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Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting.
Maschietto, Céline; Otto, Gaëtan; Rouzé, Pauline; Debortoli, Nicolas; Bihin, Benoît; Nyinkeu, Lesly; Denis, Olivier; Huang, Te-Din; Mullier, François; Bogaerts, Pierre; Degosserie, Jonathan.
  • Maschietto C; Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Otto G; COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium.
  • Rouzé P; Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Debortoli N; COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium.
  • Bihin B; Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Nyinkeu L; Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Denis O; Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Huang TD; Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Mullier F; Scientific Support Unit, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Bogaerts P; Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
  • Degosserie J; COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium.
Sci Rep ; 13(1): 6934, 2023 04 28.
Article in English | MEDLINE | ID: covidwho-2299691
ABSTRACT
Rapid and recurrent breakthroughs of new SARS-CoV-2 strains (variants) have prompted public health authorities worldwide to set up surveillance networks to monitor the circulation of variants of concern. The use of next-generation sequencing technologies has raised the need for quality control assessment as required in clinical laboratories. The present study is the first to propose a validation guide for SARS-CoV-2 typing using three different NGS methods fulfilling ISO15189 standards. These include the assessment of the risk, specificity, accuracy, reproducibility, and repeatability of the methods. Among the three methods used, two are amplicon-based involving reverse transcription polymerase chain reaction (Artic v3 and Midnight v1) on Oxford Nanopore Technologies while the third one is amplicon-based using reverse complement polymerase chain reaction (Nimagen) on Illumina technology. We found that all methods met the quality requirement (e.g., 100% concordant typing results for accuracy, reproducibility, and repeatability) for SARS-CoV-2 typing in clinical setting. Additionally, the typing results emerging from each of the three sequencing methods were compared using three widely known nomenclatures (WHO, Pangolineage, and Nextclade). They were also compared regarding single nucleotide variations. The outcomes showed that Artic v3 and Nimagen should be privileged for outbreak investigation as they provide higher quality results for samples that do not meet inclusion criteria for analysis in a clinical setting. This study is a first step towards validation of laboratory developed NGS tests in the context of the new European regulation for medical devices and in vitro diagnostics.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Sci Rep Year: 2023 Document Type: Article Affiliation country: S41598-023-34088-w

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Sci Rep Year: 2023 Document Type: Article Affiliation country: S41598-023-34088-w