Marc Johnson

We released our latest metagenomics preprint. I’m really excited about this study. The unofficial title is ‘conquer the dark matter, volume 1’ 1/ medrxiv.org/content/10.648…

New cryptic. I don't see a lot of s2m fixes these days, but one just popped up in Colorado. A very obvious BA.1-derivative, so a 4 year old infection.

We passed 3,000 metagenomic samples this week. I need a few hundred more hard drives.

6 more sightings this week. 4 from NYC, 1 from Florida and 1 from Alabama. Not explosive, but it has legs. Needs a name.

@davidmichaels @Unusual_Times @Nucleocapsoid @LongDesertTrain @jeffgilchrist @polybioRF Did they recover sequence? Not saying they are wrong if they didn't, but when sequence is recovered that is consistent the case is much stronger.

@Unusual_Times @SolidEvidence @Nucleocapsoid @LongDesertTrain @jeffgilchrist Watch the recent @polybioRF symposiums: Spring 2026 and Fall 2025. There's an active reservoir in the gut (illium) that empties when you go for a colonoscopy but refreshes within days because of activated platelets from MK cells. Gut-brain signaling causes neuroinflammation.

Useful summary article on non-retroviral RNA virus persistence mechanisms. @SolidEvidence @LongDesertTrain How people like Balloux could ever deny possibility of SARS-2 persisting is beyond me, given wealth of prior examples! H/t @jeffgilchrist 👍 nature.com/articles/s4159…

@Unusual_Times @LongDesertTrain @davidmichaels @Nucleocapsoid @jeffgilchrist Yup, that's included. The most prevalent ORF8 change in cryptics actually is 119-120DEL (in 5 cryptics). dholab.github.io/public_viz/006…

@LongDesertTrain @SolidEvidence @davidmichaels @Nucleocapsoid @jeffgilchrist Marc - do you ever sequence Orf8 in cryptics, that was our indicator that Alpha evolved in a T-Cell free environment I think

@Unusual_Times @davidmichaels @Nucleocapsoid @LongDesertTrain @jeffgilchrist I don't think gut is necessarily the only reservoir.

@SolidEvidence @davidmichaels @Nucleocapsoid @LongDesertTrain @jeffgilchrist Surely it has to be in the gut, cryptics have distinct mutations that should scream out about how they bind ? Can't be Liver or Kidneys because blood screening would pick up anomalies. Just infect a mouse with no T-Cells and see what happens, Alpha had that indication.6uu

@davidmichaels @Nucleocapsoid @LongDesertTrain @jeffgilchrist I have the most faith in the studies when they are able to recover sequence. If I can recover sequence from 600 million gallons of sewage, they should be able to recover sequence from a genuine reservoir.

@SolidEvidence @Nucleocapsoid @LongDesertTrain @jeffgilchrist Bone marrow megakaryocytes seem to be the primary reservoirs. Autopsies show SARSCoV2 in infectious tissues, even a year after infection.

@Debbie_Winslow_ @javid_lab If you can smell the chlorine, you're probably OK.

@SolidEvidence @javid_lab Question. Would you swim in a public pool this month if you were healthy? Obviously, avoid ingesting pool water.

I'm wondering if @SolidEvidence has any data and thoughts on the current cyclospora outbreak? It seems to have started at least two months ago, so there should be quite a bit of data from waste water. Can back checking lead to potential source or definitive start?

@OmicsOmicsBlog Yes, I've seen it, but it doesn't show up well from our approach.

Is any genomic surveillance of the cyclospora outbreak taking place? Does its RNA show up in wastewater sequencing? @SolidEvidence

@LongDesertTrain @CorneliusRoemer When was it submitted and when was it pulled?

@SolidEvidence @CorneliusRoemer You might be interested in this: I found an old UK sequence that was pulled from GISAID to see if I could find any hidden mutations. It turned out to be another ORF3a:H182D + C200Y. No RBM coverage but it has just about every non-RBM classic Cryptic mutation.

Two conventional sequences (not wastewater) of this variant showed up in New York City today, with collection dates June 30 and July 4. New phylogenetic tree (S:S31Y is an artifact): @SolidEvidence Still waiting for @corneliusroemer to give it an official Pango name.

We performed a metagenomic sprint this week. Samples that arrived on Tues were prepped overnight, loaded on a 10B plate Wed (25 h run), and output today. The same summer viruses continue to surge: Parechovirus 6, Rhinovirus A54, Parainfluenzavirus 3 and Coxsackievirus A9.

Three more detections of the MC.10.1.7 outlier in NYC sewersheds. Does this have a designation yet? @LongDesertTrain

@LongDesertTrain No spike coverage

@SolidEvidence Wow, Utah is quite the geographic jump. This thing might have legs. Same spike as the New York one?

@LongDesertTrain I did some scavenging to see if it was in any other sewersheds in the last month. Found 3 more, 2 more from NYC (different sewersheds) and 1 from Utah. I can't say it's taking off, but it moving around pretty quickly.

@Nucleocapsoid @LongDesertTrain There are some chronic markers in this lineage, but not many 'cryptic' mutations outside of the RBD, so it's probably at least been respiratory the whole time.

@LongDesertTrain @SolidEvidence Once particular SARS-2 virus has gad an initial opportunity to become persistent (e.g. 1st immuno-compromised host), one might expect it to acquire some mutations favoring chronic infection - such that subsequent onward infections of new hosts were ALSO more prolonged than usual?

A mysterious, unusually diverse saltation lineage descended from KP.3.1.1 (last seen early 2025) has circulated at a low level for ~8 months in Ontario (see 🧵on next post). Seemed a local anomaly, but @solidevidence just spied a weird spike in NYC WW—& it's the same one! 1/14

@LongDesertTrain When sequencing is limited enough, every branch is long.

@SolidEvidence I think it's evolving stepwise, but mostly within one person (possibly 2 or 3). I don't think there's any way those long branches happen except in the context of a chronic infection.

@holleysweetlife Always read the last data point with caution. There could be samples from that week that have not been processed yet.

@SolidEvidence I may be reading the graph wrong, but it looks like the viruses hit a peak and are now decreasing??? Or is just the normal up and down?

World Cup virus wastewater update. While I wait ‘patiently’ for the sequences from this week (which was supposed to be done already), here is a summary of the 4 lineages that have been on the rise since the games began across our 43 sampling sites. 1/