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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities.
Chiara, Matteo; D'Erchia, Anna Maria; Gissi, Carmela; Manzari, Caterina; Parisi, Antonio; Resta, Nicoletta; Zambelli, Federico; Picardi, Ernesto; Pavesi, Giulio; Horner, David S; Pesole, Graziano.
  • Chiara M; molecular biology and bioinformatics at the University of Milan.
  • D'Erchia AM; molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari.
  • Gissi C; molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari.
  • Manzari C; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari.
  • Parisi A; Genetic and Molecular Epidemiology Laboratory at the Experimental Zooprophylactic Institute of Apulia and Basilicata.
  • Resta N; Medical Genetics at the University of Bari. She heads the Laboratory Unit of Medical Genetics and the School of Specialization in Medical Genetics.
  • Zambelli F; molecular biology and bioinformatics at the University of Milan.
  • Picardi E; molecular biology and bioinformatics at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari.
  • Pavesi G; Associate Professor of bioinformatics at the University of Milan (Italy).
  • Horner DS; molecular biology and bioinformatics at the University of Milan.
  • Pesole G; molecular biology at the University of Bari and Research Associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari.
Brief Bioinform ; 22(2): 616-630, 2021 03 22.
Article in English | MEDLINE | ID: covidwho-1343634
ABSTRACT
Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our 'vademecum' for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / High-Throughput Nucleotide Sequencing / SARS-CoV-2 / COVID-19 Type of study: Clinical Practice Guide Topics: Vaccines Limits: Humans Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / High-Throughput Nucleotide Sequencing / SARS-CoV-2 / COVID-19 Type of study: Clinical Practice Guide Topics: Vaccines Limits: Humans Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article