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Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
Brejová, Brona; Borsová, Kristína; Hodorová, Viktória; Cabanová, Viktória; Gafurov, Askar; Fricová, Dominika; Nebohácová, Martina; Vinar, Tomás; Klempa, Boris; Nosek, Jozef.
  • Brejová B; Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovak Republic.
  • Borsová K; Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovak Republic.
  • Hodorová V; Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic.
  • Cabanová V; Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic.
  • Gafurov A; Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovak Republic.
  • Fricová D; Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovak Republic.
  • Nebohácová M; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic.
  • Vinar T; Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic.
  • Klempa B; Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovak Republic.
  • Nosek J; Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovak Republic.
PLoS One ; 16(10): e0259277, 2021.
Article in English | MEDLINE | ID: covidwho-1496534
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ABSTRACT
Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: Pandemics / Nanopore Sequencing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies Topics: Long Covid / Variants Limits: Humans Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pandemics / Nanopore Sequencing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies Topics: Long Covid / Variants Limits: Humans Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2021 Document Type: Article