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Marc Johnson Profile picture
@SolidEvidence
Apr 1 • 1 tweets • 1 min read • Read on X
What gets me about all these cuts and firings is that they are clearly designed to be maximally disruptive, painful, and disrespectful.

This isn't reality TV. Who treats people this way?

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More from @SolidEvidence

Marc Johnson Profile picture
Mar 17
Here is this week's analysis. One mutation popped out as increasing in frequency in the last data set.

S:G842S

Wonder what that is from.

1/ Image
Not a very common mutation. Mostly associated with with XEC.11*
2/
 cov-spectrum.org/explore/United…Image
If that's really from XEC.11*, then we should see other mutations from that lineage increasing.

So I looked up the mutations that differentiate XEC.11 from XEC:

Orf1a:V2090F
S:K182N
SV1264L
Orf3a:L85F

3/ Image
Read 8 tweets
Marc Johnson Profile picture
Mar 17
I’m very pleased to announce the launch of our LungFish Data Explorer dashboard for tracking SARS-Cov-2 lineages from wastewater.

1/
 inkfishmedical.github.io/wastewater-das…
Here’s the problem we hope this dashboard will help solve.  SARS-CoV-2 remains very prevalent in the US.

However, sequence surveillance from patients has plummeted. In addition to fewer samples, the average sequence takes >3 weeks to be reported (and it’s getting slower).

2/ Image
Fortunately, we have wastewater surveillance (primarily through CDC NWSS), which covers a large chunk of the population and has a fairly fast turnaround (<2 weeks).

3/ Image
Read 16 tweets
Marc Johnson Profile picture
Mar 1
So what's happening with medical research in the US? This is the cumulative award count from the NIH for the year.

Doesn't look so good.

But it gets worse.
1/ Image
Before grants are awarded, they have to be evaluated in meetings called study sections.

Before a study section can meet, it has to be listed in the federal registry for at least 15 days.

These are the new study section meetings listed in the federal registry this year.
2/ Image
Meetings can't even be scheduled, none of the committed funds are going out.

About 300,000 scientists are wondering if they are going to keep their jobs, and the most vulnerable are the students and postdocs.
3/
Read 4 tweets
Marc Johnson Profile picture
Feb 28
There something new on the SARS-CoV-2 landscape, and I’m not sure what it is.
1/ Image
S:S31F and S:K182N are on the rise.

The two aren’t on the same sequencing strand, but I confirmed that they are generally appearing together in the same samples.

2/
The samples are from across the country (CA, WY, LA, CT, PA, WI, etc) and more than one sequencing group, so it’s probably not a sequencing error.

3/
Read 5 tweets
Marc Johnson Profile picture
Feb 11
Brief update on the new cryptic lineage we found from Petersburg City, Virginia.

We went back and screened all of the samples from that sewershed since the beginning of 2024 and learned a few things about it.
1/ Image
First, I think I was wrong about the lineage being JN.1 derived. I thought it was JN.1 because it had 22926C (455S), but it looks like it only acquired that recently.

In samples as recent as December the lineage lacked 455S and 456L.
2/ Image
That would mean the lineage is BA.2.86-derived, which suggests it was acquired probably early 2024.

Caveat, as @LongDesertTrain points out, persist infections hate 455S. It’s possible that the lineage was JN.1, but reverted at 455, but then gained 2 nt creating 455A.
3/ Image
Read 8 tweets
Marc Johnson Profile picture
Jan 31
Wastewater variant update. This is the composite data from over 1,000 US samples collected over the last 6 weeks.
1/ Image
You have to extrapolate a little bit because several changes are shared by multiple lineages.

It appears that the new lineage I mentioned last week (MC.10.1 + 445P) is around 4% and is the fastest growing of the lot. It now has a PANGO designation - PA.1
2/
LP.8 is still expanding is is probably about 12% now. Since it is a KP.3.1.1 derivative, KP.3.1.1* might become dominant again.

LF.7 seems to be holding on too at about 4%.
3/
Read 7 tweets

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