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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2015
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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 |
format | Online Article Text |
id | pubmed-4718817 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
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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