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Marc Johnson Profile picture
Marc Johnson
@SolidEvidence
Molecular virologist, Professor, and wastewater detective. Same handle on bsky. Ignore the check, I'm doing an experiment.
16 subscribers
Jan 5 • 8 tweets • 2 min read
Interesting, it looks like Atlanta, Georgia has a REALLY old cryptic lineage.

I would call it the CDC variant, but it’s the wrong sewershed.

1/ Image I didn’t even know Georgia was doing wastewater sequencing, but a bunch of sequences appeared in SRA right after Christmas.

15 of the samples from the sewershed with pop. 190k (Cobb county) had the s2m fix.
2/
Dec 31, 2024 • 8 tweets • 3 min read
The Cleveland variant is the strangest cryptic yet. I really don’t get it.
Can someone help me figure this out.
1/ In many ways the Cleveland variant is pretty typical. In addition to the ‘s2m fix’, it has many of the convergent cryptic mutations including several of the reversions to the consensus sarbecovirus sequence.
2/ Image
Dec 29, 2024 • 23 tweets • 6 min read
I finally solved the mystery of why there are so many cryptic lineages in Northern Ohio.

This is a mystery I’ve been working on for the last 18 months.
1/ Image First, standard background.

Cryptic lineages are unique, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater.

We are fairly certain that these lineages come from individuals with very long infections (not animals).


2/
Dec 28, 2024 • 25 tweets • 6 min read
I’m pleased to share that we FINALLY submitted our latest manuscript on SARS-CoV-2 cryptic lineages and what they tell us about the origins of COVID-19.

This was a ton of work.


1/medrxiv.org/cgi/content/sh… First, standard background. Cryptic lineages are unique, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater.

We are fairly certain that these lineages come from individuals with very long infections (not animals).


2/
Dec 15, 2024 • 10 tweets • 3 min read
What are really the most prevalent SARS-CoV-2 lineages and which are increasing?

This is our latest wastewater analysis.

1/ Image We downloaded and analyzed seqs from over 3,000 US wastewater samples collected since Oct 16.

We only analyzed the US samples because there weren't any other sites we could find that covered the time period. This represented at least 80M people.
2/
 ncbi.nlm.nih.gov/sra/
Dec 7, 2024 • 7 tweets • 1 min read
I'm working on a new strategy to track lineages by making composites of all of the recent wastewater sequences.
1/ Image We downloaded about 1600 samples from the last month (~1 TB of data) and compared the frequency of mutations in the first 2 weeks versus the second 2 weeks.
2/
Nov 29, 2024 • 12 tweets • 4 min read
GISAID vs SRA/WW
I thought I would do a little comparison to see how wastewater sequencing data compares with patient sequencing data in evaluating viral trends.
1/
 cdc.gov/nwss/index.html For WW I took all of the samples from our most recent SRA download that were collected in the last month (~500 samples). This wasn’t normalized.

For the patient side I used Cov-Spectrum data (because it's public) from the last month (8,302 sequences).
2/
 cov-spectrum.org/explore/World/…
Nov 28, 2024 • 12 tweets • 3 min read
Maryland variant, retrospective analysis.

I decided to have a more careful look back at the evolution of the Maryland cryptic lineage.
1/ Image Standard explanations and disclaimers.
Cryptic lineage: unique, evolutionary advanced SARS-CoV-2 lineages detected in wastewater from an unknown source.
Cryptics are not from animals, they are long term infections.
2/
Nov 22, 2024 • 4 tweets • 1 min read
If anyone wants to follow along with the Maryland variant (or doesn't believe my analysis), have a look for yourself.

1/ Go to
Type in SRR31400336 and start alignment.

This is a sample from the Maryland sewershed collected on November 7 of this year.
2/deeperseq.genomium.org
Nov 20, 2024 • 8 tweets • 3 min read
Maryland folks, I need another favor.
There is a person from Anne Arundel county that has been infected with SARS-CoV-2 for about 3 years (Delta infection).

They probably don’t even know they are infected, but they are shedding a ton of viral material in wastewater
1/ Image I’m trying to find this person without invading their privacy, if they are willing to be found.

Here are a few threads I’ve written about this variant if you want to read up.

x.com/SolidEvidence/…
x.com/SolidEvidence/…
x.com/SolidEvidence/…
2/
Nov 17, 2024 • 12 tweets • 3 min read
Need a little help.

Does anyone know someone that works at the Patuxent Water Reclamation Facility in Crofton, MD that they could put me in touch with?

Here's why.
1/ Image There is a cryptic lineage (unique, evolutionarily advanced SARS-CoV-2 lineage detected in wastewater) that we have been detecting from a Maryland sewershed all year.

The lineage is derived from Delta, so it's from a person that was first infected about 3 years ago.

2/ Image
Nov 15, 2024 • 12 tweets • 3 min read
Postmortem.

Thanks for all of the retweets!

Late last night the twitter/x account was suspended and I also can't view the ResearchGate account anymore.

Here's a summary of some of the discussion/findings.

1/ I was going to post the full exchange I had with 'Julia', but I can't view it anymore. It was ~three exchanges and they were very benign. I stopped when I decided she was probably fake, but then she tried to reengage a few days later, which is when I investigated.
2/
Nov 14, 2024 • 16 tweets • 4 min read
I knew there were a lot of fake accounts on this platform, but they are usually obvious. I had no idea how intricate and complex the ruse could be.

Get a load of this story.
1/ About a week ago I got a DM from an account asking me a benign but specific question about my research.

This happens to me all the time. I’ve met some interesting people this way.

Sometimes people even look up my number and call my office. It happens.
2/ Image
Nov 5, 2024 • 5 tweets • 2 min read
I'm doubling down on MV.1*

This lineage has been growing rapidly recently, but it's been hard to tell if it would be a real contender since most of the infections were from Singapore.

In North America its growth has been more questionable.

But I have new data.
1/ Image You probably know that our team screens all of the wastewater sequences submitted to SRA for cryptic lineages.

One of the 'cryptic-specific' changes we look for is S:F456V, which is common in cryptic, but hadn't been seen much in circulation until recently.
2/
Oct 28, 2024 • 9 tweets • 3 min read
Cryptic lineage quarterly update, last update for now.

I save the weirdest for last. Read to the end.
1/ Image A lineage popped up in our cryptic screen because most of the seqs did not have the s2m deletion (meaning it was from 2022 or earlier).

The sample was from 9/30 in Texas. Population is 780, so it isn’t even on the NWSS map.

I don’t know where the sample was from.
2/ Image
Oct 26, 2024 • 11 tweets • 4 min read
Cryptic lineage quarterly update, part 3
Cleveland variant.
If you missed part 1 and 2, they are here.
x.com/SolidEvidence/…
x.com/SolidEvidence/…
1/ My favorite way of finding cryptic lineages by screening for what I call the ‘s2m fix’.
s2m is an RNA element at the end of the SC2 genome that has been deleted from all lineages in circulation for over 2 years.
If you see the s2m sequence, you know it is an old lineage.

2/
Oct 23, 2024 • 12 tweets • 4 min read
Cryptic lineage quarterly update, part 2
BA.1 and Delta
If you missed part 1, it is here.

1/ BA.1 cryptics. BA.1 infections all occurred in late 2021-early 2022. If there is good coverage, BA.1 lineages are easy to spot because they have a unique Spike insertion that no other lineages have had.
2/ Image
Oct 22, 2024 • 14 tweets • 5 min read
Cryptic lineage quarterly update, part 1
Recent BA.2-XBB cryptics

Cryptic lineages are unique, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater from an unknown source.

1/ Image We are almost certain that these lineages are derived from individuals that have been infected with SARS-CoV-2 for several years that are shedding a ton of viral material.

If you want to know why we think these are from humans, read this thread.

2/
Oct 2, 2024 • 4 tweets • 2 min read
Update on the Bavarian cryptic lineage that @LongDesertTrain spotted.

This lineage first popped up in August but has been consistently present since.


1/ cov-spectrum.org
Image The lineage is derived from BA.5.1.10, but taken at face value, it has over 90 additional mutations and deletions.

2/ Image
Aug 17, 2024 • 15 tweets • 5 min read
I'm giving the variant update at the SAVE meeting on Monday so I thought I'd put out a preview for comment.

We are now at our 4th 'high water' mark since the Omicron wave based on wastewater surveillance.

1/ Image I thought I would give an abbreviated summary of the last year in variants.

A little over a year ago BA.2.86 started circulating, a lineage that was almost certainly derived from a persistent infection.
2/ Image
Jul 24, 2024 • 6 tweets • 1 min read
Just returning from the CEIRR influenza annual meeting.

Here are my takeaways.

1/ First the bad news.

2.3.4.4b (which the H5 in cattle is derived from) is a bad ass. In birds it is ridiculously contagious, ridiculously promiscuous, and pretty darn deadly. It spread through typical and atypical US bird populations practically instantly.

2/