Observing evolution in action: the continual adaptation of HIV during chronic infectionIn collaboration with the group of Prof. Jan Albert at the Karolinska Institute in Stockholm, we sequence HIV populations from frozen blood samples taken from individual patients every couple of months. Using this data, we can follow the evolution of viral proteins through time and study how the viral population responds to drug treatment. This data gives us the unique opportunity to observe evolution while it is happening, rather than having to infer the dynamics from a static snapshot.
Modeling CTL escape and evolution during acute infectionDuring the months following infection, the HIV population undergoes a few (~8) rapid selective sweeps, i.e., substitutions of amino-acids. These substitutions confer an advantage somewhere from a few percent to 50 percent or more to the mutant virus and rapidly replace the founding virus. These rapid escapes inform us about how strongly the immune system targets specific epitopes in the viral proteome.