Author Topic: we are looking at the wrong retroviral model  (Read 1231 times)

Gerwyn

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we are looking at the wrong retroviral model
« on: May 20, 2011, 10:41:21 PM »
he apparent absence of HTLV-1 virions, mRNA or protein in circulating PBMCs in the majority of HTLV-1-infected people led to the conclusion that the proviral load of HTLV-1, which may reach more than 30% of peripheral blood mononuclear cells (PBMCs) and more than 50% of CD4+ cells, is maintained mainly by proliferation of provirus-containing cells (Cavrois et al., 1996; Etoh et al., 1997; Eiraku et al., 1998), rather than full-cycle virus replication mediated by reverse transcriptase. This conclusion was corroborated by the relative lack of sequence variation in HTLV-1 both within and between isolates (Daenke et al., 1990; Kinoshita et al., 1991; Komurian et al., 1991; Slattery et al., 1999), which appeared to exclude a major role of the error-prone reverse transcriptase in maintaining the proviral load.

assuming a hgrv is similar activating pmbc s prior to rna isolation to build up titre would be crucial to the success of pcr

cath

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Re: we are looking at the wrong retroviral model
« Reply #1 on: May 20, 2011, 11:16:11 PM »
So it is multiplying of infected cells.

Daughter cells will have the same provirus as the mother cell.

That means not much provirus variation.

Gerwyn

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Re: we are looking at the wrong retroviral model
« Reply #2 on: May 20, 2011, 11:52:16 PM »
So it is multiplying of infected cells.

Daughter cells will have the same provirus as the mother cell.

That means not much provirus variation.

yes

lulu

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Re: we are looking at the wrong retroviral model
« Reply #3 on: May 21, 2011, 12:40:08 AM »
Thank you Gerwyn.

cassea

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Re: we are looking at the wrong retroviral model
« Reply #4 on: May 21, 2011, 04:48:14 AM »
So if this was well known by virologists - a reasonable expectation since this study has been available since the 90's - that's another reason to say the denialists actions have been very deliberate when they try to use low variation as evidence of contamination

Tango

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Re: we are looking at the wrong retroviral model
« Reply #5 on: May 21, 2011, 03:11:47 PM »
So if this was well known by virologists - a reasonable expectation since this study has been available since the 90's - that's another reason to say the denialists actions have been very deliberate when they try to use low variation as evidence of contamination

All retrovirologist and virologists know the virus is human and associated with prostate cancer and ME.  I am tired of their stupid games and have no intention of letting them get away with crap.  There is a growing number of people who know this and will do the same.  So now they have realise it's over and start working to sort this mess out.
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

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anciendaze

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Re: we are looking at the wrong retroviral model
« Reply #6 on: May 22, 2011, 12:21:35 AM »
This is a reasonable model, and what is true of HTLV-1 is likely to be more true for HTLV-2, which appears better adapted to human hosts. 

This also has a bearing on failures to culture.  Unless you get lucky, you likely need dividing cells for viral replication.  This was not in the original Science paper, and is an easy target for critics.  (Check on the value of royalties for HIV test kits, and patent filings concerning XMRV tests, if you wonder about driving forces behind disputes over tests.  Priority is of more than academic interest.)

One caution, slow mutation after insertion says nothing about mutation of RNA prior to transcription.  I'm still betting on considerable variation from this cause.  I will also go out on a limb and say some endogenous sequences may be recent.  Molecular clock arguments don't consider mutation prior to insertion.  Arguments about descent from a common ancestor would need a better understanding of the population distribution of insertion sites than we have at present.  Horizontal transmission followed by insertion of similar sequences could look like descent from a common ancestor, if you don't know where it was inserted. 

We need better ways of recognizing virus without simply excluding anything that resembles an endogenous sequence. 

Gerwyn

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Re: we are looking at the wrong retroviral model
« Reply #7 on: May 22, 2011, 08:05:26 AM »
This is a reasonable model, and what is true of HTLV-1 is likely to be more true for HTLV-2, which appears better adapted to human hosts. 

This also has a bearing on failures to culture.  Unless you get lucky, you likely need dividing cells for viral replication.  This was not in the original Science paper, and is an easy target for critics.  (Check on the value of royalties for HIV test kits, and patent filings concerning XMRV tests, if you wonder about driving forces behind disputes over tests.  Priority is of more than academic interest.)

One caution, slow mutation after insertion says nothing about mutation of RNA prior to transcription.  I'm still betting on considerable variation from this cause.  I will also go out on a limb and say some endogenous sequences may be recent.  Molecular clock arguments don't consider mutation prior to insertion.  Arguments about descent from a common ancestor would need a better understanding of the population distribution of insertion sites than we have at present.  Horizontal transmission followed by insertion of similar sequences could look like descent from a common ancestor, if you don't know where it was inserted. 

We need better ways of recognizing virus without simply excluding anything that resembles an endogenous sequence.

They did actually activate the PMBCs prior to extraction for PCR .This is clearer in the virulence paper and as you would expect the reverse transcription PCR  using activated PMBcs as the source material delivered the headline figure of 67% of people with ME having detectable GAG sequences in the blood.When the use of culture was added to increase sensitivity then that figure rose to over 90%.Once again as would be expected if our model was accurate. mulvs tend to replicate in lymphoid tissues spleen thymus intestine lung brain and so on. This is where one would expect to see more variation generated by crossovers and so forth and evidence of dual infection if present.Time will tell.We need a lot more information about the life cycle of these viruses in humans
« Last Edit: May 22, 2011, 08:11:39 AM by Gerwyn »

anciendaze

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Re: we are looking at the wrong retroviral model
« Reply #8 on: May 22, 2011, 01:12:00 PM »
They did actually activate the PMBCs prior to extraction for PCR .This is clearer in the virulence paper and as you would expect the reverse transcription PCR  using activated PMBcs as the source material delivered the headline figure of 67% of people with ME having detectable GAG sequences in the blood.When the use of culture was added to increase sensitivity then that figure rose to over 90%...
I had been puzzled that so much controversy centered on the Science paper, when it was clear from later statements that work at WPI had moved on.  I believe the reason is that priority is central to patent claims, and ultimately a great deal of money.  If the authors deliberately withheld information needed to make the test work, then that is a trade secret which has no legal protection once secrecy is breached.  I'm afraid in this case, as in far too many others, things have become weird because attorneys are calling some of the shots. 

Since I learned of vulnerability of the virus to hypermutation, I have been working on the assumption the active virions show low replication fidelity, while the process of culturing selectively favors those with a particular genome.  This is the kind of two-stroke cycle which drives evolution by natural selection.  Latent provirus emerging unscathed by the battle with host defenses fits perfectly. 

My own hypothesis for origin says that these interactions are highly-evolved.  Laboratory accidents do not produce the constellation of adaptations this virus demonstrates.  The process likely began before vaccination was practiced.  What we saw in the 1980s was the emergence of a new strain infecting a new population with low innate immunity.  The species of mice most easily infected with XMRV tend to cluster in southeast Asia.  The area also has a number of primate species besides humans.  The Vietnam war produced a flood of refugees at the time the first cases were noticed in places like Boston and San Francisco.  This doesn't rule out sporadic earlier epidemics of limited scope as listed in the NEJM paper by Henderson and Shelokov in 1959. 

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Gerwyn

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Re: we are looking at the wrong retroviral model
« Reply #9 on: May 22, 2011, 02:37:42 PM »
I had been puzzled that so much controversy centered on the Science paper, when it was clear from later statements that work at WPI had moved on.  I believe the reason is that priority is central to patent claims, and ultimately a great deal of money.  If the authors deliberately withheld information needed to make the test work, then that is a trade secret which has no legal protection once secrecy is breached.  I'm afraid in this case, as in far too many others, things have become weird because attorneys are calling some of the shots. 

Since I learned of vulnerability of the virus to hypermutation, I have been working on the assumption the active virions show low replication fidelity, while the process of culturing selectively favors those with a particular genome.  This is the kind of two-stroke cycle which drives evolution by natural selection.  Latent provirus emerging unscathed by the battle with host defenses fits perfectly. 

My own hypothesis for origin says that these interactions are highly-evolved.  Laboratory accidents do not produce the constellation of adaptations this virus demonstrates.  The process likely began before vaccination was practiced.  What we saw in the 1980s was the emergence of a new strain infecting a new population with low innate immunity.  The species of mice most easily infected with XMRV tend to cluster in southeast Asia.  The area also has a number of primate species besides humans.  The Vietnam war produced a flood of refugees at the time the first cases were noticed in places like Boston and San Francisco.  This doesn't rule out sporadic earlier epidemics of limited scope as listed in the NEJM paper by Henderson and Shelokov in 1959. 

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hi ancientdase The supplimentary materials clearly indicate the activation of PMBCs by stating the reagents used. Any half competent virologist that reads the materials should realise it .I agree that the most likely origin is zoonosis