ixchelkali
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NIH Videocast on Viruses and CFS Featuring Lo and Alter!
- Thread starter Cort
- Start date
Bob
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Yes, I'm still optimistic as well, especially after watching the Alter/Lo video.
Yes, it's worrying that Huber is getting involved in XMRV research again, especially because she isn't able to detect it.
But personally, I don't actually believe that Huber is an enemy of ours... However annoying she might have been in expressing her opinions, I think she's a genuine researcher, who wants to detect XMRV, but wasn't able to.
Yes, Alter and Lo ran all the best contamination tests... And Alter knows what he is doing!
But unfortunately Alter and Lo didn't address the latest research that detected XMRV in a cell line (or I don't think they did anyway.)
XMRV isn't a mouse virus or mouse DNA, so if XMRV is contamination originating from a cell line, then it wouldn't show up in a test for mouse contamination.
Alter's PMRV is not XMRV though, so we don't know if that might have originated from a cell line or not...
It's very complicated!
Bob
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You gave me my chuckle for the day.
heehee...
Glad it gave you a chuckle!
When I read your quote just now, it made me chuckle as well!
It's a good thing we still have a sense of humour and can laugh at ourselves!
Bob
Senior Member
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- 16,455
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- England (south coast)
I wanted to put all of my transcription into a single post, so here it is...
I haven't transcribed the whole video, because it is too long, but I've just picked out some interesting sections...
Where there are breaks in my transcription, I've indicated it with either dots [...] or dotted lines [---].
Some of Lo's speech is a bit disjointed, and difficult to follow, but the only places that I've missed out any text in his speech is where i've placed 3 dots [...].
I've bolded some of the more interesting bits.
----------------------------
Demystifying Medicine - "Chronic Fatigue Syndrome: Is there a virus?"
Shyh-Ching Lo (FDA)
Fred Gill (NIDDK)
Harvey Alter (NIDDK)
February 22, 2011
http://videocast.nih.gov/Summary.asp?File=16477
-----------------------------
Transcription of Shyh-Ching Lo presentation:
[83.05]
"So why did many studies have different findings? This is obviously a very challenging question...
...
"...and the way the clinical sample is prepared, and the processing of this, all can make a difference.
[83.45]
And even more possible to me is that there is a variation of the PCR protocol, although everybody says we are following the same PCR assay, but if you look into all the detail, the cycles are different, annealing temperature slightly different, magnesium concentration slightly different;
All of this, we really don't know how much that's going to make a difference.
Today the topic is, is there a virus or not? is the virus responsible, or the causative agent of this, or not?
That's all very far away at the present time because, when we are looking at this, we obviously are dealing with a very low rate [or 'grade'?] of infection - a very low copy number in the blood,
and many of these difference can certainly result in the PCR disparities,
and i just want to mention... the NIH obviously, the NHLBI's, is looking into this, and have this sample, coded sample, sent to different laboratories, and to test it,
and this is the clinical [or 'critical'?] panel, the CDC's result,
and obviously ... the four of the patients,
and depends how the sample is being processed,
how long the delay of the processing of the sample, and the results are obviously different;
some are negative and some are positive,
so this is obviously, they also continue to look into this and try to solve is there any processing of the sample make a difference?
..."
[85.30]
Slide no. 93:
Why did many other studies have different findings--
-------------------------
[96.55]:
Lo describes how Harvey and Lo sent two of their positive patient samples to the CDC who then couldn't detect the PMRV's in the samples.
The CDC sent a blind coded negative control sample, from a single patient, to Harvey and Lo, which Harvey and Lo then repeatedly identified as positive, about 15 times. They repeatedly identified the same sample as being positive, even though it was blind coded. So Harvey and Lo detected PMRV in a 'negative control' from the CDC. Lo seems to be saying that this means it isn't a negative sample, but that the CDC just couldn't detect the virus in the sample.
[My thoughts: if we are talking about contamination here, then it couldn't be in the sample itself, but must enter during the testing stage. But Harvey and Lo's consistent and repeated testing of the negative control sample, as positive, suggests that it isn't contamination.]
[97.30]
[Here's the quote about the coded samples from the CDC]:
Lo:
"They [the CDC] had a negative one [sample] and then send to us to test it.
And I see, for the CDC group of patients, most of them are negative in our hands, [indiscernible],
But the interesting part; and obviously we don't want to get into the too complicated thing;
And while they kick in [?], the so called negative control from a single patient, and repeated, I forgot, 15 times, 10 times, or something;
And that particular sample; we repeatedly identified as positive.
But that's a coded sample; you know, we did not know that that particular one is a, repeat, coded negative control,
and that one is positive."
[It is difficult to understand all of Lo's speech in this section of the video, but it does suggest that there were other negative control samples that Lo consistently tested as negative, and that he consistently and repeatedly tested the one negative control as positive.]
[99.10]
Lo: "We are pushing to the very end of the sensitivity..."
---------------------------
[99.30]:
Lo says that, because they are detecting at the very limits of sensitivity, then one explanation as to why they are detecting XMRV/PMRVs in CFS patients, might be that the viruses could be ubiquitous, but that CFS patients have higher titers than the normal population, just as we do with Herpes and EBV etc., and this means that they can only detect it in CFS patient blood samples and not normal blood samples.
[Lo wasn't saying this as his opinion, he was just offering it up for discussion, saying it is a possibility, amongst other possibilities.]
------------------------------
Transcription of Harvey Alter's presentation:
[103.04]
"If the virus is indeed in the patient, i suggest about a present antibody, and i think it very important that the Whittemore Peterson group has consistently found antibody in the patients, and has found virus that they can culture in these patients; so in their data, they've done the whole gamut; we've had more trouble finding the antibody in our patients; we're working with the NCI group; but despite the fact that the Whittemore Peterson group has been able to culture it and find antibody, people still don't believe that patients were infected; so it's just a difficult field.
[103.50]
But that's the issue that we have to address, and if the patient is infected, the next issue is, is it a primary infection that causes the disease, or is it a secondary infection, due to, whatever, amino deficiency, [indiscernible] infection, or something else.
So how are you going to resolve this?
Well, the heart and lung institute and the NIAID are conducting separate studies now to assess whether these findings are reproducible and are they specific; and sensitivity is in there as well. But mostly it is to see, are they reproducible and are they specific for this disease.
So when we suggested exchanging samples between the labs that have divergent findings; we tried to do that, it wasn't sufficient, it wasn't sufficient samples, the answers were not as clear as one would hope.
But I think the most important thing is what is being done now, particularly in a study that the NIAID is sponsoring.
Dr Ian Lipkin at Columbia is heading up this study, and the idea is to take classic cases of Chronic Fatigue Syndrome; people that meet the Canadian Criteria, that had an acute onset of disease and then went into the debilitating long term effects; cases that everybody would agree are Chronic Fatigue, to the best that you can agree on that.
To take those patients, and they are from different places around the country; so they are geographically diverse; Take large volumes of their samples; send them to Dr Lipkin's lab, where they will be separated, and come overnight, and separated into various components, mostly plasma and whole blood, but maybe some PBMC's, and then coded, and the same sample will be coded in triplicate.
And then panels will be developed, and sent to the labs - who have claimed to find the virus, and those that have claimed not to have found the virus; and those labs will use their own assays, and then see how they break the code.
And the results will be published, so whatever comes out, positive or negative, the results will be published,
and the codes will be broken at the coordinating centre.
[106.34]
So what are the possible outcomes of that?
Well, if this cannot be found in these pedigree patients, in the labs who previously reported finding it, then i think that the original findings will have to be considered unconfirmed and contamination will be suspected, but all these samples will be tested for mouse DNA by the best techniques; both the techniques that Dr Lo talked about.
But if Dr Lo - he is under a lot of pressure - if he doesn't do well on the panels, then we have to say something was awry originally. However, if he does do well, if the panels show that he can consistently detect coded samples from CFS patients, and not from controls, or different ratios on patient controls, then the published findings will have been confirmed.
And that confirmation will not establish causality, it will just confirm the association, and rule out the contamination issue.
[107.35]
And the causality is going to be difficult, it's always difficult, if you don't have an animal model, it's always difficult to prove causality; it may have to be proved by controlled clinical trials using antiretroviral agents.
And Dr Mikovits has already shown that known antiretroviral agents, the whole XMRV agent is sensitive to two, but not all of the HIV antiretroviral agents.
[108.02]
So that's where it's going; this should resolve; this data should be available in the next six months and i think it's the best way to go about it. Up until that time, you can believe what you believe."
------------------------------
Q&A Session:
[110.52]
[Question about viral DNA integration into human genome.]
[111.15]
Alter:
"It's a wonderful question;
It's very difficult; it's kind of like looking for a needle in a haystack. It can be done.
People who looked for Beta retroviruses; it took them four years to find an integration site.
You have no idea where in the genome it might be and you're looking for a low titre; [a] small amount of total genome.
I'm not a molecular biologist, but i've been told it's very difficult.
We are working with a group in Canada who are trying to do it, but they don't anticipate a quick answer.
But that would be a very important thing."
[112.25]
Lo:
"For the prostate, from the tumor, they've been published, and they are flanked by the human sequence.
But even that, people do challenge that: 'is that truly from a clinical sample, or not, or a contaminant from somewhere?'
Again that is based on the PCR product, and you do the sequence."
---------------------------
Lo suggests that the discrepancies in testing might be due to the low titres.
---------------------------
[116.21]
Alter:
[Talking about CFS, referring to it as a biomedical illness]:
...
"There are similarities in an addisonian patient [referring to Addison's disease],
there's similarities in a chronic infectious mononucleosis patient.
It [CFS] smacks of, if not a viral etiology, some kind of neuroendocrine abnormality.
Something's in there that's doing something.
That's your final thing:
There's something doing something!"
----------------------------
Details from Slide 17:
Mikovits tested 50 patients from England, and found 48% positive for XMRV [by PCR?], 63% positive for XMRV antibody, and tested 78% positive in DERSE culture assay. Antibody found in 4% of controls.
Hanson tested 20 patients from New York State, and found 55% positive for polytropic sequences only (No XMRV sequences found). (This is the Maureen Hanson and Dr Bell study.) [This information doesn't match up with the abstract published at the 1st International Workshop on XMRV which says that Hanson has detected XMRV sequences.] [ETA: Now there's another abstract available that confirms that Hanson has detected p-MLV-like sequences]
----------------------------
http://videocast.nih.gov/Summary.asp?File=16477
I haven't transcribed the whole video, because it is too long, but I've just picked out some interesting sections...
Where there are breaks in my transcription, I've indicated it with either dots [...] or dotted lines [---].
Some of Lo's speech is a bit disjointed, and difficult to follow, but the only places that I've missed out any text in his speech is where i've placed 3 dots [...].
I've bolded some of the more interesting bits.
----------------------------
Demystifying Medicine - "Chronic Fatigue Syndrome: Is there a virus?"
Shyh-Ching Lo (FDA)
Fred Gill (NIDDK)
Harvey Alter (NIDDK)
February 22, 2011
http://videocast.nih.gov/Summary.asp?File=16477
-----------------------------
Transcription of Shyh-Ching Lo presentation:
[83.05]
"So why did many studies have different findings? This is obviously a very challenging question...
...
"...and the way the clinical sample is prepared, and the processing of this, all can make a difference.
[83.45]
And even more possible to me is that there is a variation of the PCR protocol, although everybody says we are following the same PCR assay, but if you look into all the detail, the cycles are different, annealing temperature slightly different, magnesium concentration slightly different;
All of this, we really don't know how much that's going to make a difference.
Today the topic is, is there a virus or not? is the virus responsible, or the causative agent of this, or not?
That's all very far away at the present time because, when we are looking at this, we obviously are dealing with a very low rate [or 'grade'?] of infection - a very low copy number in the blood,
and many of these difference can certainly result in the PCR disparities,
and i just want to mention... the NIH obviously, the NHLBI's, is looking into this, and have this sample, coded sample, sent to different laboratories, and to test it,
and this is the clinical [or 'critical'?] panel, the CDC's result,
and obviously ... the four of the patients,
and depends how the sample is being processed,
how long the delay of the processing of the sample, and the results are obviously different;
some are negative and some are positive,
so this is obviously, they also continue to look into this and try to solve is there any processing of the sample make a difference?
..."
[85.30]
Slide no. 93:
Why did many other studies have different findings--
- There could be a difference in the prevalence of the viral agents among patient groups in different geographic areas.
- Heterogeneity of CFS patient groups could be significant.
- Variations of clinical sample preparations could affect PCR amplification effectiveness and assay sensitivity.
- Variations of PCR protocols, primers, reagents or assay designs may have different sensitivity in detecting the diverse group of MLV-related virus gene sequences in the clinical samples.
- The nature of low grade infections with low titers of the virus or low copy numbers of the viral target genes in patients' blood may likely account for the inconsistence and the PCR disparity.
-------------------------
[96.55]:
Lo describes how Harvey and Lo sent two of their positive patient samples to the CDC who then couldn't detect the PMRV's in the samples.
The CDC sent a blind coded negative control sample, from a single patient, to Harvey and Lo, which Harvey and Lo then repeatedly identified as positive, about 15 times. They repeatedly identified the same sample as being positive, even though it was blind coded. So Harvey and Lo detected PMRV in a 'negative control' from the CDC. Lo seems to be saying that this means it isn't a negative sample, but that the CDC just couldn't detect the virus in the sample.
[My thoughts: if we are talking about contamination here, then it couldn't be in the sample itself, but must enter during the testing stage. But Harvey and Lo's consistent and repeated testing of the negative control sample, as positive, suggests that it isn't contamination.]
[97.30]
[Here's the quote about the coded samples from the CDC]:
Lo:
"They [the CDC] had a negative one [sample] and then send to us to test it.
And I see, for the CDC group of patients, most of them are negative in our hands, [indiscernible],
But the interesting part; and obviously we don't want to get into the too complicated thing;
And while they kick in [?], the so called negative control from a single patient, and repeated, I forgot, 15 times, 10 times, or something;
And that particular sample; we repeatedly identified as positive.
But that's a coded sample; you know, we did not know that that particular one is a, repeat, coded negative control,
and that one is positive."
[It is difficult to understand all of Lo's speech in this section of the video, but it does suggest that there were other negative control samples that Lo consistently tested as negative, and that he consistently and repeatedly tested the one negative control as positive.]
[99.10]
Lo: "We are pushing to the very end of the sensitivity..."
---------------------------
[99.30]:
Lo says that, because they are detecting at the very limits of sensitivity, then one explanation as to why they are detecting XMRV/PMRVs in CFS patients, might be that the viruses could be ubiquitous, but that CFS patients have higher titers than the normal population, just as we do with Herpes and EBV etc., and this means that they can only detect it in CFS patient blood samples and not normal blood samples.
[Lo wasn't saying this as his opinion, he was just offering it up for discussion, saying it is a possibility, amongst other possibilities.]
------------------------------
Transcription of Harvey Alter's presentation:
[103.04]
"If the virus is indeed in the patient, i suggest about a present antibody, and i think it very important that the Whittemore Peterson group has consistently found antibody in the patients, and has found virus that they can culture in these patients; so in their data, they've done the whole gamut; we've had more trouble finding the antibody in our patients; we're working with the NCI group; but despite the fact that the Whittemore Peterson group has been able to culture it and find antibody, people still don't believe that patients were infected; so it's just a difficult field.
[103.50]
But that's the issue that we have to address, and if the patient is infected, the next issue is, is it a primary infection that causes the disease, or is it a secondary infection, due to, whatever, amino deficiency, [indiscernible] infection, or something else.
So how are you going to resolve this?
Well, the heart and lung institute and the NIAID are conducting separate studies now to assess whether these findings are reproducible and are they specific; and sensitivity is in there as well. But mostly it is to see, are they reproducible and are they specific for this disease.
So when we suggested exchanging samples between the labs that have divergent findings; we tried to do that, it wasn't sufficient, it wasn't sufficient samples, the answers were not as clear as one would hope.
But I think the most important thing is what is being done now, particularly in a study that the NIAID is sponsoring.
Dr Ian Lipkin at Columbia is heading up this study, and the idea is to take classic cases of Chronic Fatigue Syndrome; people that meet the Canadian Criteria, that had an acute onset of disease and then went into the debilitating long term effects; cases that everybody would agree are Chronic Fatigue, to the best that you can agree on that.
To take those patients, and they are from different places around the country; so they are geographically diverse; Take large volumes of their samples; send them to Dr Lipkin's lab, where they will be separated, and come overnight, and separated into various components, mostly plasma and whole blood, but maybe some PBMC's, and then coded, and the same sample will be coded in triplicate.
And then panels will be developed, and sent to the labs - who have claimed to find the virus, and those that have claimed not to have found the virus; and those labs will use their own assays, and then see how they break the code.
And the results will be published, so whatever comes out, positive or negative, the results will be published,
and the codes will be broken at the coordinating centre.
[106.34]
So what are the possible outcomes of that?
Well, if this cannot be found in these pedigree patients, in the labs who previously reported finding it, then i think that the original findings will have to be considered unconfirmed and contamination will be suspected, but all these samples will be tested for mouse DNA by the best techniques; both the techniques that Dr Lo talked about.
But if Dr Lo - he is under a lot of pressure - if he doesn't do well on the panels, then we have to say something was awry originally. However, if he does do well, if the panels show that he can consistently detect coded samples from CFS patients, and not from controls, or different ratios on patient controls, then the published findings will have been confirmed.
And that confirmation will not establish causality, it will just confirm the association, and rule out the contamination issue.
[107.35]
And the causality is going to be difficult, it's always difficult, if you don't have an animal model, it's always difficult to prove causality; it may have to be proved by controlled clinical trials using antiretroviral agents.
And Dr Mikovits has already shown that known antiretroviral agents, the whole XMRV agent is sensitive to two, but not all of the HIV antiretroviral agents.
[108.02]
So that's where it's going; this should resolve; this data should be available in the next six months and i think it's the best way to go about it. Up until that time, you can believe what you believe."
------------------------------
Q&A Session:
[110.52]
[Question about viral DNA integration into human genome.]
[111.15]
Alter:
"It's a wonderful question;
It's very difficult; it's kind of like looking for a needle in a haystack. It can be done.
People who looked for Beta retroviruses; it took them four years to find an integration site.
You have no idea where in the genome it might be and you're looking for a low titre; [a] small amount of total genome.
I'm not a molecular biologist, but i've been told it's very difficult.
We are working with a group in Canada who are trying to do it, but they don't anticipate a quick answer.
But that would be a very important thing."
[112.25]
Lo:
"For the prostate, from the tumor, they've been published, and they are flanked by the human sequence.
But even that, people do challenge that: 'is that truly from a clinical sample, or not, or a contaminant from somewhere?'
Again that is based on the PCR product, and you do the sequence."
---------------------------
Lo suggests that the discrepancies in testing might be due to the low titres.
---------------------------
[116.21]
Alter:
[Talking about CFS, referring to it as a biomedical illness]:
...
"There are similarities in an addisonian patient [referring to Addison's disease],
there's similarities in a chronic infectious mononucleosis patient.
It [CFS] smacks of, if not a viral etiology, some kind of neuroendocrine abnormality.
Something's in there that's doing something.
That's your final thing:
There's something doing something!"
----------------------------
Details from Slide 17:
Mikovits tested 50 patients from England, and found 48% positive for XMRV [by PCR?], 63% positive for XMRV antibody, and tested 78% positive in DERSE culture assay. Antibody found in 4% of controls.
Hanson tested 20 patients from New York State, and found 55% positive for polytropic sequences only (No XMRV sequences found). (This is the Maureen Hanson and Dr Bell study.) [This information doesn't match up with the abstract published at the 1st International Workshop on XMRV which says that Hanson has detected XMRV sequences.] [ETA: Now there's another abstract available that confirms that Hanson has detected p-MLV-like sequences]
----------------------------
http://videocast.nih.gov/Summary.asp?File=16477
Jemal
Senior Member
- Messages
- 1,031
Thanks Bob! Most of Lo/Alter's stuff still seems to apply to the current contamination standoff.
Bob
Senior Member
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- 16,455
- Location
- England (south coast)
Yes, that's what I was thinking, Jemal. That's what made me go back and have a look at what they said in this presentation.