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...

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/

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/

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

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

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/

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

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/

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/

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?

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.

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/

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/

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

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

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/

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

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/

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/

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

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

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

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/

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/

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/

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/

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/

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

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/

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/