Do you think you've had long-term GI problems since having Covid? We are performing a study examining the characteristics of viruses, specifically persistent SARS-CoV-2 infections, in stool samples. 1/3

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?

Didn't work this time. Maybe I was wrong and this was just a X/bsky viewer difference. Or maybe the algorithm is smarter than I thought.

Thanks for the suggestions. I tried to repost a sanitized version. This worked last time, but we'll see.

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 sh!t seriously. Thanks to our collaborators/funders: Inkfish https://t.co/s7CCFCvNfO @SecureBio 23/23

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. 22/

Unknowns. A very large portion of the sequence from this data is ‘dark matter’: sequences from species that have never been characterized. (That’s what our next manuscript will be about.) 21/

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. 20/

I think this kind of monitoring 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. 19/

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. 18/ https://t.co/4cAIXmFdhu

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 it was rampant at that time. 17/

There were also a few Fall respiratory bugs we detected. Enterov!rus D68 (expected), and on off-season surge of common cold bug C42 (not expected, but nationwide). 16/

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. https://t.co/QeJsikJXuO 15/

You can see a much more detailed readout of the common cold bugs (with more sites and dates) on our dashboard. 14/ https://t.co/aTGs1iIGj8

Most of the common cold bugs also circulated in the Spring, but as I’ve noted before, the specific serotypes changed from year to year. 13/

Other respiratory bugs 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? 12/

We also detected all of the other human COVs, and IAVs. They all were most prevalent January-March, as expected. 11/

We were also monitoring SC2 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/

There was only one respiratory bug that was present year-round. You guessed it, SC2. 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 bugs were. 8/

The one time of year when the ToBRV proportion goes down is late Summer, when it is partially displaced by Tomato Mosaic v!rus (which does infect US tomatoes). This probably reflects people eating more local tomatoes when they are in season. 7/