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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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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. |
format | Online Article Text |
id | pubmed-7793244 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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