Highly sensitive PCR which Davis used in his study?

Markus83

Senior Member
Messages
166
Likes
165
As I remember Davis and his team also looked for infections in blood via PCR and found even less often pathogens in CFS vs. healthy controls.

Does someone know if these PCR testing is especially sensitive (say, compared to what you can expect at a normal university lab) and if it's possible to get tested there (on a self pay basis)? I tested negative for Chlamydia pneumoniae in blood at a german university lab, but have high antibody titers (IgG and IgA) and am pretty sure that I have chronic Cpn-infection ongoing.

Tagging @Hip, who seems to know everything ;-)
 

Hip

Senior Member
Messages
12,959
Likes
23,916
I tested negative for Chlamydia pneumoniae in blood at a german university lab, but have high antibody titers (IgG and IgA) and am pretty sure that I have chronic Cpn-infection ongoing.
You might find the Chlamydia pneumoniae section of the roadmap useful here. It basically summarizes Dr Chia's diagnostic criteria for Cpn. High IgG indicates chronic Cpn according to Chia.

Chia uses azithromycin 250 mg daily for one or two months as a treatment.
 

Markus83

Senior Member
Messages
166
Likes
165
Yes, Hip, according to Chia I have a chronic Cpn infection. However the blood-PCR at a university lab was negative. It seems that Ron Davis thinks that a chronic infection shows up in blood, at least if the sensitivity of the PCR is high enough. So I'm wondering if the PCR-testing used by Davis and his team was more sensitive that what is usually used at a university lab.
 

Hip

Senior Member
Messages
12,959
Likes
23,916
according to Chia I have a chronic Cpn infection. However the blood-PCR at a university lab was negative.
It's common in ME/CFS infections to have blood PCR negative, but IgG elevated. This is probably explained by the infections being intracellular infections, located in the tissues rather than blood.

For example, we know in the case of chronic enterovirus that it forms intracellular infections (called non-cytolytic enterovirus), and you can detect these if you test a tissue biopsy sample for enterovirus, but if you test the blood using PCR it often comes out negative (unless you are really severe, in which case you often then find enterovirus in the blood too).

Chlamydia pneumoniae is an intracellular bacterium. It lives inside cells in the tissues. So this is I believe is why ME/CFS doctors use antibody tests not blood PCR to detect chronic Cpn infection.
 

Hip

Senior Member
Messages
12,959
Likes
23,916
There is a detailed explanation here of why antibody testing rather than PCR is usually more important in ME/CFS.
 

ljimbo423

Senior Member
Messages
2,177
Likes
5,149
Location
United States, New Hampshire
Does someone know if these PCR testing is especially sensitive (say, compared to what you can expect at a normal university lab) and if it's possible to get tested there (on a self pay basis)?
Ron Davis- At 25:35 on this video, talks about the PCR test he used to look for DNA viruses in the severely ill.

EDIT- Ron also says that "the organism might not be in the blood but DNA (from the immune system attacking the virus) will be".

 
Last edited:

Markus83

Senior Member
Messages
166
Likes
165
Chlamydia pneumoniae is an intracellular bacterium. It lives inside cells in the tissues.
Cpn infects also the white blood cells and they got tested in my case (PCR from PBMCs = peripher blood mononuclear cells). I think, like you said, that one can have a chronic infection even if PCR is negative. But I'm wondering that Davis seems to think that a chronic infection is ruled out if PCR is negative. I think someone like him should know better than me? So maybe their PCRs are more sensitive than the standard PCR normally used. In that case you could test negative in a standard lab but maybe would be positive with the Stanford testing.
 

Markus83

Senior Member
Messages
166
Likes
165
Ron Davis- At 25:35 on this video, talks about the PCR test he used to look for DNA viruses in the severely ill.

EDIT- Ron also says that "the organism might not be in the blood but DNA (from the immune system attacking the virus) will be".
Yes, I think that was what I had in mind. Ok, he's talking just about viral infections. Didn't they test bacterial infections like Lyme, Cpn, bartonella, etc. ? I'm pretty sure that my PCR is falsely negative. I have not only high IgG titers against Cpn, but also IgA, which is considerd as a hint for chronic infection even by some mainstream doctors. So the question is if they have more sensitive PCRs at Stanford compared to other universities. The other possibility is that Davis is wrong about "negative PCR == no infection" or I am wrong about "high IgG + IgA && negative PCR == chronic infection anyway"...
 

Hip

Senior Member
Messages
12,959
Likes
23,916
Ron Davis used a new technique to detect the presence of DNA viruses in the tissues by detecting the viral DNA waste products of these viruses in the blood. It is not standard PCR viral test, it's a broad-spectrum test for DNA viruses.

Herpesviruses are DNA viruses, so it should detect these. I don't think the test includes any bacteria, just DNA viruses.

However, without seeing knowing details and capabilities of this test, it's not clear whether it would detect for example the abortive herpesviruses that Dr Lerner believed might cause ME/CFS. Or partially reactivated latent infections, and one study found ME/CFS may be linked to partially awakened EBV.

Also, the test does not include RNA viruses, like coxsackievirus B and echovirus. Davis is planning to test for RNA viruses in the future, but this is more difficult.
 

ljimbo423

Senior Member
Messages
2,177
Likes
5,149
Location
United States, New Hampshire
Yes, I think that was what I had in mind. Ok, he's talking just about viral infections. Didn't they test bacterial infections like Lyme, Cpn, bartonella, etc. ? I'm pretty sure that my PCR is falsely negative. I have not only high IgG titers against Cpn, but also IgA, which is considerd as a hint for chronic infection even by some mainstream doctors. So the question is if they have more sensitive PCRs at Stanford compared to other universities. The other possibility is that Davis is wrong about "negative PCR == no infection" or I am wrong about "high IgG + IgA && negative PCR == chronic infection anyway"...
Have you read Robert Naviauxs' view on why high viral and bacterial titers are found in CFS but are usually PCR negative? Naviaux is a leading ME/CFS researcher and world renown virologist of 30 years.
 

ljimbo423

Senior Member
Messages
2,177
Likes
5,149
Location
United States, New Hampshire
However, without seeing knowing details and capabilities of this test, it's not clear whether it would detect for example the abortive herpesviruses that Dr Lerner believed might cause ME/CFS. Or partially reactivated latent infections, and one study found ME/CFS may be linked to partially awakened EBV.
It seems like Ron is saying any "organism" that causes an immune system response, will cause very small amounts of DNA from that virus or bacteria to get into the bloodstream.

Which makes sense to me. I don't see how the immune system can attack an organism and not cause it to breakdown, at least a little and those breakdown products (DNA) would show up in the blood.
 

Hip

Senior Member
Messages
12,959
Likes
23,916
It seems like Ron is saying any "organism" that causes an immune system response, will cause very small amounts of DNA from that virus or bacteria to get into the bloodstream.
Consider this logic: most adults (90%) have latent EBV infections in their B-cells. Thus if Ron Davis's test could detect the DNA of latent infections like EBV, then nearly all adults would be positive on that test, and in fact the test would be useless because nearly everyone would come out positive.

Thus clearly his test does not detect latent infections.

If it cannot detect latent infection, it probably cannot detect the partially awakened EBV latent infections found in ME/CFS.

Don't forget in latent infections and partially awakened infections the virus does not leave the cell.
 

Markus83

Senior Member
Messages
166
Likes
165
Have you read Robert Naviauxs' view on why high viral and bacterial titers are found in CFS but are usually PCR negative?
No, where can I read it?

I recall that Dr Montoya also used high IgG viral titers as recruitment criteria for a Valcyte study, if I'm right. So he also didn't use PCR for that...
 

ljimbo423

Senior Member
Messages
2,177
Likes
5,149
Location
United States, New Hampshire
Here's a quote from Naviaux. The rest of what he said is here and starts about 5-6 paragraphs up from the bottom of the page.


Third, latent and reactivated viral and bacterial infections can occur, but in the case of ME/CFS that has lasted for more than 6 months, this may be the exception rather than the rule.

Some doctors and scientists have not done a good job at educating patients and other scientists about the difference between serological evidence of infection in the form of antibodies like IgM and IgG, and physical evidence of viral replication like PCR amplification of viral RNA or DNA, or bacterial DNA.

We have learned in our autism studies with Dr. Judy Van de Water that supertiters of antibodies do not mean new or reactivated viral replication. Supertiters of IgG antibodies mean that the balancing T-cell and NK cell mediated immune activity is decreased. This is a functional kind of immune deficiency that causes an unbalanced increase in antibodies.
 

Hip

Senior Member
Messages
12,959
Likes
23,916
The test should only detect active infections, that are causing an ongoing immune system activation. latent infections are by definition "inactive".
It seems that you have not come across the concept of partial reactivation in latency.

Latency does not always equate to inactive. EBV is known to have 3 latency states named latency I, latency II and latency III. Only state I is (almost) completely inactive; states II and III involve some activity (production of viral proteins).
 

Pyrrhus

Senior Member
Messages
186
Likes
531
Location
U.S., Earth
It seems like Ron is saying any "organism" that causes an immune system response, will cause very small amounts of DNA from that virus or bacteria to get into the bloodstream.
DNA debris from an immune system attack on a pathogen will be swept away and sequestered in the lymph nodes, not in the blood. Only in severe, widespread infections such as sepsis will such debris be detectable in blood.

Ron Davis has been widely misinterpreted here. He said it is sometimes possible to detect such debris in blood. He never said that you can always detect such debris in blood.
 

ljimbo423

Senior Member
Messages
2,177
Likes
5,149
Location
United States, New Hampshire
Ron Davis has been widely misinterpreted here. He said it is sometimes possible to detect such debris in blood. He never said that you can always detect such debris in blood.
At 27:05 in the video Ron says this-

"So it's been found that if you have an infection anywhere in the body, brain, heart, anywhere in the body. Some of those organisms will die, being attacked by the immune system and DNA will get into the blood from that organism."
 
Last edited:

Hip

Senior Member
Messages
12,959
Likes
23,916
So in summary:

(1) Prof Davis used a brand new viral test created by a startup company, which as far as we know has not been validated by any medical authorities such as the CDC. Many companies create new tests, but it is only when those tests become validated do they become tests we can rely on.

(2) We don't know the test's name, is technical specifications, its capabilities or its limitations, as this info is not made available.

(3) We don't know if the test is able to detect the partially reactivated EBV that has been found in ME/CFS, because this info is not available.

(4) We don't know if it is able to detect the abortive herpesvirus infections that Dr Lerner postulated may exist in ME/CFS. Abortive infections are in some ways similar to partially reactivated latency states.

(5) The test does not work for RNA viruses, so cannot detect enteroviruses, which are very important viruses in ME/CFS, and are the only virus proven to exist as chronic tissue infections in ME/CFS.
 
Last edited: