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Marc Johnson Profile picture
@SolidEvidence
Nov 1, 2022 • 7 tweets • 2 min read • Read on X
For those of you that have asked me why I am convinced that cryptic lineages are coming from people, I can finally point to a pre-print with @dho and many fantastic collaborators in the UWisc and Wisc Public Health.
medrxiv.org/cgi/content/sh…
It's pretty straightforward. We started with a sewershed that produces enough wastewater to fill about 30 olympic swimming pools a day. We sampled about a quarter cup.

But something didn't smell right.

It had a cryptic lineage, a SARS-CoV-2 RNA that was completely unknown. Image
For the next several months my collaborators continued to take sub-samples from throughout the sewershed and sent them to me to figure out which one 'didn't smell right'.

With each round of sampling we further narrowed the source of the cryptic lineage. Image
We finally narrowed the source to a single manhole, and then to a single set of bathrooms.

The sample from that bathroom contained by far the most SARS-CoV-2 RNA I had ever seen from a wastewater sample. We could have diluted it a million-fold and still detected the lineage.
This bathroom was not used by any rats or white tailed deer. The signal was coming from a person.

We also learned from this 'homogeneous sample' about the complete viral sequence. It was from a lineage that circulated over a year ago.

The person has been infected a long time.
We still don't know which person is the source (most were tested by nasal swabs and were negative), and more importantly, we don't know why the lineage is not spreading.

We suspect that the source is a long-term COVID infection of someone's GI tract.
There are still a lot of questions that need to be answered, but we have at least started to figure out what the right questions are.

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More from @SolidEvidence

Marc Johnson Profile picture
Nov 23
What should we expect this flu season?

Here’s a forecast from a wastewater perspective (because sh*t don’t lie)

1/
Background. The 4 main kinds of influenza circulating among humans (in order of severity) are:
FluA H3N2
FluA H1N1
FluB
FluC (many don’t know this one)

2/
Last season, there was a pretty even split between H1N1 and H3N2, with a little bit of FluB late in the season. At least according to CDC patient data.
3/ Image
Read 13 tweets
Marc Johnson Profile picture
Nov 21
This is wild.

Remember the NJ crytic lineage?

I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.

Some colleagues took me up on it.

Guess what they found?
1/
This preprint just came out. @wchnicholas and team reconstructed and tested the NJ Spike and found that it has the tightest ACE2 binding of any SC2 Spike ever measured.
2/
 medrxiv.org/content/10.110…
We first found the NJ variant in 2023 because this sewershed from NJ with 1.5 million people because it regularly had a sequence that was a reversion to the bat sarbeco sequence, which is common in cryptics.
3/
Read 9 tweets
Marc Johnson Profile picture
Oct 31
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?

That is the question we asked in our latest pre-print.

Turns out you can.
1/
 medrxiv.org/content/10.110…
We are not the first group to do unbiased sequencing of wastewater to monitor circulating viruses, but I think we are the first to ever do it at this scale.

Weekly wastewater samples for 18 months, totaling over 85 Billion sequence reads.

2/ Image
Among the ‘known’ viruses, there was a fairly even split between bacteria viruses (phages) and eukaryotic viruses.
This was just raw reads though, if you look at diversity there was considerably more species of phages.
3/ Image
Read 23 tweets
Marc Johnson Profile picture
Oct 24
Help me out, I’ve got another wastewater virus mystery.

This one really blows my mind.
1/
Starting in the late 2023, + @securebio have been doing ultra-deep metagenomic sequencing of the virome from Columbia, MO wastewater.

We’ve collected and sequenced sample for over 90 consecutive weeks.
2/Lung.fish
We sequence about a billion reads per sample. That’s generated about 16TB of data from this site so far.

To put this in perspective for people my age, it would take a stack of 3.5 in floppy disks 200 miles high to store this data.
3/
Read 12 tweets
Marc Johnson Profile picture
Oct 17
It looks like Coeur d’Alene, ID cryptic is gone for now, but it has still managed to answer a lot of lingering questions for me about SARS-CoV-2 evolution, and what to expect next.

Here's a whole genome summary and interpretation.
1/ Image
For a long time cryptic lineages were all from pre-Omicron lineages.

I started wondering:

Will there be Omicron cryptics?

If so, will they have the same evolutionary trajectories as the pre-Omicron cryptics?

ID shows that the answer to both questions is yes.
2/
We don’t do a lot of whole genome sequencing, so I sent 3 samples to @dho lab, who got fantastic sequences for all 3.
These samples were virtually 100% cryptic, so we have nearly complete coverage of the genome for a change.
3/ Image
Read 12 tweets
Marc Johnson Profile picture
Sep 10
This really pisses me off.

I obviously knew there was some manipulation of post metrics on social media, but I really didn’t realize just how hard this platform slams the breaks on posts it doesn’t like.

Here’s my experiment.
1/
This weekend I posted 3 threads.

1. on a cryptic lineage
2. on H5N1
3. on seasonal respiratory viruses

Each time I posted the threads on X and bsky at the same time.
2/
The three threads each got roughly the same attention on bsky.
However, on X the first 2 each had hundreds of RTs and over 1k likes.
The 3rd was practically invisible. It had only 5 RTs and 28 likes after 2 days. Over 40-times fewer views.

3/
Read 7 tweets

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