Without the “HIV” genome (poly (A)-RNA banding at 1.16 g/ml) there can be no probes or molecular clones 1 July 2004
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Eleni Papadopulos-Elelopulos,
Biophysicist
Department of Medical Physics, Royal Perth Hospital, Western Australia, 6001,
Valendar F Turner, John Papadimitriou, Barry Page, David Causer, Helman Alfonso, Sam Mhlongo, Todd Miller, Christian Fiala

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Re: Without the “HIV” genome (poly (A)-RNA banding at 1.16 g/ml) there can be no probes or molecular clones

Without the “HIV” genome (poly (A)-RNA banding at 1.16 g/ml) there can be no probes or molecular clones

 

In his rapid response:  "Re: Re: More on the photo", 25th June, Brian Foley wrote:  "The Perth Group probably does contain members who know enough molecular biology to know the difference between a probe and a clone, but they are not coming forward in this discussion".

 

When we put our questions (Q4 and Q9), regarding Lamda HXB-2, the questions were preceded with an explanation of their context including quotes from the relevant papers. (see our rapid response “Twelve simple questions to Brian Foley” 31st May 2004).   

In his rapid response “Re: Twelve simple questions to Brian Foley” 2nd June 2004, Brian Foley wrote: “The Perth group wrote:
“…
Q4. Since the "proviral DNA" was obtained by using the cDNA of the poly(A)-RNA as a probe doesn’t this mean that the "proviral DNA" is a transcript (reverse) of the poly(A)-RNA and thus that its ultimate origin is poly(A)-RNA.

Q9. Since lHXB-2 was obtained using the cDNA of poly(A)-RNA as a probe does it not mean that lHXB-2 is a transcript (reverse) of the poly(A)-RNA and thus that the ultimate origin of lHXB-2 is the poly(A)-RNA from the 1.16g/ml band.
…”

If the Perth group does not understand the difference between a lambda phage genomic library and the probe used to probe it, they should take a class in molecular genetics before attempting to convince the world that they know more about how virology should be done, than the virologists who are working in the field.”

 

 

Here Brian Foley has accused us of being ignorant and then proceeded to give us a rudimentary lesson in retrovirology.   We subsequently pointed to additional information and rephrased our questions. (see our rapid response “New and repeated questions and requests to Brian Foley” 8th June 2004).

 

 

In his rapid response “Re: New and repeated questions and requests to Brian Foley” 8th June 2004, Brian Foley wrote: “The Perth group wrote:
“…
Q4. Is It true that the "proviral DNA" is a transcript (reverse) of a poly(A)-RNA identical to the poly(A)-RNA which, in sucrose gradients, bands at the density of 1.16g/ml and thus that its ultimate origin is this RNA.
…”

No. Proviral DNA is nearly identical to viral RNA, but because of the error rate of the reverse transcription process, nearly all integrated proviral genomes contain one or more mutations relative to the RNA genome from which they were reverse transcribed. In addition to this, the viral particles contain two RNA genomes, sometimes derived from two different proviruses, and the reverse transcriptase can and does switch templates between these two genomes during the reverse transcription process. Thus any proviral genome can be a recombinant between two different viral RNAs.

Proviral genomes are similar, most often very highly similar, such as 99.98% identical, to RNA genomes from the same isolate of virus, but they are almost never “identical”.”

 

Brian Foley either deliberately or for some other reasons “muddyed the waters” and did not answer our question.   We are not asking if the proviral DNA is identical to the poly(A)-RNA which, in sucrose gradients, bands at the density of 1.16g/ml.   The question was if the poly(A)-RNA from which the proviral DNA was obtained was the same as the poly(A)-RNA (the “HIV-1” genome) which, in sucrose gradients, bands at the density of 1.16gm/ml.   We would be grateful if Brian Foley would answer our question regarding the two poly(A)-RNAs, that is, the “HIV-1” genome which bands at 1.16g/ml and the “HIV-1” genome from which the proviral DNA was obtained.  Are these two poly(A)-RNAs the same?

 

 

Brian Foley wrote: “The Perth group wrote:
“…
Q9. Is it true that the molecular clones, Lambda HXB-2 and Lambda HXB-3 were obtained from the “HIV” provirus and thus that the ultimate origin of Lambda HXB-2 is a poly(A)-RNA identical to the poly(A)-RNA from the 1.16g/ml band.
…”

We can never know the answer to that question. Robert Gallo’s lab and Luc Montagnier’s lab both ended up creating molecular clones of HIV-1 M group subtype B virus that were so nearly identical to each other as to be indicative of being derived from the very same patient. During the investigation as to how that could have possibly occurred, many other clones were made from the patients known as “LAI” and “BRU”. None of them were 100% identical to Lambda-HXB-2, Lamda-HXB-3, Lambda-BH8 (all from Gallo’s lab) or the LAV-1(BRU) clone (from Montagnier’s lab), but all of them were far more similar to all of those clones than to the clones of HIV-1 M group subtype B obtained from any other patient.”

 

It is a pity that Brian Foley again sidesteps the question and gives us an irrelevant oration.   The question has nothing to do with Luc Montagnier’s work.   The two clones were obtained by Gallo and his associates, not by Montagnier.   Most importantly, we did not ask from which patient(s) the clones originated from.   The questions are:

 

1.      Was the ultimate origin of the two clones the “HIV provirus”?

2.      Was the provirus obtained from a poly(A)-RNA that was the same as the poly(A)-RNA (the “HIV-1” genome) which, in sucrose gradients, banded at 1.16g/ml?

Competing interests: None declared