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Solid Evidence @solidevidence.bsky.social · 1d

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

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Solid Evidence @solidevidence.bsky.social · 3d

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 · 4d

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.

7/7

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Solid Evidence @solidevidence.bsky.social · 4d

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 · 4d

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

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 · 4d

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 · 4d

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 · 4d

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 · 11d

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 · 18d

Now that I’ve got a framework, I’ll try to clean it up and keep it updated as more cryptics appear.
9/9

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Solid Evidence @solidevidence.bsky.social · 18d

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 · 18d

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 · 18d

At the top you can select the page with the frequent/convergent changes.
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Solid Evidence @solidevidence.bsky.social · 18d

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 · 18d

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 · 18d

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 · 18d

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 · 18d

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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Solid Evidence @solidevidence.bsky.social · 19d

This person can't be doing well.

I'd really like to figure out who they are.

3/3

bsky.app/profile/soli...

Solid Evidence @solidevidence.bsky.social · Nov 20

Do you think you've had long-term GI problems since having Covid?

We are performing a study examining the characteristics of viruses, specifically persistent SARS-CoV-2 infections, in stool samples.

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Solid Evidence @solidevidence.bsky.social · 19d

Well, we got the sequence back from last week.

96% of the sequence is a cryptic BQ.1.1 (2.5 year old infection).

It's all coming from one person.
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Solid Evidence @solidevidence.bsky.social · 19d

Coeur d'Alene, ID continues to have by far the highest SC2 levels among the 192 wastewater SCAN sites.

Guess where it is coming from?
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Solid Evidence @solidevidence.bsky.social · 22d

you can email me. [email protected]

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Solid Evidence @solidevidence.bsky.social · 22d

I was wondering whether D68 would surge again this year. Apparently the answer is yes.

Last year it didn't peak until Early October, so it's probably still going up.

I know there have been a lot of respiratory virus infections in Columbia, I'll bet that's what it is.

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Solid Evidence @solidevidence.bsky.social · 22d

That’s all I know. There is a person in Boone, NC that has been infected with SC2 for at least 1.5 years.

How many more are there like this?
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