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Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories

The molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is key for clinical management and surveillance. Funded by the European Centre for Disease Prevention and Control, we conducted an external quality assessment (EQA) on the molecular detection and variant typing o...

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Autores principales: Mögling, Ramona, Fischer, Carlo, Stanoeva, Kamelia R., Melidou, Angeliki, Almeida Campos, Angélica C., Drosten, Christian, Biere, Barbara, Meijer, Adam, Kraus, Annette, Reusken, Chantal B. E. M., Drexler, Jan Felix
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769866/
https://www.ncbi.nlm.nih.gov/pubmed/36445090
http://dx.doi.org/10.1128/jcm.01261-22
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author Mögling, Ramona
Fischer, Carlo
Stanoeva, Kamelia R.
Melidou, Angeliki
Almeida Campos, Angélica C.
Drosten, Christian
Biere, Barbara
Meijer, Adam
Kraus, Annette
Reusken, Chantal B. E. M.
Drexler, Jan Felix
author_facet Mögling, Ramona
Fischer, Carlo
Stanoeva, Kamelia R.
Melidou, Angeliki
Almeida Campos, Angélica C.
Drosten, Christian
Biere, Barbara
Meijer, Adam
Kraus, Annette
Reusken, Chantal B. E. M.
Drexler, Jan Felix
author_sort Mögling, Ramona
collection PubMed
description The molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is key for clinical management and surveillance. Funded by the European Centre for Disease Prevention and Control, we conducted an external quality assessment (EQA) on the molecular detection and variant typing of SARS-CoV-2 that included 59 European laboratories in 34 countries. The EQA panel consisted of 12 lyophilized inactivated samples, 10 of which were SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Epsilon, Eta, parental B.1 strain) ranging from 2.5 to 290.0 copies/μL or pooled respiratory viruses (adenovirus, enterovirus, influenza virus A, respiratory syncytial virus, or human coronaviruses 229E and OC43). Of all participants, 72.9% identified the presence of SARS-CoV-2 RNA correctly. In samples containing 25.0 or more genome copies/μL, SARS-CoV-2 was detected by 98.3% of the participating laboratories. Laboratories applying commercial tests scored significantly better (P < 0.0001, Kruskal-Wallis test) than those using in-house assays. Both the molecular detection and the typing of the SARS-CoV-2 variants were associated with the RNA concentrations (P < 0.0001, Kruskal-Wallis test). On average, only 5 out of the 10 samples containing different SARS-CoV-2 variants at different concentrations were correctly typed. The identification of SARS-CoV-2 variants was significantly more successful among EQA participants who combined real-time reverse transcription polymerase chain reaction (RT-PCR)-based assays for mutation detection and high-throughput genomic sequencing than among those who used a single methodological approach (P = 0.0345, Kruskal-Wallis test). Our data highlight the high sensitivity of SARS-CoV-2 detection in expert laboratories as well as the importance of continuous assay development and the benefits of combining different methodologies for accurate SARS-CoV-2 variant typing.
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spelling pubmed-97698662022-12-22 Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories Mögling, Ramona Fischer, Carlo Stanoeva, Kamelia R. Melidou, Angeliki Almeida Campos, Angélica C. Drosten, Christian Biere, Barbara Meijer, Adam Kraus, Annette Reusken, Chantal B. E. M. Drexler, Jan Felix J Clin Microbiol Virology The molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is key for clinical management and surveillance. Funded by the European Centre for Disease Prevention and Control, we conducted an external quality assessment (EQA) on the molecular detection and variant typing of SARS-CoV-2 that included 59 European laboratories in 34 countries. The EQA panel consisted of 12 lyophilized inactivated samples, 10 of which were SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Epsilon, Eta, parental B.1 strain) ranging from 2.5 to 290.0 copies/μL or pooled respiratory viruses (adenovirus, enterovirus, influenza virus A, respiratory syncytial virus, or human coronaviruses 229E and OC43). Of all participants, 72.9% identified the presence of SARS-CoV-2 RNA correctly. In samples containing 25.0 or more genome copies/μL, SARS-CoV-2 was detected by 98.3% of the participating laboratories. Laboratories applying commercial tests scored significantly better (P < 0.0001, Kruskal-Wallis test) than those using in-house assays. Both the molecular detection and the typing of the SARS-CoV-2 variants were associated with the RNA concentrations (P < 0.0001, Kruskal-Wallis test). On average, only 5 out of the 10 samples containing different SARS-CoV-2 variants at different concentrations were correctly typed. The identification of SARS-CoV-2 variants was significantly more successful among EQA participants who combined real-time reverse transcription polymerase chain reaction (RT-PCR)-based assays for mutation detection and high-throughput genomic sequencing than among those who used a single methodological approach (P = 0.0345, Kruskal-Wallis test). Our data highlight the high sensitivity of SARS-CoV-2 detection in expert laboratories as well as the importance of continuous assay development and the benefits of combining different methodologies for accurate SARS-CoV-2 variant typing. American Society for Microbiology 2022-11-29 /pmc/articles/PMC9769866/ /pubmed/36445090 http://dx.doi.org/10.1128/jcm.01261-22 Text en Copyright © 2022 American Society for Microbiology. https://doi.org/10.1128/ASMCopyrightv2All Rights Reserved (https://doi.org/10.1128/ASMCopyrightv2) . https://doi.org/10.1128/ASMCopyrightv2This article is made available via the PMC Open Access Subset for unrestricted noncommercial re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Virology
Mögling, Ramona
Fischer, Carlo
Stanoeva, Kamelia R.
Melidou, Angeliki
Almeida Campos, Angélica C.
Drosten, Christian
Biere, Barbara
Meijer, Adam
Kraus, Annette
Reusken, Chantal B. E. M.
Drexler, Jan Felix
Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories
title Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories
title_full Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories
title_fullStr Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories
title_full_unstemmed Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories
title_short Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories
title_sort sensitivity of detection and variant typing of sars-cov-2 in european laboratories
topic Virology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769866/
https://www.ncbi.nlm.nih.gov/pubmed/36445090
http://dx.doi.org/10.1128/jcm.01261-22
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