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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.
17 subscribers
Apr 20 • 16 tweets • 4 min read
We are recruiting sewersheds for an expanding project. Basically, we want to learn everything that can be learned from wastewater.
Read on if you are interested.
1/ Image This is a collaboration with SecureBio that started about 18 months.

Basically, we isolate the viral fraction from wastewater and sequence the crap out of it (~1 billion reads/sample). This is unbiased sequencing; we don’t want to miss anything.
2/
 securebio.org
Apr 19 • 11 tweets • 3 min read
This battle between Harvard and the administration is so befuddling. The latest plot twist makes less sense than the last season of Lost.

Let me give a very quick summary for those not following along.
1/11 The last few weeks Harvard had been talking with the administration about concerns over antisemitism on campuses, but the talks lacked details, and Harvard was told that they would get a letter last Friday with more specifics.
2/
Apr 12 • 25 tweets • 7 min read
Last month there was an announcement that I thought was a major advancement in world health, but it got little attention.
I thought I would tell you all a little bit about it and why it is so important.
1/25 This breakthrough has to do with HIV, which was a zoonotic pathogen. The progenitor of HIV infects chimpanzees in Cameroon.

No one knows exactly when or how HIV crossed into humans, but the first undisputed HIV patient sample (discovered retrospectively) was from 1959 in what is now the Democratic Republic of Congo.Image
Apr 6 • 9 tweets • 2 min read
I briefly thought the SA BA.3.2 was in the US, but it turns out the virus was just messing with me again.

This was kind of interesting though.
1/ We've been screening all of the new wastewater data a few times a week for signs of BA.3.2.

One of the many screens we have is looking for reads that have C21846T+T21864C together, which are in BA.3.2 but no current lineages (it works better to look for pairs of changes).

2/
Mar 17 • 8 tweets • 3 min read
Here is this week's analysis. One mutation popped out as increasing in frequency in the last data set.

S:G842S

Wonder what that is from.

1/ Image Not a very common mutation. Mostly associated with with XEC.11*
2/
 cov-spectrum.org/explore/United…Image
Mar 17 • 16 tweets • 5 min read
I’m very pleased to announce the launch of our LungFish Data Explorer dashboard for tracking SARS-Cov-2 lineages from wastewater.

1/
 inkfishmedical.github.io/wastewater-das… Here’s the problem we hope this dashboard will help solve.  SARS-CoV-2 remains very prevalent in the US.

However, sequence surveillance from patients has plummeted. In addition to fewer samples, the average sequence takes >3 weeks to be reported (and it’s getting slower).

2/ Image
Mar 1 • 4 tweets • 2 min read
So what's happening with medical research in the US? This is the cumulative award count from the NIH for the year.

Doesn't look so good.

But it gets worse.
1/ Image Before grants are awarded, they have to be evaluated in meetings called study sections.

Before a study section can meet, it has to be listed in the federal registry for at least 15 days.

These are the new study section meetings listed in the federal registry this year.
2/ Image
Feb 28 • 5 tweets • 1 min read
There something new on the SARS-CoV-2 landscape, and I’m not sure what it is.
1/ Image S:S31F and S:K182N are on the rise.

The two aren’t on the same sequencing strand, but I confirmed that they are generally appearing together in the same samples.

2/
Feb 11 • 8 tweets • 3 min read
Brief update on the new cryptic lineage we found from Petersburg City, Virginia.

We went back and screened all of the samples from that sewershed since the beginning of 2024 and learned a few things about it.
1/ Image First, I think I was wrong about the lineage being JN.1 derived. I thought it was JN.1 because it had 22926C (455S), but it looks like it only acquired that recently.

In samples as recent as December the lineage lacked 455S and 456L.
2/ Image
Jan 31 • 7 tweets • 2 min read
Wastewater variant update. This is the composite data from over 1,000 US samples collected over the last 6 weeks.
1/ Image You have to extrapolate a little bit because several changes are shared by multiple lineages.

It appears that the new lineage I mentioned last week (MC.10.1 + 445P) is around 4% and is the fastest growing of the lot. It now has a PANGO designation - PA.1
2/
Jan 26 • 6 tweets • 2 min read
Here's the latest composite US wastewater data.

It's a little bit confusing this week.

1/ Image Clearly LP.8 is still the main lineage gaining traction. All of its changes are moving in the same direction (up).

LF.7 is much lower, but looking a little bit more alive than last week.
2/ Image
Jan 24 • 17 tweets • 5 min read
What fraction of patient sequences are derived from persistent SARS-CoV-2 infections? (volume 3)

This is something that we can actually calculate.
1/ The key is the mutation Orf1a:K1795Q, which frequently appears in persistent infections (and even more often in cryptic lineages).

2/
Jan 22 • 13 tweets • 4 min read
There was a nice paper that recently came out about a patient that had COVID for 521 days.

I find it interesting for different reasons that most though.
1/
nature.com/articles/s4152… We also study persistent infections, except we don't know who the patients are.


2/
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/