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Solid Evidence @solidevidence.bsky.social · 5h

A summary of past and ongoing cryptics is available on our dashboard.
They don’t seem to be going away.
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dholab.github.io/public_viz/0...

SARS-CoV-2 Cryptic Lineage Visualizations

dholab.github.io

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Solid Evidence @solidevidence.bsky.social · 5h

There were a few other blips of anachronistic sequences that appeared in the last month, but there wasn’t enough coverage to say if they were evolutionarily advanced, so I couldn’t I didn’t know for sure if they were ‘cryptic’.
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Solid Evidence @solidevidence.bsky.social · 5h

This graphic is only partially accurate. The RBD is so divergent it breaks our mapping program.
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Solid Evidence @solidevidence.bsky.social · 5h

The big one that has been very constant is the lineage from Lincoln, Nebraska. It was present in just about every sample last month representing about 15% of the 100k person sewershed.
That lineage is a B.1 derivative, so REALLY old. Probably infected in late 2020.
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Solid Evidence @solidevidence.bsky.social · 5h

We did get 2 more snaps of the lineage before it disappeared. Mostly stable, other than variation between 446A/D, and not all sequences had 453F. Still waiting for the WGS to get back.
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Solid Evidence @solidevidence.bsky.social · 5h

Cryptic lineage update. It looks like the Coeur d’Alene cryptic is gone for now. It was a BQ.1.1, so at least a 2.5 year infection.
Did the person move away? Get better? Something worse? We’ll probably never know.
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Solid Evidence @solidevidence.bsky.social · 2d

The closest we got is from a single bathroom, but the signal was insanely high.

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Solid Evidence @solidevidence.bsky.social · 5d

OH-1. Haven't seen it in over 2 years. I'm guessing it didn't end well.

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Solid Evidence @solidevidence.bsky.social · 5d

The basic system for fleshing out the cryptics is that we compare the cryptic sewershed to surrounding sewersheds sequenced at the same time.

Nothing is considered ‘cryptic-specific’ unless it is at least 50x more prevalent in the cryptic samples than the controls.

Enjoy.

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Solid Evidence @solidevidence.bsky.social · 5d

Finally, if anyone wants to ‘check our math’, we’re proving a link to the raw data on the mutations and the sewersheds they appeared in.
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Solid Evidence @solidevidence.bsky.social · 5d

All 4,000+ positions, and what lineages they appeared in. The columns are all sortable.
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Solid Evidence @solidevidence.bsky.social · 5d

One of the biggest updates for the variant aficionado is a complete database on mutations detected, and how frequent they were.
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Solid Evidence @solidevidence.bsky.social · 5d

Part of the reason there are more now is that I decided to include some single-detects if they were obvious enough.

I’m also now including the sewershed population where the variant was detected, and the date of last detection.

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Solid Evidence @solidevidence.bsky.social · 5d

The first big change is that I added a bunch more lineages. There are still 10-20 lineages from early on that I haven’t added yet, but this includes all the current one.

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Solid Evidence @solidevidence.bsky.social · 5d

I just updated our cryptic lineage dashboard if anyone is interested.

Viewer warning: this site contains a ton of actual data that really long persistent COVID infections are still occurring.

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

SARS-CoV-2 Cryptic Lineage Visualizations

dholab.github.io

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Solid Evidence @solidevidence.bsky.social · 13d

Had a nice visit to San Francisco this week, and I actually got to meet @jbloomlab.bsky.social in person.

Nothing happened while I was gone did it?

gladstone.org/events/viral...

Viral Landscapes: How to Comprehensively Monitor Evolutionary Trajectories

Virus-host interactions shape the evolutionary landscape of viruses and lead to the emergence of...

gladstone.org

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Solid Evidence @solidevidence.bsky.social · 19d

Now that I’ve got a framework, I’ll try to clean it up and keep it updated as more cryptics appear.
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Solid Evidence @solidevidence.bsky.social · 19d

The most common non-Spike change was Orf1a:K1795Q (shocking), which was in 17/37 lineages. This was an underestimate because 12 of the lineages only had coverage in Spike.
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Solid Evidence @solidevidence.bsky.social · 19d

The spike mutations are a bit of a mess, but the data is all there. The higher the line, the more frequent the change. The most frequence cryptic change is S:K417T, which was in 26/37 lineages.
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Solid Evidence @solidevidence.bsky.social · 19d

At the top you can select the page with the frequent/convergent changes.
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Solid Evidence @solidevidence.bsky.social · 19d

Changes are broken into 2 images: one with Spike, one with the rest of the genome.
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Solid Evidence @solidevidence.bsky.social · 19d

If you view the detailed visualization, it will show you all of the changes associated with each lineage. These are determined finding the changes that were present in the cryptic sewershed, but not any neighboring sewersheds during the same time period.

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Solid Evidence @solidevidence.bsky.social · 19d

Each lineage has some basic information about the lineage, and a timeline of when the parent lineage circulated, and when the cryptic was detected.

Georgia and Nebraska are currently tied as the oldest; both are more than 4 years old.

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Solid Evidence @solidevidence.bsky.social · 19d

The dashboard has data on 37 cryptic lineages. This isn’t even close to all of them, but I hesitate to include lineages that I’ve only seen once, even if they are clear as day.
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Solid Evidence @solidevidence.bsky.social · 19d

We finally launched our cryptic lineage dashboard.

It isn’t perfect, but ya gotta start somewhere.

Here’s a brief tutorial.
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lungfish-science.github.io/wastewater-d...

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