Brian T Foley,
Los Alamos National Lab, Los Alamos NM 87545 USA
Send response to journal:
Re: Politics vs. science.
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
(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
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:
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
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.