Andrew Urquhart

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.”

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.

@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.

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…

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.

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.

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.

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....

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.

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....

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/...

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)

Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion Coronaviruses can evolve novel transcription regulatory sequences, generating new RNA transcripts during human infection. This study identifies a prevalent subgenomic RNA in SARS-CoV-2, which produces...

More on N.iORF3 aka N*M210 aka N* can be found in Mears et al doi.org/10.1371/jour... and the Mulloy et al preprint doi.org/10.1101/2025.... Enhanced transcription of this protein may enhance XFG fitness. (3/3)

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)

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)

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

And the pendulum swings…

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/...?

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.

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.

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.

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%?

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.

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.

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...

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....

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...

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.

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

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

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

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

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

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

Neuroinvasion by Human Respiratory Coronaviruses | Journal of Virology ABSTRACT Human coronaviruses (HCoV) cause common colds but can also infect neural cell cultures. To provide definitive experimental evidence for the neurotropism and neuroinvasion of HCoV and its possible association with multiple sclerosis (MS), we have ...

SARS-CoV-2 isn’t the only neurotropic betacoronavirus. Common cold human betacoronavirus OC43 is also neurotropic. Reference Arbour et al, "Neuroinvasion by human respiratory coronaviruses", Journal of Virology (2000), doi.org/10.1128/jvi.....

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

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