I am studying the intra-patient evolution of HIV-1. We PCR amplify and
sequence 8<several<16 viruses from the virus quasispecies in the subject at
several time points and look at how virus changes.
We find the following:
TIME POINT 1:
15 out of 15 isolates have Valine in position X and Phe in position Y.
TIME POINT 2 (6 months later):
10 out of 10 isolates have Val->Ile substitution in position X and Phe->Trp in
What probably happened was that between the two time points Val->Ile & Phe->Trp
mutations occurred in one or several viruses and the progeny of these mutant
viruses comprise ~90% of the virus population in the patient by the time point
2. The important thing is that the total viral load (number of viruses in the
patient) was aproximately the same during the period of 6 months.
In other words, the viral population did not go through small total population
size, but only a few viruses from the population at time point 1 were destinned
to leave progeny by the sampling time 2.
So, the question: can this be called "bottleneck" evolution?
Please respond directly to me at gene at jmullins.stanford.edu
CA 94305-5402 USA