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/ 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…

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/

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/

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/ 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/

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/

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/

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/

https://x.com/SolidEvidence/status/1758255313440907668

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…

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/

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

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/ 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/

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/

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… As you can see, rhinovirus season (which started in the Spring) is pretty much over.
2/

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/

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/

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/

https://twitter.com/SolidEvidence/status/1958155868219777354

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/

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/ 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/

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/

A 'new' Texas cryptic lineage popped up this week.

We've got another traveler.

1/ 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/

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/ 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/

https://x.com/SolidEvidence/status/1939338601483083956

This is cool. I was poking around at the Rhinovirus (common cold) data and realized that my perception about these viruses was completely wrong.
1/ Rhinoviruses (Rhino is Greek for nose) are picornaviruses in the enterovirus genus (same as polio). Enteros can be GI or respiratory (or both), but Rhinos are usually respiratory, and are the main cause of the common cold.

2/cdc.gov/rhinoviruses/a…

I’m thrilled to announce the update of our water surveillance dashboard.

Many improvements, and our first substantial move into ‘OneHealth’.

Read to the end to find the Easter Egg.
1/
dholab.github.io/public_viz/001… The first big improvement is that the output is more precise, and interactive. For each data point we tell you the date, the reads mapped, the total reads in each sample, and the reads/billion for each pathogen.

The heat map color is dictated by reads/billion.

2/