PhD in Space Physics. Hobbyist SARS-CoV-2 lineage hunter. I will block trolls, disinformers, etc at my personal discretion. Also @wolfeagle1989.bksy.social.
Texas, USA
Joined April 2015
- Tweets2.3K
- Following415
- Followers2.8K
- Likes16.2K
Andrew Urquhart retweeted
Our BA.3.2.2 study is now published in Nature Microbiology!
Counterintuitively, we found that ancestral-strain immune imprinting protects against BA.3.2.2 through IGHV3-53/66 Class 1 antibodies, helping explain why BA.3.2.2 selectively infects children.
doi.org/10.1038/s41564-026-0…
I see 448 PJ.2.1 on GISAID, but that includes only 6 from Minnesota (MN) and 0 from Wisconsin (WI).
*But* CoV-Spectrum shows 22 PJ.2.1 from MN and 5 from WI. At least some of these also appear in UShER.
There are more PJ.2.1 that may still be in-process at GISAID.
I noticed the missing Wisconsin PJ.2.1s as I wrote lineage designation proposal github.com/sars-cov-2-varian…. I specifically noticed that UShER pulled up USA/WI-WSLH-2601700/2026 and USA/WI-WSLH-2601783/2026 on this branch. 1/2
The previous branches to designate clades 26F and 26G never got pull requests. Those may have been misfires.
But there is now a pull request github.com/nextstrain/ncov/p… to designate PJ.2.1 as clade 26F, and this is based on growth and expected growth… another signal on PJ.2.1.
My concern about PJ.2.1 is growing. US wastewater surveillance suggests it is growing. A report from Poland gov.pl/web/gis/jak-zadbac-o-… (I used Google Translate) says PJ.2.1 is dominant there. And Ontario has now reported 13 PJ.2.1 with S:A475V that form a branching tree.
On @SolidEvidence's Lungfish wastewater surveillance board, PJ.2.1 is far & away the fastest variant. Virtually all rapidly increasing mutations are PJ.2.1 muts.
Only exception is K478E—possibly a fluke as it's been very erratic over the past year.
lungfish-science.github.io/w…
The designations of SARS-CoV-2 lineages PQ.16.1.1 as clade 26C, RF.5 as clade 26D, and RK.1 as clade 26E have now been merged to the master branch. github.com/nextstrain/ncov/b… I would count these designations as official.
Andrew Urquhart retweeted
In its current form, I doubt PJ.2.1 would force a larger-than-normal winter wave. It needs to pick up an RBD mutation or 2 to do that. But we know, thanks to @yunlong_cao's work, that PJ.2.1 has very strong ACE2 binding, which is important because...
nitter.cf/yunlong_cao/status/209…
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…
I’m concerned about PJ.2.1 descendants especially with S:A475V (now observed) or with S:D420N or S:N487D (neither observed). The PJ.2.1 preprint from @yunlong_cao’s group noted all 3 mutations as potentials for PJ.2.1, and that group has a track record of good predictions.
Andrew Urquhart retweeted
Great thread summarizing the PJ.2.1 variant situation and putting it in a broader context.
5 new PJ.2.1 sequences from Spain reported yesterday. PJ.2.1 is a SARS-CoV-2 saltation variant first highlighted by @LongDesertTrain that now appears to be spreading internationally. Here is a thread on the emergence of PJ.2.1 and its potential implications.
1/4 “Regular” variants vs. saltation variants
The WHO ended the COVID-19 Public Health Emergency of International Concern in May 2023, but the virus did not disappear. SARS-CoV-2 continues to circulate globally. One important reason is its ability to evolve and evade pre-existing immunity.
Immune evasion is driven in large part by mutations in the spike protein that alter sites recognized by neutralizing antibodies. “Regular” variants emerge through stepwise evolution, accumulating relatively few mutations compared with their immediate predecessors.
Saltation variants are different. They appear with an unusually large number of mutations compared with their closest known predecessors, often including many changes in spike.
Such an evolutionary “jump” can substantially alter antigenic properties and enable increased escape from existing antibodies. But where do these highly divergent viruses come from?
One important mechanism is thought to be persistent SARS-CoV-2 infection in people with impaired immune control. Sustained viral replication over many months can provide opportunities for mutations to accumulate. In some cases, highly divergent viruses emerging during such infections may subsequently enter population-level circulation.
Occasionally, a saltation variant combining substantial immune escape with sufficient transmissibility may spread widely and contribute to a new COVID-19 wave. PJ.2.1 could potentially do so, but it is too early to know.
Andrew Urquhart retweeted
Somewhat reminiscent of BA.2.75, which wasn't immune-evasive originally, but which had such an excess of ACE2 affinity that it quickly acquired a bevy of AB-evading spike mutations & had quite a lot of success (in the form of BN.1* & CH.1.1*, & also XBB, which it formed part of).
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…
SARS-CoV-2 saltation variant PJ.2.1, significantly evolved from KP.3, has not yet evolved high neutralizing-antibody evasion, but it may have sufficient ACE2 binding capacity to trade some for antibody evasion.
This lineage may be worth watching.
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…
Andrew Urquhart retweeted
Sept 5th Update:
As mentioned in June, a relatively small late summer wave is occurring in the West and South, less than half numbers last summer. Midwest and NE are still at minimal levels.
🔸️180k infections/day
🔸️1 in 350 currently infectious
🔸️W+S about 3x MW+NE
Looking at calibrated WastewaterScan data for 1 station and all 14 TX stations, sadly Texas COVID levels are rising.
No one lineage stands out as driving this.
Likely drivers are waning immunity, the infernal seasonal heat driving people indoors, and school starting.
For a long time, we’ve needed to clean the air like we clean the water. And that became more obvious when COVID vaccines lost effectiveness so quickly in 2021 and 2022. Better late than never, I’m happy to see the Intercept Fund getting going. blog.interceptfund.com/p/end…
As of yesterday, with a merge into the master branch of github.com/nextstrain/ncov/b…, SARS-CoV-2 lineage XFG.3.4.1 has been designated Nextstrain clade 26B.
I’ve also seen John Cornyn and Greg Abbott try to attack James Talarico like this. If this is the best attack Republicans can find against Talarico, Texas is likely flipping Blue. And expect Democratic strategists to take notice.
Wow! A major American news outlet acknowledges the many of the risks of Long COVID in 2026!
Trump's policies at odds with emerging understanding of Covid's long-term harm
"The legacy of COVID is going to be long, and we are going to be learning about the chronic effects of the virus for some time to come"
cbsnews.com/news/covid-long-…
