Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity

Detalhes bibliográficos
Autor(a) principal: Bichicchi, Federica
Data de Publicação: 2023
Outros Autores: Guglietta, Niccolò, Alves, Arthur Daniel Rocha, Fasano, Erika, Manaresi, Elisabetta, Bua, Gloria, Gallinella, Giorgio
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/57671
Resumo: Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy.
id CRUZ_3a0af2a1cf9572b77ae2912a9ab596cd
oai_identifier_str oai:www.arca.fiocruz.br:icict/57671
network_acronym_str CRUZ
network_name_str Repositório Institucional da FIOCRUZ (ARCA)
repository_id_str 2135
spelling Bichicchi, FedericaGuglietta, NiccolòAlves, Arthur Daniel RochaFasano, ErikaManaresi, ElisabettaBua, GloriaGallinella, Giorgio2023-04-04T11:30:40Z2023-04-04T11:30:40Z2023BICHICHI, Federica et al. Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity. Viruses, v. 15, 217, p. 1 - 14, Jan. 2023.1999-4915https://www.arca.fiocruz.br/handle/icict/5767110.3390/v15010217engMDPIParvovirus B19Diversidade genéticaQuasispécie viralSequenciamento de próxima geraçãoEntropia de ShannonAnálise de clusterParvovirus B19Genetic diversityViral quasispeciesNext generation sequencingShannon EntropyCluster analysisNext Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversityinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleDepartment of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy.Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Desenvolvimento Tecnológico em Virologia. Rio de Janeiro, RJ, Brasil.Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy.Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy.Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy.Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy / Microbiology Section, IRCCS Sant’Orsola Hospital, 40138 Bologna, Italy.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, -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, -diversity, is a measure of the amount of inter-sample sequence heterogeneity, also incorporating information on -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 -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 -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.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/57671/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALArturRAlves_FredericaBichichi_etal_2023.pdfArturRAlves_FredericaBichichi_etal_2023.pdfapplication/pdf2610520https://www.arca.fiocruz.br/bitstream/icict/57671/2/ArturRAlves_FredericaBichichi_etal_2023.pdf87e90cb6ddba2e15c87f7e0cfb1d9b91MD52icict/576712023-09-14 15:46:42.199oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-09-14T18:46:42Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
title Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
spellingShingle Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
Bichicchi, Federica
Parvovirus B19
Diversidade genética
Quasispécie viral
Sequenciamento de próxima geração
Entropia de Shannon
Análise de cluster
Parvovirus B19
Genetic diversity
Viral quasispecies
Next generation sequencing
Shannon Entropy
Cluster analysis
title_short 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_sort Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity
author Bichicchi, Federica
author_facet Bichicchi, Federica
Guglietta, Niccolò
Alves, Arthur Daniel Rocha
Fasano, Erika
Manaresi, Elisabetta
Bua, Gloria
Gallinella, Giorgio
author_role author
author2 Guglietta, Niccolò
Alves, Arthur Daniel Rocha
Fasano, Erika
Manaresi, Elisabetta
Bua, Gloria
Gallinella, Giorgio
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Bichicchi, Federica
Guglietta, Niccolò
Alves, Arthur Daniel Rocha
Fasano, Erika
Manaresi, Elisabetta
Bua, Gloria
Gallinella, Giorgio
dc.subject.other.en_US.fl_str_mv Parvovirus B19
Diversidade genética
Quasispécie viral
Sequenciamento de próxima geração
Entropia de Shannon
Análise de cluster
topic Parvovirus B19
Diversidade genética
Quasispécie viral
Sequenciamento de próxima geração
Entropia de Shannon
Análise de cluster
Parvovirus B19
Genetic diversity
Viral quasispecies
Next generation sequencing
Shannon Entropy
Cluster analysis
dc.subject.en.en_US.fl_str_mv Parvovirus B19
Genetic diversity
Viral quasispecies
Next generation sequencing
Shannon Entropy
Cluster analysis
description Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy.
publishDate 2023
dc.date.accessioned.fl_str_mv 2023-04-04T11:30:40Z
dc.date.available.fl_str_mv 2023-04-04T11:30:40Z
dc.date.issued.fl_str_mv 2023
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv BICHICHI, Federica et al. Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity. Viruses, v. 15, 217, p. 1 - 14, Jan. 2023.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/57671
dc.identifier.issn.en_US.fl_str_mv 1999-4915
dc.identifier.doi.none.fl_str_mv 10.3390/v15010217
identifier_str_mv BICHICHI, Federica et al. Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity. Viruses, v. 15, 217, p. 1 - 14, Jan. 2023.
1999-4915
10.3390/v15010217
url https://www.arca.fiocruz.br/handle/icict/57671
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/57671/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/57671/2/ArturRAlves_FredericaBichichi_etal_2023.pdf
bitstream.checksum.fl_str_mv 5a560609d32a3863062d77ff32785d58
87e90cb6ddba2e15c87f7e0cfb1d9b91
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
_version_ 1813009108301774848

Registros relacionados