Re: "HIV" genome, clones and sequences 22 July 2003
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Christopher J Noble,
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Re: Re: "HIV" genome, clones and sequences

Eleni Papadopulos-Eleopulos writes,

'For example, "In 1977, H1N1 influenza A virus reappeared in the human population after 27 years of dormancy with sequences mainly identical to those of the 1950s virus". 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?'

No references were provided but it is easy to find articles about the re-emergence of the H1N1 influenza A strain in 1977 (1).

In fact, Influenza has an extremely high evolution rate and the reemergence of this strain with few genetic changes has been extensively studied exactly because it is an exception and not the rule. The NS gene in influenza A has a uniform and rapid evolution rate of approximately 2x10-3 substitutions per nucleotide site per year (0.2%) and can be used as a 'molecular clock'. The 1950 H1N1 strain reappeared in 1977 with only 5 nucleotide substitutions in the NS gene after 27 years - one tenth of what would normally be expected. This has been explained as the re-emergence of the 1950 strain from a frozen source (2).

I am extremely interested to know why Papadopulos-Eleopulos is presenting what is clearly an exception as if it were the rule.

1. Buonagurio et al, Science, 232, (1986) 980-2 http://www.ncbi.nlm.nih.gov:80/entrez/que ry.fcgi?cmd=Retrieve&db=PubMed&li st_uids=2939560&dopt=Abstract

2. Kendal et al, Virology, 89 (1978) 632-6 http://www.ncbi.nlm.nih.gov:80/entrez/quer y.fcgi?cmd=Retrieve&db=PubMed&list_u ids=82293&dopt=Abstract

Competing interests:   None declared