Politics vs. science. 31 July 2003
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Brian T Foley,
HIV Researcher
Los Alamos National Lab, Los Alamos NM 87545 USA

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Re: Politics vs. science.

It is becoming evident that the Perth group is not questioning the data on HIV-1 and HIV-2 but instead seeking to mislead the world with disinformation about these viruses. It seemed for some time that they may be just ignorant of how viruses are studied, and unaware that HIV-1 and HIV-2 have been more thoroughly studied and characterized than almost any other virus known to man.

1) They refer to two strains of poliomyeltis virus with just 10 single base mutations between them as being different strains, one pathogenic and the other not. At the same time, they try to claim that HIV researchers would call viruses with 40% DNA changes "identical". In fact the two viruses referred to with the 40% distance are HIV-1 M group subtype B and HIV-1 O group virus MVP-5180:
(10) Gurtler LG, Hauser PH, Eberle J, von Brunn A, Knapp S, Zekeng L, Tsague JM, Kaptue L.
A new subtype of human immunodeficiency virus type 1 (MVP-5180) from Cameroon.
(1994) J Virol 68:1581-1585

Being the experts that they are, advising the South African Government on AIDS for example, the Perth Group is clearly aware that HIV-1 M group viruses are causing the global pandemic, whereas the HIV-1 O group viruses remain more limited in distribution. In fact the first detected case of HIV-1 O group in the USA caused a large stir in 1996-1997:
Identification of HIV-1 group O infection--Los Angeles county, California, 1996.
MMWR Morb Mortal Wkly Rep. 1996 Jul 5;45(26):561-5.
because the HIV-1 ELISA and western blot test kit reagents were designed and FDA certified only for detection of HIV-1 M group viruses. Intrasubtype genetic distances for HIV-1 M group viruses are far less than the 40% distances typical between the M, N and O groups. The Perth group is very much aware that no HIV researcher would ever call a HIV-1 O group virus "Identical" to an HIV-1 M group virus.
The HIV-1 M group and O group viruses do indeed look identical to each other when viewed by electron microscopy. This is one of the reasons why electron microscopy is not the best method of studying viruses.

2) The Perth group admits that DNA sequencing is needed in all other areas of virology, such as in studying the Sabin vs. wild type polioviruses, or when noticing that a particular strain of influenza virus displays a pattern of evolution with a temporal skip, a lack of evolution over a period of time. Yet at the same time they pretend that the very same methods of research, which have lead to extraordinary discoveries about each of the 9 genes in the HIV-1 genome (Gag, Pol Env, Vif, Vpr, Vpu, Nef, Tat, Rev) are all to be dismissed.

3) The Perth group has stated "... the genomes of the most variable RNA viruses do not differ by more than 1%." When they themselves have discussed the genomes of Rous sarcoma virus and other retroviruses and they must therefor know that all RNA viruses including retroviruses have incredibly diverse genomes with rates of evolution close to 10 to the seventh power faster than the rate of evolution of mammalian DNA. They have even cited papers which discuss the rate of evolution of the human influenza virus, so they should be aware that HIV-1 and HIV-2 evolve at close to the same rate as all other exogenous viruses with RNA genomes.

Anyone can take an RNA virus gene sequence such as:
gtgtcgtgca gcctccagga ccccccctcc cgggagagcc atagtggtct gcggaaccgg tgagtacacc ggaattgccg ggaagactgg gtcctttctt ggataaaacc cactctatgc ccggagattt gggcgtgccc ccgcaagact gctagccgag tagcgttggg ttgcgaaagg ccttgtggta ctgcctgata gggtgcttgc gagtgccccg ggaggtctcg tagaccgtgc accatgagca cgaatcctaa acctcaaaga ctaaccaaaa gaaacaccaa ccgccgccca cagaacgtta agttcccggg cggcggccag atcgttggcg gggtgtactt gttgccgcgc aggggcccca gggtgggtgt gcgcgcgacg aggaagacct cggagcggtc ccaaccgcgt gggaggcgcc agcctattcc caaggctagg cccaccaccg gcaggtcctg gcaacagccg ggatatccat ggccccttta tggtaacgag ggccttgggt gggcagggtg gctcctgtct ccccagggtt ctcgcccgtc ttggggcccc accgaccccc ggcgtaggtc gcgcaacttg ggtaaggtca tcgataccct cacgtgcggc ttcgccgatc tcatggggta catacccgtc gttggcggcc cagtgggcgg ccttgccagg gctttggcgc atggcgttag agtcctggag gacggggtaa actatgcaac agggaatctt cccggttgct ccttttctat cttcctactt gctcttttct cttgcatcac catccctgcc tctgctgcgg aggtcagaaa cctatccacc tcctacatgg tgacgaacga ttgctcgaac agcagcatca cctggcagat gacagaagca gttctgcact tgccgggttg cgtcccatgt gagaaggttg gcaatggctc cagatgctgg atagccttaa caccaaacat tgcggtgtcg cgccctggcg cgctcactgg cagccttcgg actcacatag acaccatagt gatgtccgct gcaatctgct ctgccctgca tgtgggggac ttctgtggcg cgggtttaat agcttctcaa gcttttatag tctcgcctca gcaccaccag ttcgtccagg actgcaactg ttccctctat ccaggccacg tgagtggtca tcgtatggcc tgggatatga tgatgaactg gtcccccact gtgactatga tcacagcgta cgccttacgc atcccaaacc tcgtgattga ggtgatagct ggggggcatt ggggcgtgct gtttggtctc gctctcttcg gcgtgcaggg tgcctggctg aaggtagtga tcatcctcct catggtagcc ggagttgaga actccaccac cctcaccggt acagttgctg ggcggaacgc acacggcctc actgccctct ttacacctgg ggctaagcag aatatccaac ttatcaactc caatggtagc tggcacatca atcgcacggc tctgaattgc aacgactctt tgcaaacggg gttcattgcg tctctttttt acaccaataa gatcgatgcc tctggatgcc ccgagcgcat tgcctcgtgc cgttccctag actactttcg ggagggctgg ggctccttgg agtatgagga aaatgtcatc aattcacaag acatgagacc ctactgctgg cattacccgc cccgccagtg cggaatagtg ccagccactt ctgtgtgcgg cccagt

and send it to a BLAST search at:
http://www.ncbi.nlm.nih.gov/BLAST/

and find that there are tens of thousands of examples of RNA viruses that differ by far more than 1%.
I would not even know how to characterize which virus is "the most variable", because some viruses such as HIV-1 M group viruses have nomenclature committees that help to define which groups of viruses get the same names (such as HIV-1 M group subtype B) whereas other viruses are all lumped together under one name (such as feline immunodeficiency virus from lions or housecats or north American cougars).

If the Perth group, or anyone else is interested in learing about HIV-1, HIV-2 or other lentiviruses, I would be happy to help them learn. But people who only seek to spread disinformation about AIDS deserve no further response from me.

Competing interests:   None declared