Ila Singh commentary on detection in journal "Viruses"

urbantravels

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I quoted the abstract below, full text is free pdf download at the link.

http://www.mdpi.com/1999-4915/2/11/2404/

Viruses 2010, 2(11), 2404-2408; doi:10.3390/v2112404
Commentary
Detecting Retroviral Sequences in Chronic Fatigue Syndrome
Ila R. Singh email
Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
Received: 26 October 2010; in revised form: 2 November 2010 / Accepted: 2 November 2010 / Published: 3 November 2010

Abstract: XMRV or xenotropic murine leukemia virus-related retrovirus, a recently discovered retrovirus, has been linked to both prostate cancer and chronic fatigue syndrome (CFS). Recently, the teams of Drs. Shyh-Ching Lo and Harvey Alter discovered the presence of sequences closely related to XMRV in the blood of 86.5% of patients with CFS [1]. These findings are important because since the initial discovery of XMRV in CFS, several studies have failed to find XMRV in specimens collected from CFS patients. While the current study also did not find XMRV in CFS, Lo et al. did detect sequences that belong to polytropic mouse endogenous retroviruses (PMV), which share considerable similarity with XMRV. Criteria for future studies that will help bring greater clarity to the issue of retroviral sequences in CFS are proposed below.
 

eric_s

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The PMV and M-PMV share over 95% sequence identity, and the xenotropic
viruses share over 90% identity with the PMV (derived from sequences within reference [12] and
Genbank; [13,14]).Compared to this, an average pair of random isolates of HIV-1 in the U.S. are
~85-95% similar, depending on the region of the viral genome used for comparison [15,16].
Read this, all you people who say the Lo/Alter study was no confirmation. S* for brains? Sorry for the language :angel: I guess by now we have a feeling whose words are to be taken more seriously.
Edit: I'm of course not referring to anyone on the forum here, but to other scientists, journalists, etc.
 

Jim

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does anyone know why the heck lo did not blind the samples? seems it would not have been hard to do, and would have helped debate over any contamination.
 

CBS

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Sounds like Dr. Singh is describing in detail her CFS/XMRV study. Hopefully this indicates she's getting ready to publish soon.

Proving that xenotropic or polytropic viruses are present in chronic fatigue syndrome would be the first step towards determining if these viruses actually
cause disease.

Faced with a chronic, severely debilitating illness and the lack of effective and approved diagnostic or therapeutic options, some patients have begun treatment with antiretroviral agents, based on effects of these drugs on XMRV replication
in vitro [18-21]. Whether this is a wise course of action to takegiven the inconsistencies in available datacan be debated. But what cannot be debated is that there is a real need for thoughtfully designed and carefully executed studies that examine this issue more thoroughly.

At this point, it might be good to evaluate parameters essential to resolve whether XMRV and other related viruses are truly present in specimens taken from CFS patients.

A good study will need a sufficiently large set of patients that fulfill well-recognized criteria for CFS, such as those outlined by the 1994 case definition of the CDC [22], as well as the criteria defined by the Canadian consensus document on myalgic encephalitis/CFS [23].
Dr. Bateman supplied 105 patients that met the 1994 case definition and the CCDx to Dr. Singh

From this set of patients, those taking antiretroviral drugs should be excluded, as a negative result could simply mean that viral titers have decreased to an undetectable range by the drugs.
Probably safe to assume this was done.

It is also essential that the control population is large, and from the same geographical area as the patients.
200 controls from the same geographic area.

Furthermore, it is important that patient samples are collected and treated the same way as controls.
This was done by Dr. Singh.

Blinding the investigator to the identity of patient samples and controls would add an additional measure of confidence to the results.
Also done by Dr. Singh.

Another important factor in designing future studies would be making sure that there are good controls for each step of the analysis. For example, negative controls for PCR, which usually consist of water, should also go through the same nucleic acid extraction process as all human samples used in the study. Thus, contamination of samples occurring prior to amplification is likely to be detected as a positive PCR from a water control.
I would assume shes doing this if she is recommending it as an essential step.

Furthermore, the number of negative controls per plate should at least equal if not exceed the prevalence of the virus in the control population.


It is also important to characterize methods of detection in more detail than they have been so far.


Other assays, such as isolating replicating virus from plasma or detecting specific antibodies in serum will be important corroborating tests to prove the presence of an infectious virus in a set of patients.

???

Finally, an ideal study would use at least one method that has resulted in detection of XMRV in a previous study, preferably using a set of samples that were analyzed in that same previous study and are known positives or negatives. In order to avoid any possibility of contamination, it is important that these shared samples not go to any research lab for patient deidentification or aliquoting, but instead go from the phlebotomy lab directly to the researchers who will do the testing.
Repeat samples from positive WPI patients have been reported as having been collected outside of the WPI have be sent directly to Dr. Singhs lab, in some cases, bypassing the entire state of Nevada.

A study that incorporates these criteria is likely to resolve more clearly whether xenotropic or polytropic viruses are present in chronic fatigue syndrome, and move us a step closer to determining if these viruses cause disease.

I wonder what Dr. Singh already knows?
 

Otis

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After reading the commentary she did a great job of slamming the door on contamination in Lo/Alter. So take that Le Grice, now don't breathe that word again. There is still the matter of them not showing the virus replicating in a human cell line as done by Lombardo et at. I think Lo/Alter are working on this now.

Dr. Singh lays out a study design needed to "to evaluate parameters essential to resolve whether XMRV and other related viruses are truly present in specimens taken from CFS patients." She covers all the bases, and I think she's laying the groundwork for her own study due out by the end of the year, if I remember correctly. If that's the plan she may have just proactivly fended off attempts to criticize her own work and proving herself as politically savvy as she is scientifically.

Great stuff!



If she publishes a paper nailing down the corrolation we should be past replication, and shutting up most critics with the likely exception of McClure.
 

Otis

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Sounds like Dr. Singh is describing in detail her CFS/XMRV study. Hopefully this indicates she's getting ready to publish soon.

<snip>


Great summary CBS, looks like we were typing at the same time. I think Dr. Singh already knows she's met all of these criteria. :D

On your ?????? on
It is also important to characterize methods of detection in more detail than they have been so far.

Other assays, such as isolating replicating virus from plasma or detecting specific antibodies in serum will be important corroborating tests to prove the presence of an infectious virus in a set of patients.
I think the characterization has to do with specificity and sensitivity and based on her commentary - repeatability. I suspect she has an ace up her sleeve here.

As I recall she's got her own antibody test to cover the second point.

Man I can't wait for her study! I'm guessing she pulled this methodological approach largely from her own paper, it sure fits with all we know.

If she clears her own bar for the CFS/XMRV connection, with her own knack for consistently finding XMRV in prostate cancer and her incredibly meticulous approach she should finally slam the door on replicating the Science study with no "yeah buts..." to be found.

As much as I hated to hear Dr. Bateman say "slow and steady wins the race" I'm hoping this paper will be the tortes that beats all the sloppy "0/0" study hares.
 

urbantravels

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There are no flies on Dr. Singh.

I have got to believe that the cat's thoroughly out of the bag on methodological questions at this point. Nobody, at this point, could possibly publish another negative study without addressing these issues and at least modifying their idea of what "conclusions" may be drawn from negative results.

Of course, who *really* needs to be on the ball? The journal editors, that's who. They should be raising these questions with *every* XMRV study they consider for publication, and sending the studies to reviewers who know the current state of play and will ask the tough questions that Dr. Singh would ask.

And, while they are doing that highly principled painstaking review process for all other papers, they should nevertheless PUBLISH ALL OF DR SINGH'S WORK RIGHT NOW EVEN IF SHE'S NOT DONE WITH IT BECAUSE I WANT TO SEE IT NOW!!!!! That is my principled opinion on the matter.

:sofa:
 

CBS

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Dr. Singh has been working on XMRV before XMRV was cool. Can't wait for her cadaver study (started when she was at Columbia and it has been underway for over three years!)
 
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Sounds like Dr. Singh is describing in detail her CFS/XMRV study. Hopefully this indicates she's getting ready to publish soon.


That was what I thought too as I read her article. If so, should be a very good study. But also, her article does throw up how complex the process is and how many opportunities there are for things to go wrong.
 

Sean

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But also, her article does throw up how complex the process is and how many opportunities there are for things to go wrong.
Which, in an ironic kind of way, is good for us, because it would explain why so many studies have come up negative -- they have not used a sufficiently rigourous and precise protocol.

As has been mentioned before on the forums and elsewhere, most of the low hanging fruit in infectious diseases has already been picked, so it makes sense that newer discoveries are harder to make and reproduce. Which, of course, does not make them any less real or pathogenic, or important.

Gotta say I am feeling more confident than I was even straight after the Lo/Alter paper came out. I think the science is proceeding pretty well exactly as it should, all the glitches are being addressed and weeded out. It is certainly not a smooth process, technically or politically*, but it is happening.

*Historically these kind of discoveries and advances rarely have been. There have almost always been serious disputes and set backs. But the discoveries and advances still happened.
 

pictureofhealth

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I really do like Ila Singh's style, her intelligence and her level headedness.

She has presented a crystal clear, common sense guide here, which is so refreshingly free of politics and which clarifies the way forward so we can finally get some answers.

I feel quite hopeful after reading this. She is just the kind of researcher I would want on my (our) case.
 

Otis

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Of course, who *really* needs to be on the ball? The journal editors, that's who. They should be raising these questions with *every* XMRV study they consider for publication, and sending the studies to reviewers who know the current state of play and will ask the tough questions that Dr. Singh would ask.
Well said. The scrutiny that positive studies are receiving vs. what the junk 0/0 papers have gotten is pathetic. I'm all for strong positive studies and I'm willing to accept a negative study that is well done - if I ever see one.

And, while they are doing that highly principled painstaking review process for all other papers, they should nevertheless PUBLISH ALL OF DR SINGH'S WORK RIGHT NOW EVEN IF SHE'S NOT DONE WITH IT BECAUSE I WANT TO SEE IT NOW!!!!! That is my principled opinion on the matter.
Very level headed ;) and I quite agree.
 
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I agree with Singh on the easy viruses have already been found. I have been saying this for a while. Seems to me, XMRV or whatever name it or they are called, does a hide and seek game. As the Emory study said, it disappears from the blood. Also, Dr. Mikovits said it can be turned on by sex hormones, cortisol and vaccines/ infections. So, it would stand to reason it can go dormant or inactive.

I had a chance to ask her directly: is it correct to say it can go dormant? She said yes.

Specifically, in later speech, she said it can go into cells that don't replicate a lot. And then it just sits there in the DNA.

So, how many other retroviruses are there that are like this? Think of all the illnesses for which there is no explanation, no cure. MS, autism, even psychiatric illnesses, such as bi-polar disorder, not to mention the cancers. Could viruses have a role in breast cancer? Just think of the possibilities.

I am pretty sure I got this from my mom. She has strong neurological signs, but not immune system. My sister has ME/CFS, although she now prefers depression and dysautonomia, and my other sister is bi-polar with narcolepsy. My mother had breast cancer in her late 40s, thankfully cured. My grandfather was clearly, looking back on his behavior, bi-polar. How many years has XMRV, or for that matter, other retroviruses been causing havoc in the human population? OH, I forgot the obvious one, leukemia, lymphoma.

Since XMRV has different behavior than HIV, it breaks the mold. We will hopefully see a more open mind and better detection tools so that many other retroviruses with similar behavior will be discovered. As Dr. Mikovits said, this is a whole new area of science.

One day, I expect, Mikovits will hear that phone ring.

"Dr. Judy Mikovits?"

"Yes."

"My name is Dr. Gobbledy Gook from the Nobel Prize Committee. We would like to inform you that you and your partners have won the Nobel Prize for Scientific Discovery. Congratulations."

We'll see. But I won't be surprised.

Tina
 

August59

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I have a very strong feeling or opinon in that the science and technology that is being driven by the XMRV discovery (and other associated findings) is going to lead to new ground breaking discoveries in other fields of medicine. I think there will still be new viruses discovered from this science, whenever someone decides to go looking for it. XMRV is not the end of it!!
 
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An easy to read commentary article published in a journal that gives free access to the public... I think this article was written to reassure patients like us..
 

Cort

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I have a very strong feeling or opinon in that the science and technology that is being driven by the XMRV discovery (and other associated findings) is going to lead to new ground breaking discoveries in other fields of medicine. I think there will still be new viruses discovered from this science, whenever someone decides to go looking for it. XMRV is not the end of it!!
That could be - they appear to be taking a very detailed look at the whole process; of course, they could discover there was some sort of contamination but they could also discover there is a step in the normal chain of events in their PCR or sample collection or whatever that, unbeknownst to them has been wiping out a whole group of viruses. They've never seen them because they've been accidentally wiping them out. Just think of that!

That said I don't think the WPI did anything unusual in their sample collection/PCR process and the blood bank they got the healthy controls from certainly didn't either but it is possible that both did something a bit different - a little, little thing - that changed there 'terrain' so to speak. I imagine that's why they are asking researchers to provide details of their protocols they never have before.
 

Cort

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So, how many other retroviruses are there that are like this? Think of all the illnesses for which there is no explanation, no cure. MS, autism, even psychiatric illnesses, such as bi-polar disorder, not to mention the cancers. Could viruses have a role in breast cancer? Just think of the possibilities.

I am pretty sure I got this from my mom. She has strong neurological signs, but not immune system. My sister has ME/CFS, although she now prefers depression and dysautonomia, and my other sister is bi-polar with narcolepsy. My mother had breast cancer in her late 40s, thankfully cured. My grandfather was clearly, looking back on his behavior, bi-polar. How many years has XMRV, or for that matter, other retroviruses been causing havoc in the human population? OH, I forgot the obvious one, leukemia, lymphoma.

Tina
I was just talking to someone about bi-polar disorder - there are no behavioral treatments; its a chemical condition. I just read the story of a person with unipolar depression who was absolutely fine until he woke up one day and was depressed (no stressors! no abnormal behavior - just something that changed). There is infection onset depression and infection-onset obsessive compulsive disorder. (I believe there's also infectious RA), There's certainly infectious onset FM and POTS.

My understanding is that Lipkin strongly believes these and other disorders are caused by a genetic-viral connection and he believes the same in ME/CFS and this is why he is engaged in two studies on ME/CFS now.

Of course DeFreitas mentor felt two decades ago that the symptoms of ME/CFS suggested a retroviral infection in the brain.