Christopher J Noble,
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Eleni Papadopulos-Eleopulos writes:
"Re: Politics vs. Science" (5 August 2003) "It is true that a difference of up to 40% exists between HIV-1 M group subtype B and HIV-1 O group and HIV-1 group N but also within the HIV-1 M group."
"How then does Brian Foley explain that differences of up to 40% as is the case in the "HIV" sequences (10) (11) represent the genome of one and the same object?"
The reference she provides for the claim that isolates of HIV-1 M group subtype B differ by up 40% from each other is a paper by Kozal et a (1).
In fact, this paper does not support this claim. http://www.ncbi.nlm.nih.gov:80/entrez/quer y.fcgi?cmd=Retrieve&db=Pub Med&list_uids=8673920&dopt=Abstract They definitely do not say that any two isolates differed from each other by 40%. What they say is "47.5% of the 99 amino acid positions varied".
The sequences used in the study are freely available from the Entrez Nucleotide database. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nu cleotide&cmd=search&term=kozal+hiv
If you compare any two of the sequences you find at most around a 10% difference.
ie Score = 189 bits (481), Expect = 3e-52
Identities = 91/99 (91%), Positives = 94/99 (94%)
Frame = +1
Each isolate differs from each other by only a few amino acid substitutions.
To illustrate the difference we can randomly change one letter in your name.
Papadopulos-Eleopuros Papadopulos-Eleomulos Sapadopulos-Eleopulos Pipadopulos-Eleopulos Papadoxulos-Eleopulos Papedopulos-Eleopulos Papadopugos-Eleopulos Papadopulos-Fleopulos Papadopulos-Elelpulos Papadopulos-Eleopulos Paradopulos-Eleopulos Papawopulos-Eleopulos Papadipulos-Eleopulos Papadopplos-Eleopulos Papadopulus-Ezeopulos Papadopulos-Elfopulos Papadopulos-Eleopalos Papadopulos-Eleopulos Papadopulos-Eleopulzs Papadopulos-Eleopuloc
100% of the letters vary but each sequence differs from every other sequence by only 10%.
If we go back to poliovirus. I provided links to the the genetic sequences of the three Sabin poliovirus types. http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=27085396&dopt=GenBank http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=27085398&dopt=GenBank http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=27085400&dopt=GenBank
Any two of these sequences differ from each other by about 20%. However, about 30% of the nucleotides vary in just these three sequences.
My question to Eleni Papadopulos-Eleopulos is as follows. Can you find any two sequences in the Kozal et al study that differ by 40%? Please answer with either Accession numbers for the two sequences or a simple "No".
1. Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, Richman DD, Morris D, Hubbell E, Chee M, Gingeras TR. (1996). Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med 2:753-759.
Competing interests: None declared