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
Guess what we're hunting for.
November 10, 2025 at 6:41 PM
Guess what we're hunting for.
Are prickly pears or their fruit seasonal?
There are several cactus viruses that appear seasonally (Aug-Oct) just about everywhere. I can't think of any other cacti that are commonly eaten.
Or maybe it's infecting something else?
There are several cactus viruses that appear seasonally (Aug-Oct) just about everywhere. I can't think of any other cacti that are commonly eaten.
Or maybe it's infecting something else?
November 4, 2025 at 3:15 PM
Are prickly pears or their fruit seasonal?
There are several cactus viruses that appear seasonally (Aug-Oct) just about everywhere. I can't think of any other cacti that are commonly eaten.
Or maybe it's infecting something else?
There are several cactus viruses that appear seasonally (Aug-Oct) just about everywhere. I can't think of any other cacti that are commonly eaten.
Or maybe it's infecting something else?
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.
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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).
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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).
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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/
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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/
Most of the Rhinoviruses also circulated in the Spring, but as I’ve noted before, the specific serotypes changed from year to year.
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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.
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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?
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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.
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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.
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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.
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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.
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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.
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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.
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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 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.
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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.
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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/
This was just raw reads though, if you look at diversity there was considerably more species of phages.
3/
October 31, 2025 at 12:19 PM
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/
This was just raw reads though, if you look at diversity there was considerably more species of phages.
3/
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/
Weekly wastewater samples for 18 months, totaling over 85 Billion sequence reads.
2/
October 31, 2025 at 12:19 PM
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/
Weekly wastewater samples for 18 months, totaling over 85 Billion sequence reads.
2/
Here’s the one clue we have about its host. While the virus is present in every single sample, it has a huge and reproducible surge in late June/early July.
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October 24, 2025 at 4:44 PM
Here’s the one clue we have about its host. While the virus is present in every single sample, it has a huge and reproducible surge in late June/early July.
11/
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How do we know they are viruses? We can assemble the sequences and they always have very ‘virus-like’ genetics, here’s an example.
When we translate the proteins, we can usually figure out generally what kind of virus they are.
9/
When we translate the proteins, we can usually figure out generally what kind of virus they are.
9/
October 24, 2025 at 4:44 PM
How do we know they are viruses? We can assemble the sequences and they always have very ‘virus-like’ genetics, here’s an example.
When we translate the proteins, we can usually figure out generally what kind of virus they are.
9/
When we translate the proteins, we can usually figure out generally what kind of virus they are.
9/
There are other tomato viruses we detect too (e.g. Tomato Mosaic virus) that are in the US.
These mostly appear late in the growing season. Makes sense.
(This is from a paper we’re getting ready to submit)
7/
These mostly appear late in the growing season. Makes sense.
(This is from a paper we’re getting ready to submit)
7/
October 24, 2025 at 4:44 PM
There are other tomato viruses we detect too (e.g. Tomato Mosaic virus) that are in the US.
These mostly appear late in the growing season. Makes sense.
(This is from a paper we’re getting ready to submit)
7/
These mostly appear late in the growing season. Makes sense.
(This is from a paper we’re getting ready to submit)
7/
As I’ve pointed out before, SC2 only differs from the Sarbeco consensus at 23 AA positions.
Cryptics tend to revert to the Sarbeco seq and circulating lineages do not. [I think this tells us that SC2 did not come straight from a bat]
Anyway, ID is also reverting.
11/
Cryptics tend to revert to the Sarbeco seq and circulating lineages do not. [I think this tells us that SC2 did not come straight from a bat]
Anyway, ID is also reverting.
11/
October 17, 2025 at 9:21 PM
As I’ve pointed out before, SC2 only differs from the Sarbeco consensus at 23 AA positions.
Cryptics tend to revert to the Sarbeco seq and circulating lineages do not. [I think this tells us that SC2 did not come straight from a bat]
Anyway, ID is also reverting.
11/
Cryptics tend to revert to the Sarbeco seq and circulating lineages do not. [I think this tells us that SC2 did not come straight from a bat]
Anyway, ID is also reverting.
11/
The only exception is the 498/501 positions.
Cryptics tend to want to have 498H/Y and 501S/T.
Omicrons have 498R and 501Y, and so far that has remained locked in.
10/
Cryptics tend to want to have 498H/Y and 501S/T.
Omicrons have 498R and 501Y, and so far that has remained locked in.
10/
October 17, 2025 at 9:21 PM
The only exception is the 498/501 positions.
Cryptics tend to want to have 498H/Y and 501S/T.
Omicrons have 498R and 501Y, and so far that has remained locked in.
10/
Cryptics tend to want to have 498H/Y and 501S/T.
Omicrons have 498R and 501Y, and so far that has remained locked in.
10/
In fact, the Idaho cryptic is a caricature of cryptics changes, having about a third of the most common cryptic changes.
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October 17, 2025 at 9:21 PM
In fact, the Idaho cryptic is a caricature of cryptics changes, having about a third of the most common cryptic changes.
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Here was another question. Circulating lineages like to have S:K417N, while cryptics almost always select for S:K417T.
Does context matter?
Would an Omicron that starts with S:K417N still want to switch to 417T?
Yes.
8/
Does context matter?
Would an Omicron that starts with S:K417N still want to switch to 417T?
Yes.
8/
October 17, 2025 at 9:21 PM
Here was another question. Circulating lineages like to have S:K417N, while cryptics almost always select for S:K417T.
Does context matter?
Would an Omicron that starts with S:K417N still want to switch to 417T?
Yes.
8/
Does context matter?
Would an Omicron that starts with S:K417N still want to switch to 417T?
Yes.
8/
What about the death mutation.
Rarely seen in patients, but when it is, the patients have a bad habit of being reported as ‘deceased’.
Yup, there it is.
7/
Rarely seen in patients, but when it is, the patients have a bad habit of being reported as ‘deceased’.
Yup, there it is.
7/
October 17, 2025 at 9:21 PM
What about the death mutation.
Rarely seen in patients, but when it is, the patients have a bad habit of being reported as ‘deceased’.
Yup, there it is.
7/
Rarely seen in patients, but when it is, the patients have a bad habit of being reported as ‘deceased’.
Yup, there it is.
7/
Here’s another one common one, a combined S:Q1201K with a silent mutation that produces a new TRS.
I still have no idea what this TRS does for the virus, but cryptics love having it.
6/
I still have no idea what this TRS does for the virus, but cryptics love having it.
6/
October 17, 2025 at 9:21 PM
Here’s another one common one, a combined S:Q1201K with a silent mutation that produces a new TRS.
I still have no idea what this TRS does for the virus, but cryptics love having it.
6/
I still have no idea what this TRS does for the virus, but cryptics love having it.
6/