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Substitution rate and natural selection in parvovirus B19
The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075947/ https://www.ncbi.nlm.nih.gov/pubmed/27775080 http://dx.doi.org/10.1038/srep35759 |
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author | Stamenković, Gorana G. Ćirković, Valentina S. Šiljić, Marina M. Blagojević, Jelena V. Knežević, Aleksandra M. Joksić, Ivana D. Stanojević, Maja P. |
author_facet | Stamenković, Gorana G. Ćirković, Valentina S. Šiljić, Marina M. Blagojević, Jelena V. Knežević, Aleksandra M. Joksić, Ivana D. Stanojević, Maja P. |
author_sort | Stamenković, Gorana G. |
collection | PubMed |
description | The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973–2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1.03 (0.6–1.27) x 10(−4) substitutions/site/year, with higher values for analyzed genome partitions. In spite of the highest evolutionary rate, VP2 codons were found to be under purifying selection with rare episodic positive selection, whereas codons under diversifying selection were found in the unique part of VP1, known to contain B19 immune epitopes important in persistent infection. Analyses of overlapping gene regions identified nucleotide positions under opposite selective pressure in different ORFs, suggesting complex evolutionary mechanisms of nucleotide changes in B19 viral genomes. |
format | Online Article Text |
id | pubmed-5075947 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-50759472016-10-28 Substitution rate and natural selection in parvovirus B19 Stamenković, Gorana G. Ćirković, Valentina S. Šiljić, Marina M. Blagojević, Jelena V. Knežević, Aleksandra M. Joksić, Ivana D. Stanojević, Maja P. Sci Rep Article The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973–2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1.03 (0.6–1.27) x 10(−4) substitutions/site/year, with higher values for analyzed genome partitions. In spite of the highest evolutionary rate, VP2 codons were found to be under purifying selection with rare episodic positive selection, whereas codons under diversifying selection were found in the unique part of VP1, known to contain B19 immune epitopes important in persistent infection. Analyses of overlapping gene regions identified nucleotide positions under opposite selective pressure in different ORFs, suggesting complex evolutionary mechanisms of nucleotide changes in B19 viral genomes. Nature Publishing Group 2016-10-24 /pmc/articles/PMC5075947/ /pubmed/27775080 http://dx.doi.org/10.1038/srep35759 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Stamenković, Gorana G. Ćirković, Valentina S. Šiljić, Marina M. Blagojević, Jelena V. Knežević, Aleksandra M. Joksić, Ivana D. Stanojević, Maja P. Substitution rate and natural selection in parvovirus B19 |
title | Substitution rate and natural selection in parvovirus B19 |
title_full | Substitution rate and natural selection in parvovirus B19 |
title_fullStr | Substitution rate and natural selection in parvovirus B19 |
title_full_unstemmed | Substitution rate and natural selection in parvovirus B19 |
title_short | Substitution rate and natural selection in parvovirus B19 |
title_sort | substitution rate and natural selection in parvovirus b19 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075947/ https://www.ncbi.nlm.nih.gov/pubmed/27775080 http://dx.doi.org/10.1038/srep35759 |
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