Marc Johnson Profile picture
Nov 1, 2022 7 tweets 2 min read Read on X
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. Image
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. Image
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.

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More from @SolidEvidence

Jul 18
A 'new' Texas cryptic lineage popped up this week.

We've got another traveler.

1/ Image
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/ Image
It's a little surprising we found this one because the sequence coverage was kind of spotty.

It popped up in one of our screens because it had a few mutations that we've only seen in cryptics so far.
3/ Image
Read 11 tweets
Jul 9
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/ Image
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/
As promised, we've now added a standalone readout of the rhinoviruses on our wastewater dashboard.

3/
lungfish-science.github.io/wastewater-das…Image
Read 10 tweets
Jun 29
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/ Image
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…
There are 3 species of Rhinoviruses (A, B, and C), and over a hundred antigenically distinct serotypes.

3/en.wikipedia.org/wiki/Rhinovirus
Read 16 tweets
Jun 28
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/ Image
As before, we have a dropdown menu (now divided into categories) where you can do a city-to-city comparison of the different pathogens.

We hope to show more locations soon.
3/ Image
Read 17 tweets
Jun 12
Our latest cryptic lineage paper was accepted in PLoS Pathogens.

This paper has some nuanced implications about the origins of SARS-CoV-2.
1/
journals.plos.org/plospathogens/…
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/ Image
Read 11 tweets
Jun 6
This is so cool.

I’m pleased to share version 1.0 of our new dashboard for displaying data from our wastewater metagenomic project.

This is a collaborative projected between MU, U. Wisc @dho, and SecureBio; funded by Inkfish and Open Philanthropy.
1/
lungfish-science.github.io/wastewater-das…
For the last 18 months we have been getting weekly composite wastewater samples, isolating the viral fractions (the virome) and randomly sequencing everything.

We average about 1 billion reads per sample.
2/
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/ Image
Read 15 tweets

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