For those of you that have asked me why I am convinced that cryptic lineages are coming from people, I can finally point to a pre-print with @dho and many fantastic collaborators in the UWisc and Wisc Public Health. medrxiv.org/cgi/content/sh…
It's pretty straightforward. We started with a sewershed that produces enough wastewater to fill about 30 olympic swimming pools a day. We sampled about a quarter cup.
But something didn't smell right.
It had a cryptic lineage, a SARS-CoV-2 RNA that was completely unknown.
For the next several months my collaborators continued to take sub-samples from throughout the sewershed and sent them to me to figure out which one 'didn't smell right'.
With each round of sampling we further narrowed the source of the cryptic lineage.
We finally narrowed the source to a single manhole, and then to a single set of bathrooms.
The sample from that bathroom contained by far the most SARS-CoV-2 RNA I had ever seen from a wastewater sample. We could have diluted it a million-fold and still detected the lineage.
This bathroom was not used by any rats or white tailed deer. The signal was coming from a person.
We also learned from this 'homogeneous sample' about the complete viral sequence. It was from a lineage that circulated over a year ago.
The person has been infected a long time.
We still don't know which person is the source (most were tested by nasal swabs and were negative), and more importantly, we don't know why the lineage is not spreading.
We suspect that the source is a long-term COVID infection of someone's GI tract.
There are still a lot of questions that need to be answered, but we have at least started to figure out what the right questions are.
• • •
Missing some Tweet in this thread? You can try to
force a refresh
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.
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/
As before, we have a dropdown menu (now divided into categories) where you can do a city-to-city comparison of the different pathogens.
There haven’t been a ton of changes to the manuscript since I wrote a post on the preprint, so I’ll make this summary brief and focus on the things that changed. 2/
Cryptic lineages are anachronistic, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater. We are pretty certain they are all from persistent infections.
We developed techniques for finding these lineages and partially reconstruction their genomes. 3/
For the last 18 months we have been getting weekly composite wastewater samples, isolating the viral fractions (the virome) and randomly sequencing everything.
The project started with Columbia, MO in late 2023, but we’ve expanded to include Chicago, Boston, Boise, and Riverside. We are doing other sites too (and expanding), but these are the first we are reporting. 3/