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Marc Johnson Profile picture
@SolidEvidence
Apr 1, 2025 • 1 tweets • 1 min read • Read on X
What gets me about all these cuts and firings is that they are clearly designed to be maximally disruptive, painful, and disrespectful.

This isn't reality TV. Who treats people this way?

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More from @SolidEvidence

Marc Johnson Profile picture
Jan 24
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/
A good way to spot anachronistic lineages is to look for sequences that have been deleted in contemporary lineages. The virus can only undo a deletion through recombination. If we find seqs that lack the deletions, they have to be old (or contaminated with something old).
3/
Read 16 tweets
Marc Johnson Profile picture
Nov 23, 2025
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, 2025
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, 2025
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, 2025
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, 2025
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

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