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Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors
The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not require any previous functional or syntactic knowledge about th...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232212/ https://www.ncbi.nlm.nih.gov/pubmed/22162994 http://dx.doi.org/10.1371/journal.pone.0027924 |
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author | Burioni, Raffaella Scalco, Riccardo Casartelli, Mario |
author_facet | Burioni, Raffaella Scalco, Riccardo Casartelli, Mario |
author_sort | Burioni, Raffaella |
collection | PubMed |
description | The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not require any previous functional or syntactic knowledge about the sequences and it is sensitive to the correlated variations in the characters disposition. Its efficiency is improved by algorithmic tools, designed to enhance the detection of the novelty and to reduce the noise of useless mutations. We focus on the USA data from 1993/94 to 2010/2011 for A/H3N2 and on USA data from 2006/07 to 2010/2011 for A/H1N1. We show that the clusterization of the distance matrix gives strong evidence to a structure of domains in the sequence space, acting as weak attractors for the evolution, in very good agreement with the epidemiological history of the virus. The structure proves very robust with respect to the variations of the clusterization parameters, and extremely coherent when restricting the observation window. The results suggest an efficient strategy in the vaccine forecast, based on the presence of “precursors” (or “buds”) populating the most recent attractor. |
format | Online Article Text |
id | pubmed-3232212 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-32322122011-12-09 Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors Burioni, Raffaella Scalco, Riccardo Casartelli, Mario PLoS One Research Article The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not require any previous functional or syntactic knowledge about the sequences and it is sensitive to the correlated variations in the characters disposition. Its efficiency is improved by algorithmic tools, designed to enhance the detection of the novelty and to reduce the noise of useless mutations. We focus on the USA data from 1993/94 to 2010/2011 for A/H3N2 and on USA data from 2006/07 to 2010/2011 for A/H1N1. We show that the clusterization of the distance matrix gives strong evidence to a structure of domains in the sequence space, acting as weak attractors for the evolution, in very good agreement with the epidemiological history of the virus. The structure proves very robust with respect to the variations of the clusterization parameters, and extremely coherent when restricting the observation window. The results suggest an efficient strategy in the vaccine forecast, based on the presence of “precursors” (or “buds”) populating the most recent attractor. Public Library of Science 2011-12-06 /pmc/articles/PMC3232212/ /pubmed/22162994 http://dx.doi.org/10.1371/journal.pone.0027924 Text en Burioni 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Burioni, Raffaella Scalco, Riccardo Casartelli, Mario Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors |
title | Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors |
title_full | Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors |
title_fullStr | Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors |
title_full_unstemmed | Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors |
title_short | Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors |
title_sort | rohlin distance and the evolution of influenza a virus: weak attractors and precursors |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232212/ https://www.ncbi.nlm.nih.gov/pubmed/22162994 http://dx.doi.org/10.1371/journal.pone.0027924 |
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