Population genomics of intrapatient HIV-1 evolution.

Abstract:

: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 100 bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity.

journal_name

Elife

journal_title

eLife

authors

Zanini F,Brodin J,Thebo L,Lanz C,Bratt G,Albert J,Neher RA

doi

10.7554/eLife.11282

subject

Has Abstract

pub_date

2015-12-11 00:00:00

issn

2050-084X

journal_volume

4

pub_type

杂志文章

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