  Many microbial populations rapidly adapt to changing environments with
multiple variants competing for survival. To quantify such complex evolutionary
dynamics in vivo, time resolved and genome wide data including rare variants
are essential. We performed whole-genome deep sequencing of HIV-1 populations
in 9 untreated patients, with 6-12 longitudinal samples per patient spanning
5-8 years of infection. We show that patterns of minor diversity are
reproducible between patients and mirror global HIV-1 diversity, suggesting a
universal landscape of fitness costs that control diversity. Reversions towards
the ancestral HIV-1 sequence are observed throughout infection and account for
almost one third of all sequence changes. Reversion rates depend strongly on
conservation. Frequent recombination limits linkage disequilibrium to about
100bp in most of the genome, but strong hitch-hiking due to short range linkage
limits diversity.
