TY - JOUR TI - Population genomics of intrapatient HIV-1 evolution AU - Zanini, Fabio AU - Brodin, Johanna AU - Thebo, Lina AU - Lanz, Christa AU - Bratt, Göran AU - Albert, Jan AU - Neher, Richard A A2 - Chakraborty, Arup K VL - 4 PY - 2015 DA - 2015/12/10 SP - e11282 C1 - eLife 2015;4:e11282 DO - 10.7554/eLife.11282 UR - https://doi.org/10.7554/eLife.11282 AB - 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. The data can be accessed and explored via an interactive web application. 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. KW - HIV-1 KW - deep sequencing KW - evolution KW - reversion KW - fitness landscapes JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -