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Marc Johnson Profile picture
@SolidEvidence
Mar 31 • 1 tweets • 1 min read • Read on X
If anyone wants to look up what grants and contracts have been summarily terminated so far, this website has a compiled list.

It's staggering.

What's the point of having a contract anyway?

dhoconno.github.io/reporter/repor…

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More from @SolidEvidence

Marc Johnson Profile picture
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
Marc Johnson Profile picture
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
Marc Johnson Profile picture
Apr 20
We are recruiting sewersheds for an expanding project. Basically, we want to learn everything that can be learned from wastewater.
Read on if you are interested.
1/ Image
This is a collaboration with SecureBio that started about 18 months.

Basically, we isolate the viral fraction from wastewater and sequence the crap out of it (~1 billion reads/sample). This is unbiased sequencing; we don’t want to miss anything.
2/
 securebio.org
There are three main levels to the analysis of the wastewater virome.
The first is SecureBio’s main focus, which is novel pathogen detection with a particular focus on engineered pathogens.
3/
 naobservatory.org/blog/detecting…
Read 16 tweets
Marc Johnson Profile picture
Apr 19
This battle between Harvard and the administration is so befuddling. The latest plot twist makes less sense than the last season of Lost.

Let me give a very quick summary for those not following along.
1/11
The last few weeks Harvard had been talking with the administration about concerns over antisemitism on campuses, but the talks lacked details, and Harvard was told that they would get a letter last Friday with more specifics.
2/
Then last Friday Harvard got an email from the acting general counsel of HHS with a scorched earth list of demands that would have effectively ended Harvard’s autonomy in hiring, admissions and curriculum.

Here’s the letter.
3/
 nytimes.com/interactive/20…
Read 11 tweets
Marc Johnson Profile picture
Apr 12
Last month there was an announcement that I thought was a major advancement in world health, but it got little attention.
I thought I would tell you all a little bit about it and why it is so important.
1/25
This breakthrough has to do with HIV, which was a zoonotic pathogen. The progenitor of HIV infects chimpanzees in Cameroon.

No one knows exactly when or how HIV crossed into humans, but the first undisputed HIV patient sample (discovered retrospectively) was from 1959 in what is now the Democratic Republic of Congo.Image
HIV smoldered for decades before becoming widespread in the early 80s.
At the time, being diagnosed with an HIV infection was a death sentence.
There was no real cure (still isn’t) and no treatment. By any measure, HIV was one of the worst diseases of the last century.
3/
 nature.com/articles/d4158…Image
Read 25 tweets
Marc Johnson Profile picture
Apr 6
I briefly thought the SA BA.3.2 was in the US, but it turns out the virus was just messing with me again.

This was kind of interesting though.
1/
We've been screening all of the new wastewater data a few times a week for signs of BA.3.2.

One of the many screens we have is looking for reads that have C21846T+T21864C together, which are in BA.3.2 but no current lineages (it works better to look for pairs of changes).

2/
This week we had a hit. This was the genotype of the read:

C21621A|(S:T20N) A21626G|(S:T22A) T21657C|(S:F32S) T21695C|(S:S45P) A21712T|(S:S50S) CATGCTAT21758-21765del C21767-21767del C21846T|(S:T95I) T21864C|(SI101T) TTA21890-21892del|

3/
Read 9 tweets

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