K marker).

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Solid Evidence @solidevidence.bsky.social · 16/09/2026

WTH, I think I found a BA.3.2 cryptic (I hope it isn't circulating anyway). Standard RBD + A435F, S438F, P463F. Wonder if that improves ACE2 binding? It was 100% of the sequence from one sewershed. @ryanhisner.bsky.social

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Solid Evidence @solidevidence.bsky.social · 11/09/2026

I know there were groups that looked at this in mice, but I don't think there was any meaningful immunity.

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Solid Evidence @solidevidence.bsky.social · 11/09/2026

As long as you don't think about it...

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Solid Evidence @solidevidence.bsky.social · 10/09/2026

The relevant people were notified, yes.

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Solid Evidence @solidevidence.bsky.social · 10/09/2026

I picked up a carton of milk from the store this week that had H5N1 influenza in it. >150 million copies/liter! Thankfully, it was safe to drink because the milk was pasteurized, so I’m not saying what brand. Takehome: DON’T DRINK RAW MILK.

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Solid Evidence @solidevidence.bsky.social · 04/09/2026

Sure, pretty easy if you have the samples

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Solid Evidence @solidevidence.bsky.social · 04/09/2026

Sorry, missed this. It was down briefly but I think it was fixed.

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

We still don’t know most of the basics about these patients. What makes them predisposed to these persistent infections? What are their symptoms? What are the long-term consequences? Can they be treated if we knew who they were? Hopefully some day. 12/12

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Variant #1, the Lincoln variant. Detected in almost every sample from Lincoln for the last few years. Lineage is pre-Delta, so at least a 5.5-year infection. This lineage has the most divergent RBD on record. 11/ bsky.app/profile/soli...

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Variant #2. Charlotte, NC. I thought this one was gone too. I hadn’t seen it since last year, but then it popped up again in July. We now know this is a Delta-derivative (roughly a 5 year infection). It is NC-2 and NC-3 on the dashboard. 10/

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Variant #3. Cleveland, OH. I’ve been seeing this variant for a while. I thought it was gone, but it popped up again in May. It’s OH 2 on the dashboard. Another BA.1-derivative (4.5 year infection). 8/ dholab.github.io/public_viz/0...

dholab.github.io

SARS-CoV-2 Cryptic Lineage Visualizations

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Variant #4. California, sewershed population 14,465. I mentioned this one before. 7/ bsky.app/profile/soli...

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

And unsurprisingly, Colorado also has 1795Q. 6/

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Variant #5. La Plata county, Colorado. Appeared about a month ago. This one is a BA.1 derivative, so about a 4.5-year infection. Not a lot of coverage, but it has the s2m fix. 5/

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

All modern lineages look more like this. The lineage is pre-B.1.1, so it least a 4.5 year infection. 4/

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Variant #6. California, sewershed population 1.4 million. Showed up once in March of this year. Very little coverage, but there was a very telling snippet from the N gene. 3/

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Variant #7. Little Rock. This one showed up a few times this Spring. XBB-derived, so 2.5-3.5 year infection. RBD picked up 417T, 440R, 450R, 452M, 462R, 475V, and 496S. Haven’t put it on the dashboard yet. 2/

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Cryptic (gain-of-function) lineage update. There are currently 7 cryptic lineages in the US that I consider ‘active’. This is a rundown. Warning, I’m going into the weeds. Nerds only. 1/ bsky.app/profile/soli...

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Sometimes. I'd be pretty surprised if the concentrations were high enough to affect animals.

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Solid Evidence @solidevidence.bsky.social · 22/08/2026

Update. I was wrong, the sequence was normal. They just got a one-off really high sample (a hot turd). It happens.

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Solid Evidence @solidevidence.bsky.social · 20/08/2026

Something else is still hiding in plain sight.

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Solid Evidence @solidevidence.bsky.social · 20/08/2026

I'm off on the next metagenomic curiosity. Can we recover viral sequences from wine? And if so, will they be mostly plant, yeast, or insect viruses? Is there a 'viral terroir'? We shall see; I started with bottles of cheap MO and CA wine. Any predictions?

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Solid Evidence @solidevidence.bsky.social · 20/08/2026

Are you talking about Wisconsin, or something else?

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Solid Evidence @solidevidence.bsky.social · 20/08/2026

I can finally reveal the rest of our World Cup surveillance. While we were working away on wastewater metagenomics, the other side of lung.fish was on the ground doing air sampling with team Canada. Preprint just out. www.medrxiv.org/content/10.6...

lung.fish

Lungfish

Dedicated to improving environmental surveillance and tackling viruses through innovative detection strategies.

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Solid Evidence @solidevidence.bsky.social · 19/08/2026

Another appearance of the Charlotte variant. A minor branch from last time is dominant this time with the addition of [483A-484V-485S-486A]. bsky.app/profile/soli...

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Solid Evidence @solidevidence.bsky.social · 19/08/2026

Stupid SC2 lineage. SV.2 is surging and it is clogging up one of my cryptic lineage screens.

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Solid Evidence @solidevidence.bsky.social · 18/08/2026

It's a pain in the the ass, truthfully.

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Solid Evidence @solidevidence.bsky.social · 18/08/2026

Who said we aren't? With metagenomics we sequence everything that has a genome.

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Solid Evidence @solidevidence.bsky.social · 18/08/2026

There have been hints of a cryptic lineage from Anchorage for years. Who thinks they finally popped? bsky.app/profile/soli...

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Solid Evidence @solidevidence.bsky.social · 17/08/2026

Someone explain this to me. We detect deer from wastewater throughout the Midwest mostly around November, which is deer hunting season. Except in Madison, where it peaks throughout January. Why?

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Solid Evidence @solidevidence.bsky.social · 14/08/2026

Hot, I assume, and I think they are strictly plant eaters, but what do I know.

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Solid Evidence @solidevidence.bsky.social · 14/08/2026

A quick search revealed that the Houston zoo has a single pygmy hippo named Akobi. He is 6 years old and weighs around 500 pounds. Hi Akobi, I’ve been seeing you. 12/12

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Solid Evidence @solidevidence.bsky.social · 14/08/2026

This is different than the common hippopotamus we detect from Kansas city and St Louis. 11/

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Solid Evidence @solidevidence.bsky.social · 14/08/2026

There was one thing that stood out in Houston wastewater. Pygmy hippopotamus. 10/

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Solid Evidence @solidevidence.bsky.social · 14/08/2026

Norwegian rats on the other hand tend to prefer colder climates. 9/

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Solid Evidence @solidevidence.bsky.social · 14/08/2026

Like all of our warm climate sewersheds, Houston has some black rats. Black rats don’t like the cold. 8/

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Solid Evidence @solidevidence.bsky.social · 14/08/2026

We recently added a few more sites to our species dashboard, including Houston. Houston species are pretty normal. Like most places, their favorite fish seem to be Atlantic salmon, tilapia, and catfish. 7/

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