iiinova — where your digital self keeps evolving

Andrew Urquhart @wolfeagle1989.bsky.social · 4h

My concern about PJ.2.1 is growing. US wastewater surveillance suggests it is growing. A report from Poland www.gov.pl/web/gis/jak-... (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.

gov.pl

Jak zadbać o jesień bez infekcji? Główny Inspektor Sanitarny o bieżącej sytuacji epidemiologicznej - Główny Inspektorat Sanitarny - Portal Gov.pl

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Andrew Urquhart @wolfeagle1989.bsky.social · 03/10/2026

There are branches for designating clades 26F and 26G, but these have never had pull requests and have not merged to main. I would *not* count them as official.

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Andrew Urquhart @wolfeagle1989.bsky.social · 03/10/2026

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/n... I would count these designations as official.

github.com

ncov/defaults/clade_display_names.yml at 3432c85760b6c8cd0f815a85167ebb46c8131abb · nextstrain/ncov

Nextstrain build for SARS-CoV-2. Contribute to nextstrain/ncov development by creating an account on GitHub.

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Andrew Urquhart @wolfeagle1989.bsky.social · 25/09/2026

I’m concerned about PJ.2.1 descendants especially with S:A475V (now observed) or with S:D420N or S:N487D (neither observed). The preprint www.biorxiv.org/content/10.6... 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.

biorxiv.org

Increased receptor binding capability of the SARS-CoV-2 saltational variant PJ.2.1

The recently identified SARS-CoV-2 saltational variant PJ.2.1, a highly mutated descendant of MC.10.1, has achieved rapid intercontinental spread since its detection in May 2026. Here, we show that PJ...

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Andrew Urquhart @wolfeagle1989.bsky.social · 02/09/2026

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.

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Andrew Urquhart @wolfeagle1989.bsky.social · 09/07/2026

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/ending-res...

blog.interceptfund.com

Ending respiratory infections

Introducing Intercept, a $500M bet to make respiratory infections like colds and flu a thing of the past.

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Andrew Urquhart @wolfeagle1989.bsky.social · 08/07/2026

As of yesterday, with a merge into the master branch of github.com/nextstrain/n..., SARS-CoV-2 lineage XFG.3.4.1 has been designated Nextstrain clade 26B.

github.com

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Andrew Urquhart @wolfeagle1989.bsky.social · 19/01/2026

In his substack review, @marcveld.bsky.social suggested that journals like Nature or Nature Immunology were better. Soon thereafter, Aid et al, “Long COVID involves activation of proinflammatory and immune exhaustion pathways”, Nature Immunology (2025), www.nature.com/articles/s41... was published.

Screenshot of text from Aid et al reading “In this study, we evaluated the immunological and inflammatory responses in people with LC compared with convalescent controls (CCs) at 90–180 days and more than 180 days after initial COVID-19 infection using immunological assays, virological assays, transcriptomics and proteomics. The first cohort was enrolled in 2020–2021, and the second cohort was enrolled in 2023–2024. Our data show that chronic inflammation, T cell exhaustion, metabolic dysregulation and upregulation of the JAK-STAT and interleukin-6 (IL-6) signaling pathways are key features of LC.”

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Andrew Urquhart @wolfeagle1989.bsky.social · 08/12/2025

@marcveld.bsky.social This reply with your Substack review was much more helpful and enlightening than your “One swallow does not a summer make” direct reply. Your Substack review raises some good points I had missed and that I need to consider.

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/12/2025

I’m concerned about Jiang et al’s new report of immune cell population impacts for 20 months and counting after acute SARS-CoV-2 infection, and I note the authors call out that this wasn’t seen with SARS-CoV-1. See www.sciencedirect.com/science/arti.... h/t AJ Leonardi.

sciencedirect.com

Persistent Attenuation of Lymphocyte Subsets After Mass SARS-CoV-2 Infection

Growing evidence suggests that lymphocyte subsets are declined in COVID-19 patients, but it is unclear if these alterations persist after widespread e…

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Reposted by Andrew Urquhart

JPWeiland @jpweiland.bsky.social · 30/10/2025

GISAID is now blocking genomic sequencing access to critical resources like Nextstrain, Covspectrum, Outbreak-info, & others. This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.

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Andrew Urquhart @wolfeagle1989.bsky.social · 07/10/2025

Major US airports in Denver and Newark were previously reported as impacted by the US Government shutdown. Houston is now expected to be added to the list. www.khou.com/article/news....

khou.com

Government shutdown to impact travelers at both Houston airports, FAA website shows

Traveling soon? Get ready to start feeling the impact of the federal government shutdown at Houston airports.

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Andrew Urquhart @wolfeagle1989.bsky.social · 07/10/2025

The US Government shutdown is already disrupting air traffic in the USA. And if the shutdown doesn’t end, a program to provide air service to smaller communities runs out of money this coming Sunday. Source: www.wfaa.com/article/synd....

wfaa.com

Transportation secretary says government shutdown adds stress on air traffic controllers

Transportation Secretary Sean Duffy says the government shutdown is putting more stress on air traffic controllers who already have an extremely stressful job.

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Andrew Urquhart @wolfeagle1989.bsky.social · 09/09/2025

How is this going to play in farm country in the USA where Trump was so popular? From Fortune via MSN, “Farmer says ‘we’re in a very dire situation’ ahead of harvest—with zero soybean orders from China, historically the largest buyer” www.msn.com/en-us/money/...

msn.com

MSN

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Andrew Urquhart @wolfeagle1989.bsky.social · 26/08/2025

Oops. I found a typo in the second post. Correct “TRS-B was is found” to “TRS-B is found”. I’ll also note that few B.1.1 with N:G204P, especially KP.3.3, actually have the N* TRS-B broken. So *all* B.1.1 having the N* TRS-B is an overstatement. But most B.1.1 do have it. (4/3)

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Andrew Urquhart @wolfeagle1989.bsky.social · 26/08/2025

These mutations were previously seen in Gamma (P.1). The base N.iORF3 aka N*M210 aka N* TRS-B was is found in all B.1.1 including Alpha, Gamma, and Omicron, and this protein is known to enhance SARS-CoV-2 fitness including through innate immune evasion. (2/3)

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Andrew Urquhart @wolfeagle1989.bsky.social · 26/08/2025

Recent Pango lineage designation note updates such as github.com/cov-lineages... brought my attention to the emergence of the N.iORF3 aka N*M210 aka N* extended Transcription Regulation Sequence (TRS-B) enhancing mutations A28877T, G28878C several times in XFG. (1/3)

github.com

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Andrew Urquhart @wolfeagle1989.bsky.social · 22/08/2025

From The Atlantic, “COVID Revisionism Has Gone Too Far” www.msn.com/en-us/news/w... And the pendulum swings…

msn.com

MSN

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Andrew Urquhart @wolfeagle1989.bsky.social · 19/08/2025

A question: How is requiring posting of the Ten Commandments in Texas public school classrooms consistent with Article 1, Section 6 of the Texas Constitution: “no preference shall ever be given by law to any religious society or mode of worship.” statutes.capitol.texas.gov/Docs/CN/htm/...?

statutes.capitol.texas.gov

THE TEXAS CONSTITUTION ARTICLE 1. BILL OF RIGHTS

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/08/2025

That’s my point: If “COVID-AIDS” occurs, most likely there would also be “SARS-AIDS”. And SARS acute infections were two decades ago giving plenty of time for a “SARS-AIDS” to emerge. But has such a thing emerged? As best I know, no. So the probability of “COVID-AIDS” emerging is greatly diminished.

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/08/2025

I think I missed an important point on this thread: Some people are concerned that after several years COVID will lead to an HIV-like immune collapse. My point is that SARS1 is quite similar to COVID. Not the same, but quite similar. And an HIV-like immune collapse has not happened with SARS1.

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Andrew Urquhart @wolfeagle1989.bsky.social · 05/08/2025

There are some who worry that COVID is “Airborne AIDS” with a near-100% occurrence nasty post-acute syndrome. That’s the motive behind my comparison with SARS.

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Andrew Urquhart @wolfeagle1989.bsky.social · 05/08/2025

For comparison of post-acute SARS risks with post-acute HIV risks aka AIDS, the post-acute sample size for SARS probably is big enough. In the absence of treatment, what is the rate of immune collapse within 15 years post acute HIV infection? Just shy of 100%?

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Andrew Urquhart @wolfeagle1989.bsky.social · 05/08/2025

As far as I’m aware, most antibodies to SARS-CoV-2 target the Spike, N, and ORF8. And many of those aren’t neutralizing especially outside the Spike RBD and NTD targets. So yeah, there’s not much antibody response against the main protease or other replication complex proteins.

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Andrew Urquhart @wolfeagle1989.bsky.social · 04/08/2025

I haven’t heard of significant antibody responses to the main protease, and I’ve only heard of significant neutralizing responses to the spike. However, the main protease is the target of Paxlovid and some other antivirals.

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Andrew Urquhart @wolfeagle1989.bsky.social · 04/08/2025

This is interesting: A second COVID protein, the main protease, triggers blood clotting. This protein is *not* in vaccines used in developed countries, but it is highly conserved in coronaviruses including common cold coronaviruses. Ref Pagotto et al, www.nature.com/articles/s42....

nature.com

The main protease (Mpro) from SARS-CoV-2 triggers plasma clotting in vitro by activating coagulation factors VII and FXII - Communications Biology

SARS-CoV-2 main protease (Mpro) directly activates coagulation by cleaving factors VII and XII, showing a broader protease specificity and revealing a novel mechanism linking COVID-19 infection to thr...

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Andrew Urquhart @wolfeagle1989.bsky.social · 02/08/2025

Don’t miss that *influenza* awakens dormant cancer cells in lungs (Chia et al, “Respiratory viral infections awaken metastatic breast cancer cells in lungs”, Nature (2025), www.nature.com/articles/s41...). Maybe we need to be more concerned about *all* respiratory viruses.

nature.com

Respiratory viral infections awaken metastatic breast cancer cells in lungs - Nature

Mouse models show that respiratory infections from viruses such as influenza and SARS-CoV-2 can trigger metastasis of dormant breast cancer cells in the lungs, a finding supported by epidemiological d...

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Andrew Urquhart @wolfeagle1989.bsky.social · 29/07/2025

Finally, quoting from Strauss and Howe’s older “The Fourth Turning” (p. 318): “Classic virtues that didn’t necessarily pay off in an Unraveling (traits like trust, reliability, patience, perseverance, thrift, and selflessness) will become hard currency in a Crisis.” 6/6

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Andrew Urquhart @wolfeagle1989.bsky.social · 29/07/2025

As the world is highly interconnected now, and foreign dignitaries may well be implicated in the Epstein Files, this realignment may start in America but spread throughout the world. 5/6

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Andrew Urquhart @wolfeagle1989.bsky.social · 29/07/2025

I’m in that 89% and 92%. And anyone who wants the Epstein Files released is my ally. If you want the Epstein Files released, you’re my ally whether you’re MAGA, or you’re Never Trumper, or you’re a Democrat, or you’re Progressive/Socialist/Leftist. 4/6

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Andrew Urquhart @wolfeagle1989.bsky.social · 29/07/2025

A July 16-18, 2025 CBS News YouGov poll found 89% of Americans wanted the Epstein Files released and 92% thought those files likely implicated powerful or wealthy people (Source Q40 and 41 at d3nkl3psvxxpe9.cloudfront.net/documents/cb...) In a badly divided America, this agreement is remarkable. 3/6

d3nkl3psvxxpe9.cloudfront.net

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Andrew Urquhart @wolfeagle1989.bsky.social · 29/07/2025

Quoting Neil Howe’s “The Fourth Turning Is Here” (p. 190): “In every other case, society’s first regeneracy, after giving birth to two or more dominant groups, eventually weakens. These groups then fragment and reassemble during a second regeneracy.” 2/6

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Andrew Urquhart @wolfeagle1989.bsky.social · 29/07/2025

America, we may be approaching a Strauss-Howe “second regeneracy”. Current Republican vs Democrat, rural vs urban polarization may be changing to alignment by accountability vs impunity, justice vs exploitation, for vs against release of the Epstein Files. 1/6

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

With all this said, I don’t want to minimize the impact Long COVID has had on people. Long COVID is real and is a problem that needs to be taken seriously and addressed. However, we need to pay attention to and address other Post Acute Infection Syndromes as well. 8/8

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

As to longer-term Long COVID risks, we have 2 decades of history from human infections of another virus in the same species, SARS-CoV-1, and its post-acute syndrome Long SARS. Have highly delayed post-acute SARS-1 risks been reported? Is SARS-1 *that* different from COVID? 7/8

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

Gandhi, The Lancet Infectious Diseases (2024), www.thelancet.com/journals/lan... summarizes the situation well. See the screenshot with this post or its alt text. 6/8

The public's awareness of post-viral sequelae has been heightened by the COVID-19 pandemic, but infectious diseases experts have been aware of persisting symptoms following viral infections for more than a century. Post-influenza (an RNA virus) syndromes were first described following the 1918 influenza pandemic, including “encephalitis lethargica”, a relatively vague syndrome of “marked lethargy” often accompanied by neurological symptoms. Post-viral syndromes have been described following Epstein-Barr virus, cytomegalovirus, herpes simplex virus (all DNA viruses), and measles (an RNA virus) infections, with chronic inflammation in the setting of elevated antibody titres to these viruses invoked as the pathophysiological mechanism.

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

Part of what seems to have happened is the high acute case rates with COVID brought more awareness of post-acute infection syndromes (PAIS). But PAIS have in fact been known from other infectious illnesses including influenza. Long Flu happens too. 5/8

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

The spreadsheet has links to the studies both direct and through Digital Object Identifiers. For clarity, the quantitative study titles as well as some qualitative related study links are at github.com/alurqu/relat.... 4/8

github.com

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

Why do I say this? I’ve summarized the findings from multiple quantitative studies I found on this topic in a spreadsheet I’ve posted at github.com/alurqu/relat.... The post-acute rate ratios between COVID and other pathogens just aren’t that big. 3/8

github.com

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

The answer I’m finding is that it depends on the sense of “significantly”. In a statistical sense, for comparisons against some infectious illnesses, the answer is yes. But in a sociological sense, like is the rate more than double per case, the answer appears to be no. 2/8

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Andrew Urquhart @wolfeagle1989.bsky.social · 06/07/2025

Recently I’ve been examining the question “On a per-case basis for the same acute severity, is the rate of post-acute cognitive or neurological syndromes, or post-acute syndromes in general, significantly higher after COVID than after other infectious illnesses such as flu?” 1/8

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Andrew Urquhart @wolfeagle1989.bsky.social · 02/07/2025

More XFG.2 continues to be reported, but not in shockingly high numbers. It may have happened to be detected early after a relatively late start compared to other XFGs. I’m concluding this thread at least for now.

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Andrew Urquhart @wolfeagle1989.bsky.social · 27/06/2025

Additionally, perhaps Texans are beginning to realize that the “Big, Beautiful Bill” budget proposal is principally a wealth transfer from those already struggling financially to the wealthiest in society, and that runs against the interests of the MAGA base.

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Andrew Urquhart @wolfeagle1989.bsky.social · 27/06/2025

Trump’s popularity in Texas may also be taking hits due to DOGE’s indiscriminate instead of surgical reductions in the federal workforce including at the National Weather Service Consider that Texas has some wild weather and also has significant population on a hurricane-exposed coast.

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Andrew Urquhart @wolfeagle1989.bsky.social · 27/06/2025

3 more XFG.2: 3 Scotland, UK (totals Scotland 5, UK 10). Global total known now XFG.2 408.

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Andrew Urquhart @wolfeagle1989.bsky.social · 27/06/2025

That’s a good question. My guess would be that ICE raids may be eroding Trump’s support in Texas’s large Hispanic/Tejano community that increased in 2024. And then there Trump’s tariff policies in contrast with his campaign promises to bring down prices. And there may be other issues.

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Andrew Urquhart @wolfeagle1989.bsky.social · 27/06/2025

3 more XFG.2: 2 Puerto Rico (total Puerto Rico 2); 1 Vermont (VT), USA (totals VT 6, local USA 372, USA including travelers 377). Global total known now XFG.2 405.

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Andrew Urquhart @wolfeagle1989.bsky.social · 26/06/2025

If this trend continues, it could be huge. If Republicans start losing Texas, they probably can’t win the Presidency. And this might also put pressure on Texas’s Senate seats. www.newsweek.com/donald-trump...

newsweek.com

Donald Trump's approval rating goes negative in Texas

A new poll delivered a warning sign to Republicans about Trump's approval in the Lone Star State.

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