Research-level and emerging tests for persistent/chronic infections

There are various theories about persistent infections causing chronic illness. Some emerging tests are affordable ($2K or less) and are slowly working their way into clinical use. As well move out into the research-level realm, there are 2 problems:

  1. They still don’t find everything.
  2. We don’t know how to interpret the results!

One key scientific question in the scientific literature has to do with pathobionts - organisms that can cause harm under certain circumstances. Scientists don’t know why they are harmful in some contexts but not others. So even if we could profile everything living inside your body, we often don’t know what causes the problem and we often don’t know how to fix it.

However, there are some infections that we do know how to treat - HIV, Hep C, chronic Lyme, shingles, toxoplasma, parasites, etc. So those tests are currently quite relevant. Emerging tests like metagenomic NGS are also useful for patients with meningitis.

What emerging tests are finding

Gene sequencing technology has been advancing at breakneck speed, similar to how computers have become faster and faster over time. Its cost has come down dramatically. This will drive up usage over time.

One technology is called metagenomic next generation sequencing. It has discovered many micro-organisms living inside the human body that we didn’t know about. Wilson and colleagues (DOI:10.1056/NEJMoa1803396) describe their experience with metagenomic NGS for meningitis patients:

A total of 58 infections of the nervous system were diagnosed in 57 patients (27.9%). Among these 58 infections, metagenomic NGS identified 13 (22%) that were not identified by clinical testing at the source hospital.

13 out of the 58 infections found would not have been detected were it not for metagenomic NGS. The technology helped a lot in treating patients. At the same time, meningitis was still a mystery in many patients so this kind of testing did not find everything.

Clinicians in the UK can order metagenomic NGS through this webpage:

  • £1350 for tissue biopses
  • £700 for CSF

Cancer - interesting but not useful at the moment

A paper by Sven Borchmann (DOI:10.1186/s40168-021-01039-4) provides a review of bacteria and viruses that are associated with cancer in tumor tissue and blood. Research has found weird stuff like Ralstonia pickettii, an obscure bacteria that only has 2 full paragraphs in its Wikipedia page. Historically, it has not been thought of as a bacteria that regularly lives in humans, causes cancer, or is pathogenic. While it is sometimes found in cancer patients and is almost absent in healthy donors, its detection does not lead to any actionable change in treatment.

This type of research suggests that we will find weird stuff in healthy and unhealthy patients. But, we don’t yet know how to help patients based on that informatin.

Exotic tests

HIV treatment can bring HIV down to levels ‘undetectable’ with traditional methods. Researchers have discovered that new tools (e.g. single cell sequencing) allow them to detect extremely low levels of HIV hiding out in infected cells.

These more exotic tests can find things that other tests miss.

Theories about infections causing chronic illness

  • ME/CFS: John Chia believes that enteroviruses are a major cause of ME/CFS while other infectious and non-infectious causes play a role. He successfully treated his son. Steven Phillips’ book Chronic discusses vector-borne illnesses; he successfully treated himself after a 2-year battle that left him bedridden and unable to work.
  • Long COVID: Some point to reactivated shingles (herpes zoster), EBV, CMV, etc. Reactivated infections are also seen in post-vax.
  • Mysterious diseases that turned out to be caused by infections: Syphilis and (acute) Lyme infections were commonly misdiagnosed as something else until we understood these infections and how to treat them. Patients who have symptoms of multiple sclerosis are normally tested for various infections. Ruling them out is necessary for a MS diagnosis.

The good news - treat to test

The good news is that the lack of testing doesn’t stop patients from recovering. Patients (with appropriate supervision) can trial treatments to find effective treatment and to possibly generate some information to help figure out what’s happening. This is what John Chia does when tests come back negative.

That being said, you shouldn’t assume that your chronic illness is definitely caused by an infectious agent. To prove out those theories, we need to find the infections and we clearly haven’t done that yet. It’s possible that other things are going on; I maintain a list of various Long COVID and post-vax theories on this Long Haul Wiki page.

The current reality is that the treatments are ok and the testing is bad. Because testing is not very good, having access to the best medical tests does not seem to really help people recover. We know that the Long COVID and post-vax patients tested at the NIH do not seem to have exceptional results. See the conversation between Avindra Nath and Takashi Yamamura from Nov 2021. We know that a lot of people have gotten cytokines panels and have tried the suggestions of Patterson concierge docs. And we know of some people who have purchased auto-antibody tests from CellTrend, Berlin Cures, etc. But where we really seem to see results are from the people who have tried the better treatments (fasting, ivermectin, HCQ, black seed oil from Nigella Sativa, high ATA HBOT, statins).

So while testing is interesting, it has been fairly disappointing in terms of helping people recover.

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