Re: A paraphrased request and a question to Brian Foley 14 May 2004
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Brian T Foley,
HIV Researcher
Los Alamos National Lab, Los Alamos, NM 87545

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Re: Re: A paraphrased request and a question to Brian Foley

The Perth group wrote:
“…
Our request to Brian Foley is: Is it true that

(a) In 1983/85 Montagnier’s and Gallo’s groups claimed to have purified “HIV” and from this “purified” “HIV” to have obtained the “HIV” poly- (A) RNA, that is, the “HIV” genome (and thereby some of the best known and still most often used “HIV” molecular clones). But neither group published electron micrographs (EM) to confirm their purification;

(b) In 1997 Montagnier admitted that his group did not purify “HIV” and in his view neither did Gallo’s group. In fact Montagnier stated that they did not publish any EM because in the “purified” “HIV” they could not find any particles “with the morphology typical of retroviruses”;

(c) In the only EM of “purified” “HIV” published to date the vast majority of the material is microvesicles, that is, cellular fragments amongst which there are a small number of particles which the authors claim to be “HIV” but none of which has all the morphological characteristics attributed to “HIV”.

Yes or no?
…”

No; maybe but not relevant; and no:

(a) In the 1983 to 1985 time period Montagnier’s and Gallo’s groups published dozens of papers, all of which are relevant to the discovery of group of viruses now known as the HIV-1 M group subtype B viruses. This subtype of the HIV-1 M group is the subtype responsible for the epidemics of AIDS that were first detected among homosexual men in New York and Los Angeles in 1981, and later detected among Haitian immigrants to the USA, homosexuals in other cities, IV drug users, hemophiliacs, spouses of hemophiliacs, sex partners of drug users, and transfusion recipients who had received blood from members of these “risk groups”.

In none of those 1983-1985 papers were claims made that the virus (referred to variously as HTLV-III, LAV, ARV, and other names) was “purified” to 100% purity. Such claims are not necessary for proper isolation, description and cloning of a virus, despite the delusions of the Perth group about this. If the Perth group has some evidence that a talk given at the Pasteur Institute in 1973 became the “law to end all laws” about how viruses must be studied, they should provide a transcript of that talk, and some evidence that at least one virus has ever been “isolated” by the protocol laid out in that talk. Otherwise, they should begin to admit that maybe the virologists of the world know more about virology than the Perth group does.

In the 1983-1985 time period Montagnier’s and Gallo’s groups did indeed publish electron micrographs of the virus. None of the EMs showed the virus was 100% pure, but that is not necessary. They usually published EMs of virus budding from cells and in the intercellular spaces rather than EMs virus harvested from the supernatant. They published Southern, northern and western blots of viral RNA, proviral DNA and viral proteins. They showed that antibodies reactive to multiple proteins produced by this virus were found in AIDS patients and a subset of people who were at very high risk for developing AIDS, but not found among the general population.

If the Perth group or anyone else thinks there was something wrong with any of this research, they should present a formal case, and not “debate” it on the internet and then attempt to inject it into the politics of South Africa without any formal examination of the evidence.

Only one of the dozens of molecular clones of the HIV-1 M group subtype B viruses described in the 1983-1985 time period eventually became proven to be an infectious molecular clone, and went on to become one of the best known infectious molecular clones of subtype B. That clone is Lambda-HXB-2, sequenced in 1985 by Ratner et al. [1] and shown to be infectious by Fisher in 1986 [2].

(b) I have read one report, parroted to dozens of different web sites on the internet, stating that Montagnier claimed not to have “purified” the virus. However, the statements he made are essentially identical to what I have been attempting to inform the Perth group for the past several years; that “purification” to 100% purity is NOT a requirement for the proper study of a virus. I am not sure what Montagnier meant, if he stated that the material in the 1.16 g/ml bands his Lab produced contained no “particles with the morphology typical of retroviruses”. He may have only meant that he found the cone-shaped cores of this lentivirus to be unique. Another possibility is that something when wrong between collecting the band and preparing microscope slides, such that the viral particles were disrupted. Any comments on that should be made by the workers in Montagnier’s lab who did the work, and not by those of us who can only speculate on the dozens of possibilities.

(c) Although the Perth group continually attempts to mislead people into believing that only one or a very few EMs of HIV exist, there have actually been several electron micrographs of HIV-1 obtained from 1.16 g/ml bands [3,4 for examples]. There have been dozens more EMs of HIV-1 pelleted through a sucrose cushion and resuspended [5,6,7 for examples]. None of these shows 100% pure virus particles. The virus particles in those EMs look like HIV-1 or any other lentivirus to me. Whether or not they contain “all” of the morphological characteristics attributed to HIV-1 depends on what list of characteristics you are referring to. I would not expect the envelope glycoprotein spikes often seen on virus as it is budding from cells [8,9,10 for examples] to always survive untracentifugation, for example.

In the center panel of Figure 3 of [4] which is stated to be virus from the HIV-1(MN)/H9 Clone 4 preparation with a p24-capsid to human HLA ratio of 4.61 to 1 as shown in table 1, there are many more viral particles than cellular vesicles, so I would claim that the Perth group is attempting to mislead people when they state that in the only EM of purified HIV ever published to date, the vast majority of the material is microvesicles.

If anyone has any doubt that these viral particles are directly encoded by the infectious molecular clones that they are claimed to be encoded by, papers which describe mutant morphologies linked to mutated genomes should help to convince them [11,12 for examples]. Likewise there are many studies which show that cloned viruses shares antigens with uncloned viruses [13,14 for examples].

The Perth group wrote:
“…
Let us paraphrase our request: Would Brian Foley please give us a summary of the evidence (not just the title) of a study as well as the evidence from a few confirmatory studies where the existence of an “infectious molecular clone” (as defined by Brian Foley) of “HIV-1” has been proven.
…”

I have repeatedly told the Perth group that I do not consider it my job to spoon feed them everything they need to know to understand HIV. If they cannot read and understand the papers I have pointed out to them, there is no reason for them to trust my interpretation of those papers. The whole point of this discussion on the politics of AIDS in South Africa is not to teach the Perth group or other denialists that they are wrong; it is to point out that finding the “truth” about a technical subject requires a bit of homework. If one person says HIV has not been properly isolated and another (or 50,000 others) say that is has, one side or the other must not be telling the truth. Asking each of them to repeat their assertions is no substitute for looking at the raw data.

This is the last time that I will attempt to appease the Perth group in this way. As the Perth group has stated; “their definition” of an infectious molecular clone is:
“… by infectious molecular clone of a virus is meant the introduction of the viral genome (molecular clone) into suitable cells leading to the appearance of virus particles identical (regarding both appearance and composition) to the ones from which the genome was obtained”.

I have previously cited more than 50 papers which describe clones meeting those criteria and more, but I will go through one of them [14] step-by-step as requested by the Perth group. In this paper the authors describe the creation and preliminary analyses of an infectious molecular clone of a HIV-1 M group subtype C isolate named 93IN101, isolated in India in 1993 from a cohort of individuals described in [15], and deposited in the NIH AIDS Reagent Repository [16]. The infectious molecular clone was named plasmid-Indie-C1. Virions produced from the cloned virus are shown in figure 2B. Virions produced from the pIndie-C1 infectious molecular clone were proven to infect cells by using the CCR5 coreceptor, and not the CXCR4 coreceptor as shown by their ability to infect the MAGIC5E cell line (which expresses the CCR5 coreceptor) but not the parental MAGI cell line (which does not express the CCR5 coreceptor). Production of viral proteins from cells infected with virus particles derived from the pIndie-C1 infectious molecular clone was similar to the production of viral proteins produced by another, well-characterized infectious molecular clones of HIV-1 (pNL43 as shown in figure 2D).

Cells transfected with the pIndie-C1 plasmid showed marked cytopathic effects (figure 2A). The gp120 Envelope protein produced by the pIndie-C1 clone reacted more strongly with sera from individuals infected with HIV-1 M group subtype C viruses (figure 3A lane d, bottom two blots) than with sera from individuals infected with HIV-1 M group subtype B viruses (figure 3A lane d, top two blots), whereas gp120 produced from subtype B infectious molecular clones pNL43 and pSF2 reacted more strongly with the sera from the individuals infected with subtype B (figure 3A lanes b and c). No reactivity was detected from the uninfected control cells (figure 3A lane a).

As shown in figure 3B, top frame (note that the lanes were loaded in a different order; a-control, b-pNL43, c-pSF2, d-pIndie-C1), the 4H4 monoclonal antibody, which recognizes the Nef epitope shown below [17], reacted strongly with the Nef proteins produced from the pIndie-C1 and pNL43 clones, but not with the pSF2 clone, as might be expected by the many differences in this region of the pSF2 epitope:

4H4 Epitope            MGGKWSKSSVVGWPTVRERMRRAPTVRERMRRAEPAADGVGAA
C.93IN101              -------C-I----AI------..........-----E-----
B.pNL43                ----------I-----------..........------R----
B.pSF2                 ---.--....AIRERM-RAEP-..........----------V

As shown in figure 3B, bottom frame, a mixture of three monoclonal antibodies which each recognize a different Vpr epitope, reacted equally strongly with the Nef proteins produced by all three clones.

The complete genome of the virus inserted in the pIndie-C1 plasmid was sequenced and found to contain complete open reading frames for all HIV-1 proteins. The sequence, including both proviral LTRs was 9,680 bases in length, and was shown to be phylogenetically related to the genomic sequences obtained from other HIV-1 M group subtype C viral isolates from India as shown in figure 1.

REFERENCES:

1: Ratner L, Haseltine W, Patarca R, Livak KJ, Starcich B,
Josephs SF, Doran ER, Rafalski JA, Whitehorn EA,
Baumeister K, et al.
Complete nucleotide sequence of the AIDS virus, HTLV-III.
Nature. 1985 Jan 24-30;313(6000):277-84.
PMID: 2578615

2: Fisher AG, Collalti E, Ratner L, Gallo RC, Wong-Staal F.
A molecular clone of HTLV-III with biological activity.
Nature. 1985 Jul 18-24;316(6025):262-5.
PMID: 2410792

3: Gluschankof P, Mondor I, Gelderblom HR, Sattentau QJ.
Cell membrane vesicles are a major contaminant of
gradient-enriched human immunodeficiency virus type-1
preparations.
Virology. 1997 Mar 31;230(1):125-33.
PMID: 9126268

4: Bess JW Jr, Gorelick RJ, Bosche WJ, Henderson LE, Arthur LO.
Microvesicles are a source of contaminating cellular proteins
found in purified HIV-1 preparations.
Virology. 1997 Mar 31;230(1):134-44.
PMID: 9126269

5: Kuznetsov YG, Victoria JG, Robinson WE Jr, McPherson A.
Atomic force microscopy investigation of human
immunodeficiency virus (HIV) and HIV-infected lymphocytes.
J Virol. 2003 Nov;77(22):11896-909.
PMID: 14581526

6: Briggs JA, Wilk T, Welker R, Krausslich HG, Fuller SD.
Structural organization of authentic, mature HIV-1
virions and cores.
EMBO J. 2003 Apr 1;22(7):1707-15.
PMID: 12660176

7: Yu X, Matsuda Z, Yu QC, Lee TH, Essex M
Vpx of simian immunodeficiency virus is localized primarily
outside the virus core in mature virions.
J Virol. 1993 Jul;67(7):4386-90.
PMID: 8510227

8: http://www.hiv.lanl.gov/content/hiv-db/REVIEWS/Gelderblom.html

9: Zhu P, Chertova E, Bess J Jr, Lifson JD, Arthur LO, Liu J,
Taylor KA, Roux KH.
Electron tomography analysis of envelope glycoprotein trimers
on HIV and simian immunodeficiency virus virions.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15812-7.
PMID: 14668432

10: McKeating JA, McKnight A, Moore JP.
Differential loss of envelope glycoprotein gp120 from virions
of human immunodeficiency virus type 1 isolates: effects on
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J Virol. 1991 Feb;65(2):852-60.
PMID: 1898972

11: Tang S, Murakami T, Agresta BE, Campbell S, Freed EO,
Levin JG.
Human immunodeficiency virus type 1 N-terminal capsid
mutants that exhibit aberrant core morphology and are
blocked in initiation of reverse transcription in
infected cells.
J Virol. 2001 Oct;75(19):9357-66.
PMID: 11533199

12: Reicin AS, Ohagen A, Yin L, Hoglund S, Goff SP.
The role of Gag in human immunodeficiency virus type
1 virion morphogenesis and early steps of the viral life
cycle.
J Virol. 1996 Dec;70(12):8645-52.
PMID: 8970990

13: Meerloo T, Parmentier HK, Osterhaus AD, Goudsmit J,
Schuurman HJ.
Modulation of cell surface molecules during HIV-1 infection
of H9 cells. An immunoelectron microscopic study.
AIDS. 1992 Oct;6(10):1105-16.
PMID: 1466841

14: Mochizuki N, Otsuka N, Matsuo K, Shiino T, Kojima A,
Kurata T, Sakai K, Yamamoto N, Isomura S, Dhole TN,
Takebe Y, Matsuda M, Tatsumi M.
An infectious DNA clone of HIV type 1 subtype C.
AIDS Res Hum Retroviruses. 1999 Sep 20;15(14):1321-4.
PMID: 10505681

15: Brookmeyer R, Mehendale SM, Pelz RK, Shepherd ME,
Quinn T, Rodrigues JJ, Bollinger RC.
Estimating the rate of occurrence of new HIV infections
using serial prevalence surveys: the epidemic in India.
AIDS. 1996 Jul;10(8):924-5.
PMID: 8828

16: http://www.aidsreagent.org/ specifically: http://www.aidsreagent.org/ecommerce/de fault.cfm?Action=Detail&ItemID=299426

17: http://www.hiv.lanl.gov/content/immunology/ab_search?action=results;ab_id=906

Competing interests: None declared