Solid Evidence
@solidevidence.bsky.social
Molecular virologist, sewage sage and wastewater wizard.
Professor at University of Missouri, School of Medicine
Professor at University of Missouri, School of Medicine
I really wish I'd been doing more sites that season. Was it a nationwide outbreak of FluC? I'd bet it was.
November 2, 2025 at 3:13 PM
I really wish I'd been doing more sites that season. Was it a nationwide outbreak of FluC? I'd bet it was.
Not published yet, but at least public.
October 31, 2025 at 1:21 PM
Not published yet, but at least public.
Ribosomes are pretty biophysically similar to viruses. We tried depleting, but we lost some things that we didn't want to lose in the process. I'm convinced that the rRNA data is going to be useful eventually.
October 31, 2025 at 1:20 PM
Ribosomes are pretty biophysically similar to viruses. We tried depleting, but we lost some things that we didn't want to lose in the process. I'm convinced that the rRNA data is going to be useful eventually.
Eventually sequencing will be cheaper, databases will be more complete, and this kind of study will be routine (maybe 5-10 years).
Meanwhile, keep pooping, we take this shit seriously.
22/22
Thanks to our collaborators/funders:
Inkfish, @securebio.org, naobservatory.org/casper/
Meanwhile, keep pooping, we take this shit seriously.
22/22
Thanks to our collaborators/funders:
Inkfish, @securebio.org, naobservatory.org/casper/
Nucleic Acid Observatory - Reliable early warning for catastrophic pandemics
The world is demonstrably vulnerable to biological threats. COVID-19 was a disaster, but future pandemics could be far worse. To protect society from future catastrophe, we need reliable early warning...
naobservatory.org
October 31, 2025 at 12:19 PM
Eventually sequencing will be cheaper, databases will be more complete, and this kind of study will be routine (maybe 5-10 years).
Meanwhile, keep pooping, we take this shit seriously.
22/22
Thanks to our collaborators/funders:
Inkfish, @securebio.org, naobservatory.org/casper/
Meanwhile, keep pooping, we take this shit seriously.
22/22
Thanks to our collaborators/funders:
Inkfish, @securebio.org, naobservatory.org/casper/
False positives. Even many human viruses are not characterized.
Every week we find sequences whose closest match is polio, but it's never polio.
It’s always viruses related to polio that just aren’t in the database.
It's annoying, and time consuming checking them all.
21/
Every week we find sequences whose closest match is polio, but it's never polio.
It’s always viruses related to polio that just aren’t in the database.
It's annoying, and time consuming checking them all.
21/
October 31, 2025 at 12:19 PM
False positives. Even many human viruses are not characterized.
Every week we find sequences whose closest match is polio, but it's never polio.
It’s always viruses related to polio that just aren’t in the database.
It's annoying, and time consuming checking them all.
21/
Every week we find sequences whose closest match is polio, but it's never polio.
It’s always viruses related to polio that just aren’t in the database.
It's annoying, and time consuming checking them all.
21/
Unknowns. A very large portion of the sequence from this data is ‘dark matter’: sequences from species (largely viruses) that have never been characterized.
(That’s what our next manuscript will be about.)
20/
(That’s what our next manuscript will be about.)
20/
October 31, 2025 at 12:19 PM
Unknowns. A very large portion of the sequence from this data is ‘dark matter’: sequences from species (largely viruses) that have never been characterized.
(That’s what our next manuscript will be about.)
20/
(That’s what our next manuscript will be about.)
20/
Price, right now the sequencing alone is at least ~$500-1000 per sample.
However, it keeps going down. There was a noticeable decrease in price even during the duration of this study.
19/
However, it keeps going down. There was a noticeable decrease in price even during the duration of this study.
19/
October 31, 2025 at 12:19 PM
Price, right now the sequencing alone is at least ~$500-1000 per sample.
However, it keeps going down. There was a noticeable decrease in price even during the duration of this study.
19/
However, it keeps going down. There was a noticeable decrease in price even during the duration of this study.
19/
I think this kind of surveillance is the way of the future, but we’re not there yet.
1. Price: too expensive.
2. Unknowns: most sequences are 'unknown'.
3. False positives: requires careful curation.
18/
1. Price: too expensive.
2. Unknowns: most sequences are 'unknown'.
3. False positives: requires careful curation.
18/
October 31, 2025 at 12:19 PM
I think this kind of surveillance is the way of the future, but we’re not there yet.
1. Price: too expensive.
2. Unknowns: most sequences are 'unknown'.
3. False positives: requires careful curation.
18/
1. Price: too expensive.
2. Unknowns: most sequences are 'unknown'.
3. False positives: requires careful curation.
18/
The data in this paper is from one sewershed Jan.2024-June 2025.
If you want to know about more sites and more recent data, visit our dashboard. It’s updated at least once a week.
17/
lungfish-science.github.io/wastewater-d...
If you want to know about more sites and more recent data, visit our dashboard. It’s updated at least once a week.
17/
lungfish-science.github.io/wastewater-d...
𓆞 lung.fish Data Explorer
lungfish-science.github.io
October 31, 2025 at 12:19 PM
The data in this paper is from one sewershed Jan.2024-June 2025.
If you want to know about more sites and more recent data, visit our dashboard. It’s updated at least once a week.
17/
lungfish-science.github.io/wastewater-d...
If you want to know about more sites and more recent data, visit our dashboard. It’s updated at least once a week.
17/
lungfish-science.github.io/wastewater-d...
There were other things we saw that we REALLY didn’t expect. For instance, H5N1 B3.13 (which wasn't in MO) appeared in Spring of 2024.
We’re pretty sure this came from a dairy in town that imports their milk from Texas, where H5N1 was rampant at that time.
16/
We’re pretty sure this came from a dairy in town that imports their milk from Texas, where H5N1 was rampant at that time.
16/
October 31, 2025 at 12:19 PM
There were other things we saw that we REALLY didn’t expect. For instance, H5N1 B3.13 (which wasn't in MO) appeared in Spring of 2024.
We’re pretty sure this came from a dairy in town that imports their milk from Texas, where H5N1 was rampant at that time.
16/
We’re pretty sure this came from a dairy in town that imports their milk from Texas, where H5N1 was rampant at that time.
16/
There were also a few Fall respiratory viruses we detected. Enterovirus D68 (expected), and on off-season surge of rhinovirus C42 (not expected, but nationwide).
15/
15/
October 31, 2025 at 12:19 PM
There were also a few Fall respiratory viruses we detected. Enterovirus D68 (expected), and on off-season surge of rhinovirus C42 (not expected, but nationwide).
15/
15/
We also saw a year-to-year turnover in Parechovirus serotypes (causes meningitis).
This exactly matched what our colleagues down the road in KC found in pediatric patients.
pubmed.ncbi.nlm.nih.gov/40712199/
14/
This exactly matched what our colleagues down the road in KC found in pediatric patients.
pubmed.ncbi.nlm.nih.gov/40712199/
14/
October 31, 2025 at 12:19 PM
We also saw a year-to-year turnover in Parechovirus serotypes (causes meningitis).
This exactly matched what our colleagues down the road in KC found in pediatric patients.
pubmed.ncbi.nlm.nih.gov/40712199/
14/
This exactly matched what our colleagues down the road in KC found in pediatric patients.
pubmed.ncbi.nlm.nih.gov/40712199/
14/
You can see a much more detailed readout of the rhinovirus (with more sites) on our dashboard.
13/
dholab.github.io/public_viz/0...
13/
dholab.github.io/public_viz/0...
Rhinovirus Serotypes Dashboard
dholab.github.io
October 31, 2025 at 12:19 PM
You can see a much more detailed readout of the rhinovirus (with more sites) on our dashboard.
13/
dholab.github.io/public_viz/0...
13/
dholab.github.io/public_viz/0...
Most of the Rhinoviruses also circulated in the Spring, but as I’ve noted before, the specific serotypes changed from year to year.
12/
12/
October 31, 2025 at 12:19 PM
Most of the Rhinoviruses also circulated in the Spring, but as I’ve noted before, the specific serotypes changed from year to year.
12/
12/
Other respiratory viruses circulated later. For instance, ParaInfluenza 3 circulated from April-June both years.
This was expected, but I still don’t understand it epidemiologically. Why then?
11/
This was expected, but I still don’t understand it epidemiologically. Why then?
11/
October 31, 2025 at 12:19 PM
Other respiratory viruses circulated later. For instance, ParaInfluenza 3 circulated from April-June both years.
This was expected, but I still don’t understand it epidemiologically. Why then?
11/
This was expected, but I still don’t understand it epidemiologically. Why then?
11/
We also detected all of the other human coronaviruses, and influenza viruses. They all were most prevalent January-March, as expected.
10/
10/
October 31, 2025 at 12:19 PM
We also detected all of the other human coronaviruses, and influenza viruses. They all were most prevalent January-March, as expected.
10/
10/
We were also monitoring SARS-CoV-2 in these samples the old-fashioned way (dPCR) and it was nice to see that the amount detected from sequencing (normalized or not normalized) correlated pretty well with the dPCR results.
10/
10/
October 31, 2025 at 12:19 PM
We were also monitoring SARS-CoV-2 in these samples the old-fashioned way (dPCR) and it was nice to see that the amount detected from sequencing (normalized or not normalized) correlated pretty well with the dPCR results.
10/
10/
There was only one respiratory virus that was present year-round. You guessed it, SARS-CoV-2.
It’s still here.
9/
It’s still here.
9/
October 31, 2025 at 12:19 PM
There was only one respiratory virus that was present year-round. You guessed it, SARS-CoV-2.
It’s still here.
9/
It’s still here.
9/
Although human pathogens were a tiny fraction of the total sequences, there was still plenty of sequences to figure out what the circulating human pathogens were.
8/
8/
October 31, 2025 at 12:19 PM
Although human pathogens were a tiny fraction of the total sequences, there was still plenty of sequences to figure out what the circulating human pathogens were.
8/
8/
The one time of year when the ToBRV proportion goes down is late Summer, when it is partially displaced by Tomato Mosaic virus (which does infect US tomatoes).
This probably reflects people eating more local tomatoes when they are in season.
7/
This probably reflects people eating more local tomatoes when they are in season.
7/
October 31, 2025 at 12:19 PM
The one time of year when the ToBRV proportion goes down is late Summer, when it is partially displaced by Tomato Mosaic virus (which does infect US tomatoes).
This probably reflects people eating more local tomatoes when they are in season.
7/
This probably reflects people eating more local tomatoes when they are in season.
7/
What’s sort of surprising is that ToBRFV isn’t even in US tomatoes.
That explains why we see it year round though. These are probably from imported tomatoes and tomato products.
6/
en.wikipedia.org/wiki/Tomato_...
That explains why we see it year round though. These are probably from imported tomatoes and tomato products.
6/
en.wikipedia.org/wiki/Tomato_...
Tomato brown rugose fruit virus - Wikipedia
en.wikipedia.org
October 31, 2025 at 12:19 PM
What’s sort of surprising is that ToBRFV isn’t even in US tomatoes.
That explains why we see it year round though. These are probably from imported tomatoes and tomato products.
6/
en.wikipedia.org/wiki/Tomato_...
That explains why we see it year round though. These are probably from imported tomatoes and tomato products.
6/
en.wikipedia.org/wiki/Tomato_...
What plant viruses you may ask? The most prominent one is a virus called Tomato Brown Rugose Fruit Virus (ToBRFV).
This was true everywhere in the country.
Americans eat a lot of tomatoes.
5/
This was true everywhere in the country.
Americans eat a lot of tomatoes.
5/
October 31, 2025 at 12:19 PM
What plant viruses you may ask? The most prominent one is a virus called Tomato Brown Rugose Fruit Virus (ToBRFV).
This was true everywhere in the country.
Americans eat a lot of tomatoes.
5/
This was true everywhere in the country.
Americans eat a lot of tomatoes.
5/
Focusing on the eukaryotic viruses, you see that the vast majority of the eukaryotic viruses are Virgaviridae, which infect plants.
4/
4/
October 31, 2025 at 12:19 PM
Focusing on the eukaryotic viruses, you see that the vast majority of the eukaryotic viruses are Virgaviridae, which infect plants.
4/
4/