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Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history

An often-returning question for not only HIV-1, but also other organisms, is how predictable evolutionary paths are. The environment, mutational history, and random processes can all impact the exact evolutionary paths, but to which extent these factors contribute to the evolutionary dynamics of a p...

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Autores principales: Bons, Eva, Leemann, Christine, Metzner, Karin J., Regoes, Roland R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793244/
https://www.ncbi.nlm.nih.gov/pubmed/33370289
http://dx.doi.org/10.1371/journal.pbio.3001010
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author Bons, Eva
Leemann, Christine
Metzner, Karin J.
Regoes, Roland R.
author_facet Bons, Eva
Leemann, Christine
Metzner, Karin J.
Regoes, Roland R.
author_sort Bons, Eva
collection PubMed
description An often-returning question for not only HIV-1, but also other organisms, is how predictable evolutionary paths are. The environment, mutational history, and random processes can all impact the exact evolutionary paths, but to which extent these factors contribute to the evolutionary dynamics of a particular system is an open question. Especially in a virus like HIV-1, with a large mutation rate and large population sizes, evolution is expected to be highly predictable if the impact of environment and history is low, and evolution is not neutral. We investigated the effect of environment and mutational history by analyzing sequences from a long-term evolution experiment, in which HIV-1 was passaged on 2 different cell types in 8 independent evolutionary lines and 8 derived lines, 4 of which involved a switch of the environment. The experiments lasted for 240–300 passages, corresponding to approximately 400–600 generations or almost 3 years. The sequences show signs of extensive parallel evolution—the majority of mutations that are shared between independent lines appear in both cell types, but we also find that both environment and mutational history significantly impact the evolutionary paths. We conclude that HIV-1 evolution is robust to small changes in the environment, similar to a transmission event in the absence of an immune response or drug pressure. We also find that the fitness landscape of HIV-1 is largely smooth, although we find some evidence for both positive and negative epistatic interactions between mutations.
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spelling pubmed-77932442021-01-27 Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history Bons, Eva Leemann, Christine Metzner, Karin J. Regoes, Roland R. PLoS Biol Research Article An often-returning question for not only HIV-1, but also other organisms, is how predictable evolutionary paths are. The environment, mutational history, and random processes can all impact the exact evolutionary paths, but to which extent these factors contribute to the evolutionary dynamics of a particular system is an open question. Especially in a virus like HIV-1, with a large mutation rate and large population sizes, evolution is expected to be highly predictable if the impact of environment and history is low, and evolution is not neutral. We investigated the effect of environment and mutational history by analyzing sequences from a long-term evolution experiment, in which HIV-1 was passaged on 2 different cell types in 8 independent evolutionary lines and 8 derived lines, 4 of which involved a switch of the environment. The experiments lasted for 240–300 passages, corresponding to approximately 400–600 generations or almost 3 years. The sequences show signs of extensive parallel evolution—the majority of mutations that are shared between independent lines appear in both cell types, but we also find that both environment and mutational history significantly impact the evolutionary paths. We conclude that HIV-1 evolution is robust to small changes in the environment, similar to a transmission event in the absence of an immune response or drug pressure. We also find that the fitness landscape of HIV-1 is largely smooth, although we find some evidence for both positive and negative epistatic interactions between mutations. Public Library of Science 2020-12-28 /pmc/articles/PMC7793244/ /pubmed/33370289 http://dx.doi.org/10.1371/journal.pbio.3001010 Text en © 2020 Bons et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Bons, Eva
Leemann, Christine
Metzner, Karin J.
Regoes, Roland R.
Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history
title Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history
title_full Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history
title_fullStr Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history
title_full_unstemmed Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history
title_short Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history
title_sort long-term experimental evolution of hiv-1 reveals effects of environment and mutational history
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793244/
https://www.ncbi.nlm.nih.gov/pubmed/33370289
http://dx.doi.org/10.1371/journal.pbio.3001010
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