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Marc Johnson Profile picture
Marc Johnson
@SolidEvidence
Molecular virologist, Professor, and wastewater detective. Same handle on bsky. Opinions are my own and do not reflect those of my employer or anyone else.
Jun 10 • 7 tweets • 2 min read
I’m so excited. My secret (not so secret) observational experiment is about to begin.

This is a once in a lifetime opportunity for wastewater surveillance.

FIFA World cup.
1/
 @SecureBio
scientificamerican.com/article/the-wo… Starting this week, over 5 million international visitors from at least 48 countries will be descending on 16 cities in North America.
The average visitor will stay 1-3 weeks.
2/
Apr 30 • 4 tweets • 1 min read
This is crazy.

Imagine a hole the size of a football field that is 700 feet deep.

Now fill it up with wastewater, and remove a tablespoon.

That was our starting material for this study.

1/ Image Using an untargeted sequencing approach, we were not only able to identify a single measles patient from that sample, but we were able to confirm that the sequence of the virus specifically matched the virus from that patient.

2/
 evidence.nejm.org/doi/pdf/10.105…
Apr 28 • 5 tweets • 2 min read
BA.3.2 is strange is so many ways.

It's now 17 months old, which is really quite old for a COVID lineage.

Every so often there is a sweeping lineage that displaces everything in circulation, but when that doesn't happen the existing 'clans' fight it out with each other.
1/ The longest running clan is the current one. BA.2.86 emerged around July 2023 and is still going strong.

This is the RBD of the original BA.2.86, and some of its descendants from 17 months later.

2/ Image
Apr 4 • 10 tweets • 3 min read
I’m amazed.
It’s really true: the BA.3.2 COVID lineage is infecting children at a much higher rate than previous lineages.

I’m late to this party, but I couldn’t really believe it was true until I did the analysis for myself.
1/ Most countries do not include patient ages with the sequence, so I restricted my analysis to

1. countries with reliable age info,
2. only included sequences submitted since Dec 2025
3. only included countries with over 50 BA.3.2 sequences.

2/
Mar 23 • 9 tweets • 3 min read
A new cryptic lineage popped up in St Louis a few weeks ago.

I’ve been sampling this sewershed (500k people) twice a week for years and the first time I see this cryptic lineage it is 5 years old and makes up 50% of the sample.
1/ Image I believe the cryptic is a B.1.1 (circulated until early 2021), but it’s possibly even a B.1.
Clearly pre-Omicron though.
2/ Image
Jan 24 • 16 tweets • 4 min read
We found a new (I think) cryptic lineage this week.
I know I say this all the time, but this is really weird.
Warning, this thread is for nerds only.
1/ Here’s what we do. Every week we download all of the new sequences from SRA and run a bunch of screens to look for anachronistic or cryptic lineages.

This new one popped up in 3 different screens.
2/
Nov 23, 2025 • 13 tweets • 3 min read
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/
Nov 21, 2025 • 9 tweets • 3 min read
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…
Nov 3, 2025 • 23 tweets • 7 min read
Can you take a quarter cup of composite wastewater, 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
Oct 31, 2025 • 23 tweets • 7 min read
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
Oct 24, 2025 • 12 tweets • 3 min read
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
Oct 17, 2025 • 12 tweets • 4 min read
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/
Sep 10, 2025 • 7 tweets • 2 min read
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/
Sep 9, 2025 • 18 tweets • 5 min read
Our wastewater dashboard was updated yesterday (we’re behind because of an equipment failure).

I’d like to point out some things you can learn from the dashboard about respiratory virus [post v.2, bleeped version].

1/

lungfish-science.github.io/wastewater-das…Image As you can see, rhinovirus season (which started in the Spring) is pretty much over.
2/ Image
Sep 6, 2025 • 18 tweets • 5 min read
Our wastewater dashboard was updated yesterday (we’re behind because of an equipment failure).

I’d like to point out some things you can learn from the dashboard about respiratory virus [and stupid vaccine policy].
1/
 lungfish-science.github.io/wastewater-das… As you can see, rhinovirus season (which started in the Spring) is pretty much over.
2/ Image
Sep 6, 2025 • 10 tweets • 3 min read
I’ve found cryptic lineages from sequencing wastewater.

I’ve found cryptic lineages from screening databases.

This is the first time I’ve found a cryptic lineage from social media.

This was an interesting story.
1/ Earlier this summer someone poked me to ask what the deal was with Coeur d’Alene, ID whose COVID numbers were consistently the highest in the country (by far).

I couldn’t find the post, so if this was you, please take credit.
2/ Image
Aug 22, 2025 • 11 tweets • 3 min read
It’s been 2 days, 143 comments, and I’ve been called lots of bad names.
Here’s what I learned about protein based Novavax (NV) vs mRNA COVID vaccines.
1/ The pretty universally agreed on difference is that Novavax has fewer side effects.
If you have bad vaccine reactions, it is probably the better choice.
2/
Aug 17, 2025 • 13 tweets • 4 min read
It’s been 2 years since BA.2.86 first appeared (and I’m give the variant update to SAVE on Monday), so I thought I would do a little summary about this era of SARS-CoV-2 evolution.
1/ Image SARS-CoV-2 lineages come up with new constellations of mutations in 3 main ways.
1. Sequential acquisition of mutations during normal circulation.
2. Recombination.
3. Sweeping new lineages (almost certainly from persistent infections).
2/
Aug 16, 2025 • 10 tweets • 2 min read
I read @EricTopol's Super Agers book while we were traveling this summer.

Wow. That was the most rigorous (>1,500 refs), comprehensive, and bullshit-free book on health I’ve ever seen.

Too much info for a thread, but I’ll mention some highlights.

1/simonandschuster.com/books/Super-Ag… Fact 1, it’s not just genetics.
@EricTopol spent years sequencing the genomes of the ‘wellderly’ (people over 80 that have never had a chronic illness) to find the genes associated with healthy aging.
Their conclusion – there wasn’t much there. It’s not just genetics.
2/
Jul 18, 2025 • 11 tweets • 3 min read
A 'new' Texas cryptic lineage popped up this week.

We've got another traveler.

1/ Image This one was from a Texas sewershed from July 1 with a population of 1,000,000, which means it had to have been one of the Dallas sewersheds.

2/ Image
Jul 9, 2025 • 10 tweets • 4 min read
I've always found this frustrating.

You or your child has a respiratory infection. It's not flu or COVID. Your doctor can only tell you, 'you have a virus'.

Could it be a little bit more specific?

We hope to help answer this question, non-invasively, and for free.
1/ Image Contrary to my prior assumptions, many of the most common pathogens are not everywhere, all the time. They occur in discrete waves, often nationwide.

I wrote about this recently with Rhinoviruses, the most frequent cause of the common cold.

2/