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Marc Johnson Profile picture
Marc Johnson
@SolidEvidence
Molecular virologist, Professor, sewage sage and wastewater wizard.
16 subscribers
Oct 28 • 8 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/…
1/ 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.

2/
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.

2/
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.

1/ 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.

2/
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.
2/
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.
2. Image
Jun 5 • 7 tweets • 2 min read
Update on the unexpected H5 detections from wastewater.

Thanks to all that helped figure this out.

1/ 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.

2/
 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.
1/ 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.
2/
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.
2/ Image
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.

1/ 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.

2/
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.

26/ 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.

27/
Mar 11 • 7 tweets • 2 min read
Our paper is finally out in Lance Microbe.

In this study we tracked the source of a SARS-CoV-2 cryptic lineage from the main treatment plant in a WI city all the way to a single set of bathrooms... using nothing but wastewater sampling and sequencing.

1/
 thelancet.com/journals/lanmi… This is the same study that I discussed recently on the Freakonomics podcast.


2/freakonomics.com/podcast/water-…
Mar 10 • 19 tweets • 5 min read
Imagine that you were to experience a thunderstorm for the first time as an adult.

The sky turns dark in the middle of the day and lightning bolts start coming out of the sky.

This couldn’t seem natural.

This is kind of how I see things with COVID origins debates.
1/ Image I’m from the Midwest, so tornadoes and violent thunderstorm seem normal to me.

I’m also a virologist, so some of the wild stuff that Coronaviruses do seems normal too.

2/
Mar 9 • 11 tweets • 2 min read
Back to curating the viruses we find from randomly sequencing the wastewater virome.

I've been a virologist for 30 years, how have I not heard of some of these viruses?

I don't think we knew about smacoviruses when I went to grad school. Quail influenza? Who has pet quail and is flushing their waste? And please stop.

Could be a duck or chicken host, but still.
Mar 3 • 4 tweets • 1 min read
One more round.

We've started a project where we are doing unbiased sequencing of the wastewater 'virome'.

Dec/Jan SARS-CoV-2 was the most common human RESPIRATORY virus detected, but what else was in the top 5? You all have gotten most of them.
#1 SARS-CoV-2
#2 Adenoviruses
#3 AlphaCoronaviruses (229E & NL63)
#4 other BetaCoronaviruses (HKU1 & OC43)
#5 is an Influenza, but which one?
#6 is RSV (A+B)

I know, the grouping was not consistent.
Mar 2 • 11 tweets • 5 min read
We found an interesting cryptic lineage from Charlotte, NC recently.

[cryptic lineage = an unique evolutionarily advanced SARS-CoV-2 lineage found in wastewater from an unknown source]

1/ Image This is one that popped up in a screen for sequences with the s2m ‘fix’.

Explained here.

2/
Image
Mar 2 • 13 tweets • 4 min read
Ohio cryptic lineage update.

Many people have asked what happened with the Ohio cryptic lineage, so I thought I would give an Ohio update.

[cryptic lineage = an unique evolutionarily advanced SARS-CoV-2 lineage found in wastewater from an unknown source]

1/ Image Background.

Last year we described a cryptic lineage that was regularly detected in wastewater samples from Columbus, Ohio and Washington Court House (WCH), a town about 40 miles away.

2/