Christopher J Noble,
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John Kirkham writes, "The Halpern paper he cites (1) does indeed say 50% although the data given is for all papilloma viruses, not just human papilloma viruses amongst themselves. This 50% figure is based on the MY09/11 segment of L1 not whole papilloma virus genomes."
The paper in question also states, "Second, viruses infecting humans are found in several separate regions of the tree, intermingled with viruses infecting animals."
The human papilloma viruses are spread throughout the phylogenetic tree and are as distantly related to each other as they are to the animal papilloma viruses. Look at figure 2. HPV41 and HPV13 (both human papilloma viruses) are as divergent as any other pair.
The paper also states, " First, the most divergent isolates differ from one another by as much as 50% on the nucleotide level, even in the most conserved regions of the genome."
The phylogenetic tree in figure 2 is indeed based on the MY09/11 segment of the L1 gene. The author, however, clearly states that the 50% figure relates to even the most conserved regions of the genome not just the L1 gene.
John Kirkham further states, "The Halpern paper he cites does not support his contention that the genetic variability of HPV is the same as that of HIV as the following extracts from page 46 show, added comments are in square brackets:"
I have never claimed that the mutation rate or evolution rate of HPV is similar to HIV. HIV is a retrovirus, HPV is a DNA virus. HPV has a much slower evolution rate than HIV.
Eleni Papadopulos-Eleopulos previously wrote, "Our interest is not in the evolution rates as such, but the genomic differences at a given time. In this regard, the differences in the RNA viruses genomes are significantly less than in the "HIV" genome."
This is exactly the point that I am addressing here. Please do not attempt to sidetrack the discussion. You appear to be desperately trying to find some way in which Eleni Papadopulos-Eleopulos can be corrrect. The simple truth is that she is wrong.
RNA viruses such as influenza A and even DNA viruses such as HPV show much more genetic diversity than 1%. The hemagglutin gene in different influenza A subtypes varies by an average of 50%. Isolates of HPV differ by as much as 50% at the nucleotide level even in highly conserved regions of the genome.
Nevertheless, the statements made by Eleni Papadopulos-Eleopulos have been uncritically accepted as fact by a large number of people, including yourself, since 1996.(2) The fact that she has consistently repeated these claims for the past 7 years during which she was advising the President of South Africa on matters including the HIV genome makes it extremely difficult for me to believe that it was an accidental mistake or purely due to ignorance.
They have been cited many times by self styled AIDS dissidents as evidence for the non-existence of HIV. Take this recent example from last week (3) 'Another important point: the so-called "isolates" of "SIV" are very genetically different from each other and from so-called isolates of "HIV", far beyond the 1% sequence difference that is considered to represent "extreme variability" in RNA viruses.'
Isn't it about time to admit that you and hundreds of other so-called AIDS dissidents have been misled by Eleni Papadopulos-Eleopulos?
(1) Halpern, A., Journal of Clinical Virology 19 (2000) 43-56
(2) http://www.virusmyth.net/aids/data/epreplypd.htm http://www.virusmyth.net/aids/perthgroup/geneva/slide27.htm
(3) http://groups.msn.com/aidsmythexposed/general.msn w?action=get_message&mview=1&ID_Message=2838
Competing interests: None declared