Share this page!

Enter URL or ID to Unroll

You can paste full URL like: https://x.com/threadreaderapp/status/1644127596119195649
or just the ID like: 1644127596119195649

How to get URL link on X (Twitter) App

  1. On the Twitter thread, click on or icon on the bottom
  2. Click again on or Share Via icon
  3. Click on Copy Link to Tweet
  4. Paste it above and click "Unroll Thread"!
  5. More info at Twitter Help
Marc Johnson Profile picture
Marc Johnson
@SolidEvidence
Molecular virologist, Professor, sewage sage and wastewater wizard.
Dr Bob (now on Mastodon) Profile picture Potato Of Reason Profile picture Masahiro Sakai Profile picture Loofymectin aka Jan Masleid Profile picture MakeChange Profile picture 16 subscribed
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/
Feb 26 • 9 tweets • 3 min read
Swiss variant update, another record is broken.

1/ Image Late last year the Swiss deposited a whole bunch of wastewater sequences going back a few years. We screened the data and found a cryptic lineage from Lousanne in 2021.

I don’t think I ever posted about it because it wasn’t that exotic, and it disappeared 2 years ago.

2/ Image
Feb 26 • 8 tweets • 3 min read
I found (or rediscovered) another cryptic lineage this weekend, and this is the weirdest one yet.

Sometimes it almost feels like someone is playing an extremely elaborate prank on me.

I'm not sure even I believe this one.

1/ The lineage is from a sewershed in Switzerland. The group submitted hundreds of sequences recently and the lineage appeared twice in samples from late last year, both times from the same sewershed.

2/
Feb 23 • 13 tweets • 4 min read
How common are SARS-CoV-2 persistent infections (revisited).

Last summer I tried to calculate how frequent persistent SARS-CoV-2 infections were from sequence info.

Since there was a recent paper on this, I thought I would revisit my calculations.
1/
 My calculations depend on 2 assumptions.

1. Sequences with Orf1a:K1795Q usually (>80% of the time) come from persistent infections (excluding Gamma and BS.1).

2. About 4-10% of all long persistent infections acquire Orf1a:K1795Q.

2/
Feb 17 • 17 tweets • 3 min read
Biosafety restrictions and Biothreat assessment: a rant.

Regulations are fine, but double standards are frustrating.

1/ Background, my lab studies cryptic lineages: evolutionarily advanced SARS-CoV-2 lineages detected in wastewater from an unknown source (we are now pretty certain cryptics are from long persistent infections).

We’ve found scores of these.

2/
 doi.org/10.1371/journa…
Feb 15 • 16 tweets • 5 min read
New Jersey Cryptic lineage update.

Background: Cryptic lineages are evolutionarily advanced SARS-CoV-2 lineages detected in wastewater from an unknown source.

We are fairly certain that these are derived from patients with persistent SARS-CoV-2 infections.

1/ Image If you are curious why we believe that cryptic lineages are from individual patients and not some non-human source, please read this thread. The paper on this should be coming out soon.

2/
Feb 10 • 5 tweets • 2 min read
Wow, check out the RBD from this cryptic lineage from wastewater samples; it's still circulating in some poor patient in Newark, NJ.

1/ Image We've actually been seeing snippets of this lineage for a while, but we didn't get a good look at its RBD until recently.
2/
Feb 1 • 13 tweets • 4 min read
Another highly divergent circulating BA.2 was just announced in South Africa.

Do we need to be worried?

1/
The key question with a new variant is if it has the ability to get through our first major line of defense, our neutralizing antibodies (NA).

The vast majority (>90%) of NAs target the receptor binding domain of Spike, so that is where I look for answers.

2/
Jan 27 • 6 tweets • 2 min read
COVID numbers always seem to go down early in the year, but this year is more optimistic than most.
1/ Image In January 2021 numbers were rapidly declining, but there was uncertainty because the first major variants of concern (Alpha, Beta, Gamma) were moving in.

Those 3 didn’t have much impact, but unforeseen was Delta, which arrived in May.
2/ Image
Jan 15 • 7 tweets • 3 min read
Missouri wastewater variant update.
Relative vs absolute numbers.
1/ Image DHSS just updated their wastewater data, so I can share my analysis now.
2/
 storymaps.arcgis.com/stories/f7f549…
Jan 13 • 11 tweets • 3 min read
With the introduction of new variants, I’ve noticed a tendency of some to conflate relative abundance, with absolute abundance, which can result in misleading conclusions.
1/ Image With variants, relative abundance is the fraction of all sequences on a particular date that is a particular variant. As of the start of the year, over 70% of all samples sequenced were JN.1.
2/ Image