The Politics of AIDS in South Africa: 6 November 2003
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Brian T Foley,
HIV Researcher
Los Alamos National Lab, Los Alamos, NM 87545

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Re: The Politics of AIDS in South Africa:

On Nov 4th, the Perth group wrote:
”... Would Christopher Noble please tell us what evidence “databases of genetic sequences and phylogenetic trees” give us regarding the existence of a virus? We have always thought that to prove the existence of the “HIV” virus, you have to isolate/purify it and then proceed to define its genome and genomic sequences and its proteins. Otherwise, how do you know that the genomic sequences are those of “HIV” and the proteins are coded by these sequences? It is obvious that you cannot start with impure material to define the origin of the genome. If Christopher Noble has another way would he please tell us what it is?
...”

We have repeatedly told you that you thought wrong. No organism has ever been “purified” 100%, no virus has ever been “isolated” by the full criteria which you have designed to be impossible. The study of microorganisms has never involved 100% “purity” and “isolation” from all other living and non-living matter, and it never will. Separation techniques, such as passing a culture supernatant through a series of filters with progressively smaller pore sizes tells us if a pathogen is cell-sized (fungi, protist, cancer cell, etc.) bacteria-sized, or virus-sized. It is not necessary to show that the filtrate is 100% “pure”, only that the pathogen is in the filtrate. After size is determined, other methods such as serology and genomic sequencing can be employed to determine which component found in the infectious filtrate is the pathogen.

It was very clear by 1982, from conventional epidemiology, such as contact tracing of sex partners, needle sharing partners and blood donors, that AIDS was caused by a pathogen that was transmitted only by close contact and not by casual contact. It remains clear today that AIDS is not caused solely by environmental factors or toxins or malnutrition, even if other health problems somewhat similar to AIDS are sometimes caused by such factors (1-23).

As to the utility of databases; if a freshman high-school student is asked to write an original work of fiction and his or her essay begins with this text:
“Call me Ishmael. Some years ago - never mind how long precisely - having little or no money in my purse, and nothing particular to interest me on shore, I thought I would sail about a little and see the watery part of the world.”
You do not have to “isolate” the original draft text of Herman Melville’s Moby Dick and analyze the handwriting of that draft to prove that Herman Melville and not your freshman student, deserves the true credit for this text. If you simply go to GOOGLE and search for “and nothing particular to interest me on shore” you immediately find that this text is most likely not be the original work of the freshman, despite what he or she may argue about an infinite number of monkeys typing for an infinite amount of time... A very little further analysis of the student's paper and Melville's Moby Dick, will be needed to support your initial analysis.

When a DNA sequence is determined from an organism, now that the DNA sequences of tens of thousands of organisms have been depositied in electronic databases, it is usually trivial to determine what type of organism the new DNA sequence is derived from. This is why it took only a few weeks of research, once samples began to be analyzed, to determine that the Sin nombre hantavirus was the cause of an unexplained group of deaths in the southwest USA. It is also the reason why it also took only weeks to determine that a previously undiscovered coronavirus was the cause of SARS. No coronavirus and no hantavirus has ever been 100% “purified” by any procedure similar to what you have described. Not only is your full procedure not necessary, it is impossible. Serology and DNA sequencing alone are often sufficient to get started until complete infectious molecular clones or other materials become available for confirmatory work.

The retroviruses and other viruses have been extensively studied since the early 1900s, long before either DNA sequencing or gradient density ultracentrifugation were discovered. The tools and techniques used to study viruses continue to evolve over time as new techniques are found to be superior to older techniques. Many techniques, such as serology have not been replaced, but only improved upon. The 1984 Nobel Prize in physiology or medicine for the techniques related to the production of monoclonal antibodies is one example of a major improvement.

The Perth group has been repeatedly informed that they are deluded in their beliefs about the techniques and procedures used to study viruses. See for example: Micheal Coon, August 2000 Robin Weiss, 1999

Yet they continue to repeat the same rhetoric, as if repetition will make it more true. The subject of these rapid responses is not the “isolation” of HIV, but the “The politics of AIDS in South Africa: beyond the controversies”. This non peer reviewed exchange cannot and will not have any impact whatsoever on viral research, nor setting ground rules for genomics. This discussion can only have a small impact on uncovering the thinking that has lead the Perth group to attempt to misinform the government of South Africa about what it should do to mitigate the AIDS epidemic in that country. The Perth groups’ use of quotes about influenza and polio viruses, shows that they are not ignorant of all aspects of virology. Instead they are quite clever about selecting tidbits of information in an attempt to support their ideology. It is my opinion that the South African government should have set rules for the discussion of HIV and AIDS by their panel (such as rules stipulationg that the participants tell the truth, the whole truth and nothing but the truth) and established penalties for breaking those rules. Without any such rules and penalties, in the South African panel deiscussion or here in Rapid Responses, there can be no expectation of a credible or fair outcome. This does not mean that such panels and discussions are worthless, but it does place some constraints on their usefulness.

For my own part in this, I feel I must clear up at least one point that I was incorrect or misleading on above:
The Bess et al result of a ratio of 150:1 was indeed from a cell line that does not express the HLA DR gene, the best result with an HLA DR-producing cell reported by Bess was 119:1. But it should also be noted that the ratio is based on the sum of both HLA DR and Beta 2 microglobulin, and not just HLA DR as the header of the figure (p24 to HLA ratio) might imply. None of that has anything to do with "proof" of the existence of HIV, it only shows that reagents made from density gradient ultracentifugation and fractionation contain human proteins both from the cellular envelope (which surrounds all enveloped viruses) and from extra-viral material in the form of cellular vessicles and debris. For that reason, other methods of purification of viral proteins, such as cloning viral genes for protein production in bacteria, may sometimes be necessary or desirable.

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[No authors listed]
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PMID: 6819440

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PMID: 6819439

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N Engl J Med. 1982 Dec 9;307(24):1521-2.
PMID: 6983029

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PMID: 6817061

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[No authors listed]
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22) Severe acquired immunodeficiency in male homosexuals, manifested by chronic perianal ulcerative herpes simplex lesions.
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Competing interests: None declared