rates of HIV evolution
Prabhav suggested comparing rates of viral evolution within patients to those within a transmission cluster.
We could measure/compare rates of adoptation to treatment to rates of adoptation to a new host.
The confound is that we identify the transmission clusters via genetic distance. It would be easier if we had a known transmission chain.
Alternately, EuResist does have ~6000 cases with two samples taken under one treatment. We could compare rates here with rates after a treatment change.