Solid Evidence

It's probably an infection of the GI tract, anatomically contained.

It's way more divergent than Omicron was, but yeah.

I volunteered to give a talk about the cryptic lineage at the Nebraska Center for Virology retreat next week.

This will be the second time I've given a talk where the topic of the talk (the cryptic) is conceivably in the audience.

Exciting.
2/2

newsroom.unl.edu/announce/mic...

The most prominent cryptic lineage in the world right now is from Lincoln, Nebraska.

It's a B.1 infection (about 5 years old) that has been detected in their wastewater every week for about the last 18 months.

Sooo....
1/

Thinking about it, a better experiment would be to restore the key sarbeco consensus sequences to SC2 and see if that enhances its fitness in bats. I'll bet they would.

Know anyone with a bat colony?

LOL, if I had a Time Machine I would use it to collect wastewater samples from the past.

I'm guessing that it would be a complete dud in any of them. Evidence from cryptic continues to mount. Some of reversions to Sarbeco concensus occur in over 50% of cryptics; that is ridiculously strong positive selection. I don't think they would have been tolerated in their native environment.

It's a testable hypothesis. Infect a horseshoe bat with SC2. If this is correct, it should be just as fit as other sarbecoviruses.

I'd be willing to bet that it is a dud in comparison.

The only experiments I know of used other species of bat, so it's hard to draw a conclusion.

Hopefully our next manuscript will be in a few months and will be our first pass at characterizing the ‘normal’ wastewater virome, which is mostly bacterial and plant viruses that have never been characterized.
Stay tuned.
10/10

The outputs of most of this data is publicly available on our lungfish dashboards.
9/
lungfish-science.github.io/wastewater-d...

Despite being untargeted, we still detected all of the relevant pathogens, and with the appropriate seasonality.
8/

An important point is that this project happened now because the cost of sequencing keeps going down. This study would have been impossibly expensive to perform 10 years ago.
7/

This is my favorite part. The data from this manuscript was uploaded to the public SRA database.

Currently, 50% of ALL wastewater sequencing data in this database came from this project.
6/

We collected a lot of data from a lot places (and these are just the locations that agreed to make their data public, there are more that did not).
5/

The manuscript largely just lays out the places we did surveillance, and our methods.
4/

(CASPER = Coalition for Agnostic Sequencing of Pathogens from Environmental)
3/

Although most of the sequencing was done in MO, the project is a collaboration with a group called CASPER.

This includes @securebio.org and partners across the country that contribute to acquisition and analysis of the data.
2/
naobservatory.org/casper/

Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this cap...

Happy to report that we submitted a new manuscript this week.

The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social
1/
medrxiv.org/cgi/content/...

But are there any Asian markets in Ottumwa?

Actually, it turns out there are at least 3, and one of them (JM) is praised for its frozen fish section.

Whew. Sanity restored.
8/8

Apparently small frozen pompano are a fairly common staple in Asian stores. Even more surprising, when I went further down the aisle and found this.
7/

This week I was buying some spices at a local Asian store and was wandering through the frozen section, and there it was.
6/

I’d never seen pompano at the store, and I’d never seen at a restaurant (not even in sushi).
I wondered if it was used in pet food, fish sticks, imitation crab, etc. Couldn’t find any evidence that it’s used for any of those things.
5/

While the parrotfish signal did not persist, the pompano signal did.
We see it just about everywhere.

But where is it coming from?

When you google ‘pompano’ you find pictures like this.

Are these anglers bringing their catch home from ocean fishing trips?
4/

In the same sample we saw a large fraction of Pompano, another ocean fish.

I really thought we had mixed up with a Hawaiian sample.
3/

When I lived in the Keys I was told that Parrotfish tastes bad and has really soft flesh, but I suppose it’s a matter of taste. I never tried it, but I’d never seen it for sale at any store.
2/

Pompano and other mystery fish. The reveal.

About a year ago I was looking at the species distribution in wastewater from Ottumwa, Iowa and found a surprise. Parrotfish?
There’s no ocean in Iowa, and you don’t keep parrotfish as pets.
1/

Mystery solved.

Those who follow me know that I puzzle over species I detect in WW that don't make sense.

One I've mentioned before is Pompano; we've detected 177 times to date from all over the place.

Who knows where it is from?

I'll post the answer tomorrow.

clearly, cleanly. What did I mean?

Enjoy.
6/6

We’re also tightening up the output. Many of the sequences of perfect matches to more than 1 species. Rather than giving a generic and imprecise name for the group, we are no listing all of the species that are perfect matches.
5/