Solid Evidence

BA.3.2 update. A few more patient sequences appeared, so the score is now 119 to 4.

The 2 states where it has been most prevalent (Maine and Rhode Island) have had virtually no patient sequencing.

#shitdon'tlie

Wait, sorry. Not the Alpha. It's the BA.1 cryptic that jumps around a lot.

The sample shows up in multiple Cleveland sewersheds, as well as Akron. Just in case.

bsky.app/profile/soli...

4/47 of the ones I've tracked.

I don't.

You mean Alpha specifically?

I was always afraid this would happen. There are 2 cryptic in the same Cleveland sewershed.
An Alpha and a BA.1.

Oops, thought I did.

While I was at it I updated the other cryptics that still appear to be active (Lincoln and Cleveland). BTW, the Alpha from Cleveland didn’t have any RBD coverage, so I haven’t added it yet.

3/3

It is pretty strange that 2 cryptics that are both pre-B.1.1 and appeared over a year apart from the same sewershed. However, the sequences look completely different.
Note: NC-2 is another one that killed its FCS.
2/

The North Carolina variant appeared again in December, so I decided to add it to the dashboard. NC-2
1/
dholab.github.io/public_viz/0...

BA.3.2 update. We're up to 89 US wastewater detections. It's around 2% of the total now.

I don't know who they are.

I assume that everyone that talks about how awful AI is for the planet rode their bike to work today.

(chart generated by AI)

GISAID does have some wastewater data, but it is consensus data, which is fairly useless for wastewater unless it is a single dominant variant.

The BA.3.2 data is coming from SRA, but it's not the easiest screen to do. Once we find the positives it is fairly straightforward for anyone to verify them though.

Small landmark. As of last week we've identified over 1,000 unique vertebrate 12s sequences from our species diversity project.

60% are fish.

dholab.github.io/public_viz/0...

There have been some studies, but in general those cases are pretty rare, and if you are sequencing, they are obvious.

So far there has only been one US patient reported with BA.3.2.

Meanwhile, these are the wastewater detections to date.

Want to know what's really going on? Check the wastewater; we don't miss shit.

I'm not sure. It's possible they pretreat the penguin waste. I detect other things from their zoo, like black bear.

We detect a lot of Capuchin monkey from Boston too, and I was surprised to learn that was not coming from the zoo.

We didn’t detect penguins in any of the 8 places that didn’t have penguins in their zoo. The only place that has penguins that we didn’t detect them is Boston.

I’m starting to think this technique works.
7/7

Check, check, check.
6/

Finally, we detected 3 penguins from KC. The same banded signal, a great penguin (King or Emperor), and a Gentoo.
5/

It checked out though. This time it was presumably the Humboldt penguin from the Brookfield zoo.
4/

Second detection was from Chicago. Same sequence as in Boise.

I’m amazed this worked, Chicago has the largest treatment plant in the US, 700 million gallons/day.
3/

Based on the Boise zoo website, it was probably a Magellanic.

2/

More zoo creatures. We’ve detected 3 different penguin species across our 12 sampling sites.

The first site was Boise, where we detected a banded penguin (matches Humboldt, African, or Magellanic).
1/

I missed this, there is a second site (Boston) where Hippos showed up in our data, but there it was pygmy hippopotamus.

Checks out, apparently they have a colony at the New England zoo in Boston.

We've made some updates to our dashboard if you want to check it out.

Influenza C is having a strong year.
dholab.github.io/public_viz/0...

ends of the sequence