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

Even more from the G24077A+T24079A screen.

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 · 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 · 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 · 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 · 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

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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Solid Evidence @solidevidence.bsky.social · 11/08/2026

This was not random, these genes are all CMV surface proteins. In fact, it was 5 of the 6 genes that CMV expresses on its surface. 6/ www.mdpi.com/1999-4915/10...

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Solid Evidence @solidevidence.bsky.social · 11/08/2026

Our algorithms flag anything that is elevated. If you went to the website this week you saw this banner at the top alerting to a surge in CMV detection in Boston. I had a pretty good idea what this was, but I decided to investigate. 4/

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Solid Evidence @solidevidence.bsky.social · 11/08/2026

The biggest program is our metagenomics project. We get weekly wastewater samples from 44 US sites (~30 million people). We isolate the viral fraction, and we quickly sequence the crap out of it. 3/

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Solid Evidence @solidevidence.bsky.social · 07/08/2026

These lineages usually either repair or abolish the s2m. This one destroyed it with 2 novel deletions. 7/

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Solid Evidence @solidevidence.bsky.social · 07/08/2026

2 more classics. R683Q (bye-bye FCS) and L828F (what the heck does that change do?). 6/

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Solid Evidence @solidevidence.bsky.social · 07/08/2026

The RBD reminds you of some other lineages we are seeing now. 417T, 439K, 440S, 445A, 446D, 449R, 452Q, 453F, 455W, 486S, 496T, 498Y, 500S, 501T, 504D. Massive convergent evolution. 4/

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Solid Evidence @solidevidence.bsky.social · 07/08/2026

A few highlights. Like most gain-of-function lineages, this lineage has 1795Q. Also, the Sarbeco reverting V38A and Orf3:I10L. 3/

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Solid Evidence @solidevidence.bsky.social · 07/08/2026

Taken at face value, the lineage has 481 mutations. I had trouble determining what exactly it was derived from before, but nextstrain now says that it is a Delta-derivative, so a 4-5 year infection. 2/

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Solid Evidence @solidevidence.bsky.social · 07/08/2026

The Charlotte Gain-of-function lineage is back, last seen in Dec, 2025. It’s from a different sewershed, but same city. Although this is clearly the same lineage as ‘NC-2’, I decided to designation this as ‘NC-3’ on my dashboard so you can see ‘how much it’s grown’. 1/

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Solid Evidence @solidevidence.bsky.social · 30/07/2026

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?

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Solid Evidence @solidevidence.bsky.social · 27/07/2026

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.

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

Hawaii has hundreds of fish species and many of them we don’t see anywhere else. The most prevalent by far is a fish called Akule, or Bigeye Scad. I had never heard of it, but apparently it is very tasty fried whole. 14/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

Largemouth bass is surprisingly prevalent in Palo Alto and Sacramento. Unlikely other places where it is mostly caught only in Spring and Fall, it seems to be in season in Northern California all year long. 13/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

The most prevalent fish in Ottumwa, Iowa is Freshwater Drum (river fish), particularly in Spring and Fall. 12/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

There are quite a few fish species that are highly elevated in Boston, such as whiting/pollack. 11/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

The thing with the most diversity across sites is fish. The most prevalent fish overall is Atlantic salmon, but it is particularly pronounced in Boston where there is a lot of fish processing. 10/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

I didn’t know there were cattle egrets in Hawaii, but apparently that’s another invasive species. 9/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

But I think it is probably related to the Oscar Mayer plant in Columbia that makes 140 million pounds of hot dogs a year. 8/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

Moving on to birds, the 2 birds most detected everywhere are chicken and turkey. I was never sure why there was so much turkey in Columbia. 7/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

I didn’t know that there was mongoose in Hawaii, but apparently it’s kind of a problem. 6/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

It’s obvious which sites have zoos. That hippo signal from Kansas city is all derived from Liberty and Cairo. 5/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

Black rats on the other hand like warm locations near the coast, like in California. 4/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

Speaking of gross things, there are a lot of rats among us that show up in locations with combined sewersystem. But there is variation. Norwegian rats are most prevalent in colder climates and inland (Chicago, Boston, etc). 3/

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Solid Evidence @solidevidence.bsky.social · 18/07/2026

The main change we made is that you can select any species in the legend and see the distribution of that species across sites. Take dog for instance. People apparently flush dog poop everywhere. People are weird. 2/

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Solid Evidence @solidevidence.bsky.social · 05/07/2026

The weirdest of the bunch is Parechovirus 6. Parechoviruses are also picornaviruses and can cause cold, GI issues, and occasionally meningitus. New Parechoviruses surges aren’t as common. Also, the surges have been asynchronous across many sites. 6/

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Solid Evidence @solidevidence.bsky.social · 05/07/2026

Next is Coxsackievirus A9. This is another picornavirus that can cause flu-like symptoms, rashes, and other things. It was pretty high last Fall too, but is seeming to have a second wind this summer in some places. 5/

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Solid Evidence @solidevidence.bsky.social · 05/07/2026

This is the Rhinovirus A54 distribution from our private dashboard. You don’t need to know where the locations are to see that it is new and it is surging everywhere. 4/

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Solid Evidence @solidevidence.bsky.social · 05/07/2026

Second is Rhinovirus A54 (common cold). The 100+ Rhinoviruses strains are always taking turns surging and apparently, it’s A54’s turn. 3/

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Solid Evidence @solidevidence.bsky.social · 05/07/2026

While there hasn’t been any new viruses that were clearly introduced by World cup, there are certain viruses that surge this time of year. The first is Parainfluenzavirus 3, which surges everywhere in late Spring to early summer every year (no idea why). 2/

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Solid Evidence @solidevidence.bsky.social · 03/07/2026

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/

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Solid Evidence @solidevidence.bsky.social · 24/06/2026

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.

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Solid Evidence @solidevidence.bsky.social · 15/06/2026

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?

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