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HIV-1 vs HIV-2

Ulrich Melcher umelcher at BMB-FS1.BIOCHEM.OKSTATE.EDU
Fri Mar 17 09:29:05 EST 1995

Do others take an HIV molecular clock seriously?
     As I understand it, there are estimates of the frequency of occurrence
of changes in the HIV-1 genome for samples whose divergence time can be
estimated accurately.  These estimates when applied to the different
subtypes of HIV-1 yield divergence dates consistent with other information.
This estimate is then applied assuming a constant frequency (a uniformly
ticking clock) to earlier divergences (from HIV-2 and from other primate
immunodeficiency viruses).
     Since HIV-1 seems to be a recently evolved virus and is probably still
rapidly evolving, I question whether a constant clock can be applied to
these earlier divergences.  I expect that the frequencies of substitutions
can change dramatically in situations where viruses are adapting to new
niches.  Thus, I take estimates of distant divergence times with several
grains of salt.
     Other opinions?

Ulrich Melcher                 umelcher at bmb-fs1.biochem.okstate.edu
Department of Biochemistry     Tel: 405-744-6210
  and Molecular Biology        FAX: 405-744-7799
Oklahoma State University
Stillwater OK 74078-0454 USA

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