Ulrich Melcher wrote:
> Is it possible that there are only a limited
> number of regions of sequence space (corresponding to subtypes)
> compatible with a successful HIV-1? This would mean that the sequence
> space between subtypes consists of HIV-1's with poor "fitness". It
> would also mean that the subtypes were generated by rare events of a
> virus of one subtype jumping into another peak in sequence space.
It doesn't seem unlikely that coding-sequence changes in something as
fine-tuned as HIV might fall into only a few allowable combinations,
but how about looking at third position changes and other sites which
are relatively less likely to be important to natural selection? If
the multiple HIV classes are created by leaps between selective peaks,
rather than long periods of gradual evolution, the non-coding sites
should show a rather different pattern from the coding ones.
You could argue that even third positions are under selection (for speed
of replication, speed of transcription, etc.) but surely it's weaker
than the selection on coding positions, and not as prone to
combinatorial effects.
Mary Kuhner mkkuhner at genetics.washington.edu
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