Marc Johnson Profile picture
Molecular virologist, Professor, sewage sage and wastewater wizard. Same handle on bsky.
16 subscribers
Nov 22 4 tweets 1 min read
If anyone wants to follow along with the Maryland variant (or doesn't believe my analysis), have a look for yourself.

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Go to
Type in SRR31400336 and start alignment.

This is a sample from the Maryland sewershed collected on November 7 of this year.
2/deeperseq.genomium.org
Nov 20 8 tweets 3 min read
Maryland folks, I need another favor.
There is a person from Anne Arundel county that has been infected with SARS-CoV-2 for about 3 years (Delta infection).

They probably don’t even know they are infected, but they are shedding a ton of viral material in wastewater
1/ Image I’m trying to find this person without invading their privacy, if they are willing to be found.

Here are a few threads I’ve written about this variant if you want to read up.

x.com/SolidEvidence/…
x.com/SolidEvidence/…
x.com/SolidEvidence/…
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Nov 17 12 tweets 3 min read
Need a little help.

Does anyone know someone that works at the Patuxent Water Reclamation Facility in Crofton, MD that they could put me in touch with?

Here's why.
1/ Image There is a cryptic lineage (unique, evolutionarily advanced SARS-CoV-2 lineage detected in wastewater) that we have been detecting from a Maryland sewershed all year.

The lineage is derived from Delta, so it's from a person that was first infected about 3 years ago.

2/ Image
Nov 15 12 tweets 3 min read
Postmortem.

Thanks for all of the retweets!

Late last night the twitter/x account was suspended and I also can't view the ResearchGate account anymore.

Here's a summary of some of the discussion/findings.

1/ I was going to post the full exchange I had with 'Julia', but I can't view it anymore. It was ~three exchanges and they were very benign. I stopped when I decided she was probably fake, but then she tried to reengage a few days later, which is when I investigated.
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Nov 14 16 tweets 4 min read
I knew there were a lot of fake accounts on this platform, but they are usually obvious. I had no idea how intricate and complex the ruse could be.

Get a load of this story.
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About a week ago I got a DM from an account asking me a benign but specific question about my research.

This happens to me all the time. I’ve met some interesting people this way.

Sometimes people even look up my number and call my office. It happens.
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Nov 5 5 tweets 2 min read
I'm doubling down on MV.1*

This lineage has been growing rapidly recently, but it's been hard to tell if it would be a real contender since most of the infections were from Singapore.

In North America its growth has been more questionable.

But I have new data.
1/ Image You probably know that our team screens all of the wastewater sequences submitted to SRA for cryptic lineages.

One of the 'cryptic-specific' changes we look for is S:F456V, which is common in cryptic, but hadn't been seen much in circulation until recently.
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Oct 28 9 tweets 3 min read
Cryptic lineage quarterly update, last update for now.

I save the weirdest for last. Read to the end.
1/ Image A lineage popped up in our cryptic screen because most of the seqs did not have the s2m deletion (meaning it was from 2022 or earlier).

The sample was from 9/30 in Texas. Population is 780, so it isn’t even on the NWSS map.

I don’t know where the sample was from.
2/ Image
Oct 26 11 tweets 4 min read
Cryptic lineage quarterly update, part 3
Cleveland variant.
If you missed part 1 and 2, they are here.
x.com/SolidEvidence/…
x.com/SolidEvidence/…
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My favorite way of finding cryptic lineages by screening for what I call the ‘s2m fix’.
s2m is an RNA element at the end of the SC2 genome that has been deleted from all lineages in circulation for over 2 years.
If you see the s2m sequence, you know it is an old lineage.

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Oct 23 12 tweets 4 min read
Cryptic lineage quarterly update, part 2
BA.1 and Delta
If you missed part 1, it is here.

1/ BA.1 cryptics. BA.1 infections all occurred in late 2021-early 2022. If there is good coverage, BA.1 lineages are easy to spot because they have a unique Spike insertion that no other lineages have had.
2/ Image
Oct 22 14 tweets 5 min read
Cryptic lineage quarterly update, part 1
Recent BA.2-XBB cryptics

Cryptic lineages are unique, evolutionarily advanced SARS-CoV-2 lineages detected from wastewater from an unknown source.

1/ Image We are almost certain that these lineages are derived from individuals that have been infected with SARS-CoV-2 for several years that are shedding a ton of viral material.

If you want to know why we think these are from humans, read this thread.

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Oct 2 4 tweets 2 min read
Update on the Bavarian cryptic lineage that @LongDesertTrain spotted.

This lineage first popped up in August but has been consistently present since.


1/ cov-spectrum.org
Image The lineage is derived from BA.5.1.10, but taken at face value, it has over 90 additional mutations and deletions.

2/ Image
Aug 17 15 tweets 5 min read
I'm giving the variant update at the SAVE meeting on Monday so I thought I'd put out a preview for comment.

We are now at our 4th 'high water' mark since the Omicron wave based on wastewater surveillance.

1/ Image I thought I would give an abbreviated summary of the last year in variants.

A little over a year ago BA.2.86 started circulating, a lineage that was almost certainly derived from a persistent infection.
2/ Image
Jul 24 6 tweets 1 min read
Just returning from the CEIRR influenza annual meeting.

Here are my takeaways.

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First the bad news.

2.3.4.4b (which the H5 in cattle is derived from) is a bad ass. In birds it is ridiculously contagious, ridiculously promiscuous, and pretty darn deadly. It spread through typical and atypical US bird populations practically instantly.

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Jul 6 7 tweets 2 min read
MO COVID wastewater update. Although it's not major, there has been a noticeable uptick on COVID levels the last few weeks.

1/ Image In my thinking, there are 3 things that contribute to these fluctuations: the viral lineage, host immunity, and human behavior.
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Jun 7 8 tweets 3 min read
Update on the Maryland variant, the highly diverse Delta variant from a sewershed South of Baltimore.
1/ Image This sewershed only started sequencing earlier this year, so I don't know how long it has been around, but it is clearly Delta-derived, which means the infection probably occurred in the second half of 2021, nearly 3 years ago.
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Jun 5 7 tweets 2 min read
Update on the unexpected H5 detections from wastewater.

Thanks to all that helped figure this out.

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There were 4 sewersheds that had detectable H5 from states that have not been reported to have infected herds. Those 4 were from Minnesota and Iowa.

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data.wastewaterscan.org/tracker?charts…
May 4 9 tweets 2 min read
A few points about the H5N1 outbreak that I'd like to share.

1. If we had a pan-influenza wastewater screen in place nationally that differentiates the influenza sources by sequencing (which isn't that hard to do), we probably would have detected this outbreak months ago.
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BTW, we submitted a CDC proposal earlier this year to do exactly this, but the topic was pulled from the BAA so the proposal wasn't even reviewed.
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May 4 7 tweets 2 min read
Classic new cryptic lineage from Maryland (South of Baltimore). It's a Delta-derivative (2-3 year old infection).
1/ Image This one is practically a caricature of a cryptic. It has 6 of the classic Sarbeco reversions.
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Apr 14 4 tweets 2 min read
This is weird. I was going through public wastewater sequences and found another BA.1.1 lineage that didn't get the memo that it is supposed to be extinct.

This time is was from Sioux City, Iowa (which is on the Nebraska border) in February.
1/ Image However, then I checked and realized that there were actually 3 BA.1.1 sequences deposited from Nebraska in the last month. They are very divergent, but closely related to each other, and they are from at least 2 different patients.
2/ Image
Mar 25 28 tweets 7 min read
This is amazing.

Can cryptic lineages tell us anything about the origins of SARS-CoV-2 (SC2)?

The answer may surprise you, it surprised the hell out of me.

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Cryptic lineages are unique, evolutionarily advanced SC2 lineages detected in wastewater from an unknown source.

We are pretty certain that these are coming from people with persistent infections, and they are likely gut infections.

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sciencedirect.com/science/articl…
Mar 25 9 tweets 2 min read
Cryptic lineages desperately want to restore this glycosylation site (I've seen it restored 4 different ways), but the reversion is EXTREMELY rare in circulating lineages.

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Then there is the RBD. The cryptic lineages really want Q498H (the sequence in bats) or 498Y. As I mentioned, these changes are extremely rare in circulating lineages.

Seems this change probably has more to do with the tissue than with the species.

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