Solid Evidence

Yeah, that made me some lasting enemies. I was only reporting data from a public database, but some had a real problem with it.

Something like that.

Yes to all 3.

HIPAA DOES NOT APPLY TO MUNICIPAL WASTEWATER TESTING.

Just needed to get that off my chest.

Geez, the cryptic are starting to come out of the woodwork. This week it's a Delta (I think) from California.

I don't have the full analysis yet, but the RBD is classic:
440K-441R-449R-450D-452Q-453F-456Y-460K-484A-486I-498Y-501T-504D.

And here's the non-Spike changes.
2/2

@ryanhisner.bsky.social complained he couldn't see all of the Atlanta variant mutations. Here is an updated version of Spike.

This lineage is about 2-times more divergent than Omicron was in 2021. If it were to start circulating it would be big trouble.

1/

To be clear, the Atlanta variant is not in circulation and is almost certainly a single persistent infection that is not spreading.

However, to answer your question, the lineage is about 2-times more divergent than Omicron was, or 4 times more divergent than BA.2.86 was.

There is nothing contemporary that is really even in the same ballpark.

Hopefully we'll have it live soon so the interactive features work.
4/

The non-spike mutations were just as bad. Unsurprisingly it had 1795Q.
3/

I need to work on the display, the GA-1 lineage had so many mutations I couldn't make them all fit on a graphic, but here's an overview.
It has a lot of the hits. 417T, 498Y (out of frame) and others.
2/

This is a preview of our new Cryptic lineage dashboard.

I added the Atlanta variant (GA-1), which recently reappeared.

We added a timeline to highlight the lag between virus circulation and cryptic detection.

GA-1 was below the RADAR for years before it appeared as a cryptic.
1/

That's it for now. Have fun.
9/9

But in Boston the number one ‘alternative’ bird is the pigeon.
I think that checks out.
8/

Most places this is followed by various song birds. (not sure how they end up in there)
7/

Likewise, the most common birds everywhere are chicken, turkey, and duck.
6/

But if you go to a closed sewershed like Columbia you still see the dog, but not the rat.
Followed by the other mammals people like to eat: sheep and goat.
5/

But if you deselect human, pig and cattle, you see the other mammals.

Rat and Dog are next on the list (about even), followed by sheep.
4/

Another new feature is that you can double click on any species and it will be removed from the analysis so you can more easily see the less common species.

In Chicago the dominant mammalian species is human (duhh).
3/

The data is up to date through mid-July.
One of the new features is that when you hover over any species it will show all of the times it was detected.

This helps you see that White Bass has been in season in Ottumwa for a while.
2/

You might think the animals contributing to wastewater are about the same everywhere.
If so, you would be wrong.
Check out our updated Wastewater Species dashboard.
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dholab.github.io/public_viz/0...

Update on the Atlanta variant. It is unquestionably the same lineage we detected about at year ago.

The lineage is a B.1.1-derivative. Probably B.1.1.29.

That means it infected the person 4.5 years ago, and is currently the dominant signal in a sewershed with 190k people.

More to come.

New cryptic from Georgia, not sure yet if it's the same one from last summer. Looks like a pre-Omicron derivative.

I'm working on a live cryptic dashboard, hopefully will have a Beta version ready this.

A few of our sites are rural. We are targeting some sites of human/animal interface. The virome from smaller places can be less diverse, but it's not fundamentally different.

Eventually, but for now we are just sharing the data in real time.

hmm, thanks

Like I said at the beginning, this is a beta test and there are probably mistakes.
Let me know what you think.
17/17

I really can’t wait to more sites over time with this data. BTW, we are still enrolling sewersheds for this project with @securebio.org .
16/

More recently it appears to be the Catfish that are biting, which checks out.
15/