@LongDesertTrain
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Teacher "Be ruthless with systems and be kind to people." Michael Brooks, 1983-2020
Joined May 2018
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7 of 19 sequences (37%) just uploaded from New Brunswick, Canada, are PJ.2.1, including 4/7 collected since Sept 1. This is the highest local percentage we've seen yet.
Reminder: PJ.2.1 is a saltation variant that originated in Ontario, Canada. Ancestral mutation profile below.
These don't appear to be the result of a single introduction to New Brunswick. Bottom 4 seqs sprout from the major PJ.2.1 branch, but the top 3 descend from a branch with seqs from California, Colorado, and New Jersey—and are right next door to a US travel sequence from Cuba.
"Value of the US stock market is ~$80 trillion. If the AI bubble bursts, it can easily lose 20-30%... a loss of wealth of $16-$24 trillion. It is quite plausible the drop would be even larger.... The drop in demand...would be 3-4% of GDP. That is a very severe recession."
If we are about to see the collapse of an AI bubble, then worries about government debt make no sense. If there is no AI bubble, then worries about government debt make no sense. We have other things to worry about deanbaker22.substack.com/p/t…
One of nine PJ.2.1 sequences uploaded from NYC today has A475V, which escapes some major class 1 antibodies. One of 2 two mAbs tested by @yunlong_cao that most potently neutralized PJ.2.1 (IC50=0.001) & to which it was much more vulnerable then XFG, is ~entirely escaped by A475V.
SARS-CoV-2 saltation variant PJ.2.1 has raised concerns over another JN.1-like event.
Here we found:
1. PJ.2.1 shows markedly higher ACE2 binding.
2. PJ.2.1's antigenicity remains comparable to the JN.1 family.
3. No increased immune evasion against human plasma.
While PJ.2.1 currently lacks the immune evasion capabilities of other contemporary strains (XFG, PQ.16.1.1, BA.3.2.2...), its robust baseline receptor-binding strength mirrors the early evolutionary trajectory of BA.2.86 to JN.1, necessitating continued genomic, epidemiological, and virological surveillance of the PJ.2.1 lineage.
Details can be found in the recent BioRxiv manuscript:
biorxiv.org/content/10.64898…
It's not clear if A475V will give PJ.2.1 a major advantage, but regardless, I expect that, given its high ACE2 affinity, it will accumulate spike mutations, similar to BA.2.86 & BA.2.75 before it, which may give it an edge over its competitors, at least in USA/Europe.
Credit to @Nucleocapsoid for pointing out that A475V was one of three mutations @yunlong_cao and co-authors suggested might appear in PJ.2.1.
biorxiv.org/content/10.64898…
New paper from phylogenetics/evolution arch-guru Richard Neher and Luca Sesta! Tantalizing title ("Epistasis and the changing fitness landscapes of SARS-CoV-2") and abstract.
Paywalled, unfortunately.
academic.oup.com/genetics/ad…
Ryan Hisner retweeted
A child attempting to rescue an aid worker is killed by an Israel.
His name was Mohammed Al-Zeinati.
This is Zionism.
Ryan Hisner retweeted
Tracking emerging variants such as PJ.2.1 has become increasingly difficult as sequencing activity has declined.
This decline reflects shifting public health priorities and financial constraints.
However, the emergence of highly divergent variants such as BA.3.2, which disproportionately affects children, and PJ.2.1, which may have the potential for wider geographic spread, has clear public health implications.
These developments underscore the importance of maintaining at least a baseline level of genomic surveillance. #PJ21
A new PJ.2.1 detection in Murcia, Spain 🇪🇸.
Most detections so far have been reported from the Barcelona area. Beyond Barcelona, PJ.2.1 has also been detected in Oviedo and Murcia.
These cities are geographically distant from one another, suggesting that the variant is circulating in several parts of the country.
Most detections came through baseline surveillance. However, PJ.2.1 was also detected through sentinel ARI surveillance in a 1-year-old girl and an 82-year-old woman.
Thus, as expected, PJ.2.1 infection can also be associated with symptomatic respiratory disease.
Most PJ.2.1 detections in Spain so far have been reported in older adults, in agreement with data from Canada and the US. Let's see whether this pattern continues as more cases are identified. #PJ21
Ryan Hisner retweeted
PJ.3.2 seems to be hitting the accelerator. These are the wastewater samples deposited in just the last week where it was present (based on 439K marker).
Ryan Hisner retweeted
A new/old SARS-CoV-2 paper for us is now in @NatureComms
nature.com/articles/s41467-0…
We submitted first in 2023 and due to a variety of reasons, it is now out, in 2026.
The manuscript details our look into conserved SARS-CoV-2 Omicron mutations outside the receptor binding domain.
WHOA. Did not expect this. It's remarkable that in its >1.5 years of circulation, I've never seen a BA.3.2 chronic infection sequence. My assumption is that the loss of ORF7a—which I think plays a vital role in most chronic infections—is a major hit to T cell evasion.
WTH, I think I found a BA.3.2 cryptic (I hope it isn't circulating anyway).
Standard RBD + A435F, S438F, P463F.
Wonder if that improves ACE2 binding?
It was 100% of the sequence from one sewershed.
@LongDesertTrain
Today two PJ.2.1 international US-airport seqs showed up from Cuba & Germany (Aug 31, Sept 1 collection), adding to the list of countries we've seen PJ.2.1 in. We've had ~zero recent seqs from Cuba or Germany, so this is, at the very least, a sign that PJ.2.1 is not rare there.
As Fede Gueli points out, @SolidEvidence's wastewater variant dashboard makes it clear that PJ.2.1 is the fastest-growing lineage in the US. I've inserted arrows pointing to some of the PJ.2.1 mutations. The farther above the dotted diagonal line, the faster the growth. 1/6
The first two PJ.2.1 seqs from New Jersey also appeared today. Until yesterday, it wasn't 100% clear whether PJ.2.1 was growing quickly, but @SolidEvidence's Lungfish wastewater data, together with the bevy of recent seqs make it pretty clear: PJ.2.1 is pretty fast.
As Fede Gueli points out, @SolidEvidence's wastewater variant dashboard makes it clear that PJ.2.1 is the fastest-growing lineage in the US. I've inserted arrows pointing to some of the PJ.2.1 mutations. The farther above the dotted diagonal line, the faster the growth. 1/6
As it's hard for to keep track of all these variants, I'm trying to include background threads at the end of these threads. Here's my original thread on this saltation variant from about 2 months ago.
nitter.cf/LongDesertTrain/status…
A mysterious, unusually diverse saltation lineage descended from KP.3.1.1 (last seen early 2025) has circulated at a low level for ~8 months in Ontario (see 🧵on next post).
Seemed a local anomaly, but @solidevidence just spied a weird spike in NYC WW—& it's the same one!
1/14
And here's a shorter thread from a couple weeks later with some more detail on PJ.2.1.
nitter.cf/LongDesertTrain/status…
