Re: HIV genome, clones and sequences 24 July 2003
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Christopher J Noble,
postdoctoral fellow
Bern, Switzerland

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Re: Re: HIV genome, clones and sequences

Eleni Papadopulos-Eleopulos writes, 'The difference between the sequences of the chimpanzee genome and the human genome is less than 2%, while the genomes of RNA viruses do not differ by more than 1% and even this 1% sequence differences are considered to represent "extreme variability".'

Even in influenza A, one of the examples of RNA viruses given by Papadopulos-Eleopulos, considerably more variation than 1% is seen. (1)

Papadopulos-Eleopulos continues, 'For example, "The type 3 Sabin poliovirus vaccine differed from its neurovirulent progenitor at only 10 nucleotide positions after 53 in vitro and 21 in vivo passages in monkey tissues.'

This quote is again deceptive. Poliovirus has an extremely high mutation rate of approximately 10-4 to 10-5 subtsitutions per site per replication. Papadopulos-Eleopulos apparently does not understand the difference between mutation rates and evolution rates. The latter is highly dependent on the selective conditions. Sabin was trying to produce a strain with less replication fitness. This is clearly not the normal selective conditions as can be seen with unfortunate results in cases of vaccine-related paralytic poliomyelitis. In some individuals more than 100 genetic changes can be seen during a single passage of the Sabin strain. (2)

Papadopulos-Eleopulos continues, 'In other words, if a mere difference of less than 2% leads to the appearance of two totally different objects (namely, humans and chimpanzees), how then can differences of up to 40% lead to the appearance of the same object (namely "HIV")? Indeed, if the sequence variation was the only fact one knew about these nucleic acids sequences the only conclusion one could come to is they are not the nucleic acids of a retrovirus or indeed any virus. Or, as Peter Duesberg has so aptly stated, "there is a range, a small range, in which you can mutate around without too much penalty, but as soon as you exceed it you are gone, and you are not HIV any longer, or a human any longer...then you are either dead or you are a monkey, or what have you". '

I find the comparison between viruses and primates to be totally artificial and deliberately deceptive. A better comparison would be with the human papillomavirus (HPV) which shares many phylogenetic similarities with HIV including a large divergence of up to 50% between isolates. (3)

(1) Xu X, Cox NJ, Bender CA, Regnery HL, Shaw MW. Virology. 224 (1996) 175-83. http://www.ncbi.nlm.nih.gov:80/entrez/ query.fcgi?cmd=Retrieve&db=Pub Med&list_uids=8862412&dopt=Abstract

(2) Kew OM, Nottay BK, Hatch MH, Nakano JH, Obijeski JF. J Gen Virol. 56 (1981) 337-47 http://www.ncbi.nlm.nih.gov:80/entrez/ query.fcgi?cmd=Retrieve&db=Pub Med&list_uids=6273502&dopt=Abstract

(3) Halpern AL, J Clin Virol. 19 (2000) 43-56 http://www.ncbi.nlm.nih.gov:80/entrez/ query.fcgi?cmd=Retrieve&db=Pub Med&list_uids=11091147&dopt=Abstract

Competing interests:   None declared