| Author | Bichicchi, Federica | |
| Author | Guglietta, Niccolò | |
| Author | Alves, Arthur Daniel Rocha | |
| Author | Fasano, Erika | |
| Author | Manaresi, Elisabetta | |
| Author | Bua, Gloria | |
| Author | Gallinella, Giorgio | |
| Access date | 2023-04-04T11:30:40Z | |
| Available date | 2023-04-04T11:30:40Z | |
| Document date | 2023 | |
| Citation | BICHICHI, Federica et al. Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity. Viruses, v. 15, 217, p. 1 - 14, Jan. 2023. | en_US |
| ISSN | 1999-4915 | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/57671 | |
| Language | eng | en_US |
| Publisher | MDPI | en_US |
| Rights | open access | |
| Subject in Portuguese | Parvovirus B19 | en_US |
| Subject in Portuguese | Diversidade genética | en_US |
| Subject in Portuguese | Quasispécie viral | en_US |
| Subject in Portuguese | Sequenciamento de próxima geração | en_US |
| Subject in Portuguese | Entropia de Shannon | en_US |
| Subject in Portuguese | Análise de cluster | en_US |
| Title | Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity | en_US |
| Type | Article | |
| DOI | 10.3390/v15010217 | |
| Abstract | 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. | en_US |
| Affilliation | Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy. | en_US |
| Affilliation | Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Desenvolvimento Tecnológico em Virologia. Rio de Janeiro, RJ, Brasil. | en_US |
| Affilliation | Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy. | en_US |
| Affilliation | Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy. | en_US |
| Affilliation | Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy. | en_US |
| Affilliation | Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy / Microbiology Section, IRCCS Sant’Orsola Hospital, 40138 Bologna, Italy. | en_US |
| Subject | Parvovirus B19 | en_US |
| Subject | Genetic diversity | en_US |
| Subject | Viral quasispecies | en_US |
| Subject | Next generation sequencing | en_US |
| Subject | Shannon Entropy | en_US |
| Subject | Cluster analysis | en_US |
| xmlui.metadata.dc.subject.ods | 10 Redução das desigualdades | |
