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Population genomics of intrapatient HIV-1 evolution

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 popula...

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Autores principales: Zanini, Fabio, Brodin, Johanna, Thebo, Lina, Lanz, Christa, Bratt, Göran, Albert, Jan, Neher, Richard A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718817/
https://www.ncbi.nlm.nih.gov/pubmed/26652000
http://dx.doi.org/10.7554/eLife.11282
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author Zanini, Fabio
Brodin, Johanna
Thebo, Lina
Lanz, Christa
Bratt, Göran
Albert, Jan
Neher, Richard A
author_facet Zanini, Fabio
Brodin, Johanna
Thebo, Lina
Lanz, Christa
Bratt, Göran
Albert, Jan
Neher, Richard A
author_sort Zanini, Fabio
collection PubMed
description 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. DOI: http://dx.doi.org/10.7554/eLife.11282.001
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spelling pubmed-47188172016-03-17 Population genomics of intrapatient HIV-1 evolution Zanini, Fabio Brodin, Johanna Thebo, Lina Lanz, Christa Bratt, Göran Albert, Jan Neher, Richard A eLife Genomics and Evolutionary Biology 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. DOI: http://dx.doi.org/10.7554/eLife.11282.001 eLife Sciences Publications, Ltd 2015-12-11 /pmc/articles/PMC4718817/ /pubmed/26652000 http://dx.doi.org/10.7554/eLife.11282 Text en © 2015, Zanini et al http://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Genomics and Evolutionary Biology
Zanini, Fabio
Brodin, Johanna
Thebo, Lina
Lanz, Christa
Bratt, Göran
Albert, Jan
Neher, Richard A
Population genomics of intrapatient HIV-1 evolution
title Population genomics of intrapatient HIV-1 evolution
title_full Population genomics of intrapatient HIV-1 evolution
title_fullStr Population genomics of intrapatient HIV-1 evolution
title_full_unstemmed Population genomics of intrapatient HIV-1 evolution
title_short Population genomics of intrapatient HIV-1 evolution
title_sort population genomics of intrapatient hiv-1 evolution
topic Genomics and Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718817/
https://www.ncbi.nlm.nih.gov/pubmed/26652000
http://dx.doi.org/10.7554/eLife.11282
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