Last week, we got news that our paper on “Loss and recovery of genetic variation in adapting HIV populations” is accepted for publication in PLoS Genetics! My coauthors on this paper are Sergey Kryazhimskiy and John Wakeley. You can find an earlier version of the paper on the arXiv, and a related blog post on Haldane’s Sieve.
In a nutshell, this is what the paper is about: we analyze longitudinal data on 30 patients in which the virus evolves to become drug resistant. We see that
1. known resistance mutations mostly fix one at a time,
2. these fixations are associated with a reduction in genetic diversity due to hitchhiking,
3. the fixations involve both soft and hard sweeps (see pictures), and
4. recovery of genetic diversity is slow for synonymous sites and faster for non-synonymous sites.