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Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity

Parvovirus B19 (B19V) is a ssDNA human virus, responsible for an ample range of clinical manifestations. Sequencing of B19V DNA from clinical samples is frequently reported in the literature to assign genotype (genotypes 1–3) and for finer molecular epidemiological tracing. The increasing availabili...

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Autores principales: Bichicchi, Federica, Guglietta, Niccolò, Rocha Alves, Arthur Daniel, Fasano, Erika, Manaresi, Elisabetta, Bua, Gloria, Gallinella, Giorgio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9863757/
https://www.ncbi.nlm.nih.gov/pubmed/36680257
http://dx.doi.org/10.3390/v15010217
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author Bichicchi, Federica
Guglietta, Niccolò
Rocha Alves, Arthur Daniel
Fasano, Erika
Manaresi, Elisabetta
Bua, Gloria
Gallinella, Giorgio
author_facet Bichicchi, Federica
Guglietta, Niccolò
Rocha Alves, Arthur Daniel
Fasano, Erika
Manaresi, Elisabetta
Bua, Gloria
Gallinella, Giorgio
author_sort Bichicchi, Federica
collection PubMed
description Parvovirus B19 (B19V) is a ssDNA human virus, responsible for an ample range of clinical manifestations. Sequencing of B19V DNA from clinical samples is frequently reported in the literature to assign genotype (genotypes 1–3) and for finer molecular epidemiological tracing. The increasing availability of Next Generation Sequencing (NGS) with its depth of coverage potentially yields information on intrinsic sequence heterogeneity; however, integration of this information in analysis of sequence variation is not routinely obtained. The present work investigated genomic sequence heterogeneity within and between B19V isolates by application of NGS techniques, and by the development of a novel dedicated bioinformatic tool and analysis pipeline, yielding information on two newly defined parameters. The first, α-diversity, is a measure of the amount and distribution of position-specific, normalised Shannon Entropy, as a measure of intra-sample sequence heterogeneity. The second, σ-diversity, is a measure of the amount of inter-sample sequence heterogeneity, also incorporating information on α-diversity. Based on these indexes, further cluster analysis can be performed. A set of 24 high-titre viraemic samples was investigated. Of these, 23 samples were genotype 1 and one sample was genotype 2. Genotype 1 isolates showed low α-diversity values, with only a few samples showing distinct position-specific polymorphisms; a few genetically related clusters emerged when analysing inter-sample distances, correlated to the year of isolation; the single genotype 2 isolate showed the highest α-diversity, even if not presenting polymorphisms, and was an evident outlier when analysing inter-sample distance. In conclusion, NGS analysis and the bioinformatic tool and pipeline developed and used in the present work can be considered effective tools for investigating sequence diversity, an observable parameter that can be incorporated into the quasispecies theory framework to yield a better insight into viral evolution dynamics.
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spelling pubmed-98637572023-01-22 Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity Bichicchi, Federica Guglietta, Niccolò Rocha Alves, Arthur Daniel Fasano, Erika Manaresi, Elisabetta Bua, Gloria Gallinella, Giorgio Viruses Article Parvovirus B19 (B19V) is a ssDNA human virus, responsible for an ample range of clinical manifestations. Sequencing of B19V DNA from clinical samples is frequently reported in the literature to assign genotype (genotypes 1–3) and for finer molecular epidemiological tracing. The increasing availability of Next Generation Sequencing (NGS) with its depth of coverage potentially yields information on intrinsic sequence heterogeneity; however, integration of this information in analysis of sequence variation is not routinely obtained. The present work investigated genomic sequence heterogeneity within and between B19V isolates by application of NGS techniques, and by the development of a novel dedicated bioinformatic tool and analysis pipeline, yielding information on two newly defined parameters. The first, α-diversity, is a measure of the amount and distribution of position-specific, normalised Shannon Entropy, as a measure of intra-sample sequence heterogeneity. The second, σ-diversity, is a measure of the amount of inter-sample sequence heterogeneity, also incorporating information on α-diversity. Based on these indexes, further cluster analysis can be performed. A set of 24 high-titre viraemic samples was investigated. Of these, 23 samples were genotype 1 and one sample was genotype 2. Genotype 1 isolates showed low α-diversity values, with only a few samples showing distinct position-specific polymorphisms; a few genetically related clusters emerged when analysing inter-sample distances, correlated to the year of isolation; the single genotype 2 isolate showed the highest α-diversity, even if not presenting polymorphisms, and was an evident outlier when analysing inter-sample distance. In conclusion, NGS analysis and the bioinformatic tool and pipeline developed and used in the present work can be considered effective tools for investigating sequence diversity, an observable parameter that can be incorporated into the quasispecies theory framework to yield a better insight into viral evolution dynamics. MDPI 2023-01-12 /pmc/articles/PMC9863757/ /pubmed/36680257 http://dx.doi.org/10.3390/v15010217 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Bichicchi, Federica
Guglietta, Niccolò
Rocha Alves, Arthur Daniel
Fasano, Erika
Manaresi, Elisabetta
Bua, Gloria
Gallinella, Giorgio
Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
title Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
title_full Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
title_fullStr Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
title_full_unstemmed Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
title_short Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
title_sort next generation sequencing for the analysis of parvovirus b19 genomic diversity
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9863757/
https://www.ncbi.nlm.nih.gov/pubmed/36680257
http://dx.doi.org/10.3390/v15010217
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