A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) amplicon contamination was discovered due to next-generation sequencing (NGS) reads mapping in the negative controls. Environmental screening was undertaken to determine the source of contamination, which was suspected to be evaporati...

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Autores principales: Mwangi, Peter, Mogotsi, Milton, Ogunbayo, Ayodeji, Mooko, Teboho, Maringa, Wairimu, Sondlane, Hlengiwe, Nkwadipo, Kelebogile, Adelabu, Olusesan, Bester, Philip Armand, Goedhals, Dominique, Nyaga, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Vienna 2022
Materias:
Brief Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8926888/
https://www.ncbi.nlm.nih.gov/pubmed/35298714
http://dx.doi.org/10.1007/s00705-022-05411-z
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author Mwangi, Peter
Mogotsi, Milton
Ogunbayo, Ayodeji
Mooko, Teboho
Maringa, Wairimu
Sondlane, Hlengiwe
Nkwadipo, Kelebogile
Adelabu, Olusesan
Bester, Philip Armand
Goedhals, Dominique
Nyaga, Martin
author_facet Mwangi, Peter
Mogotsi, Milton
Ogunbayo, Ayodeji
Mooko, Teboho
Maringa, Wairimu
Sondlane, Hlengiwe
Nkwadipo, Kelebogile
Adelabu, Olusesan
Bester, Philip Armand
Goedhals, Dominique
Nyaga, Martin
author_sort Mwangi, Peter
collection PubMed
description Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) amplicon contamination was discovered due to next-generation sequencing (NGS) reads mapping in the negative controls. Environmental screening was undertaken to determine the source of contamination, which was suspected to be evaporation during polymerase chain reaction (PCR) assays while using the coronavirus disease 2019 (COVID-19) ARTIC protocol. A decontamination strategy is hereby documented to assist laboratories that may experience similar amplicon contamination. Routine molecular laboratory environmental screening as a quality control is highly recommended. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-022-05411-z.
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spelling pubmed-89268882022-03-17 A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory Mwangi, Peter Mogotsi, Milton Ogunbayo, Ayodeji Mooko, Teboho Maringa, Wairimu Sondlane, Hlengiwe Nkwadipo, Kelebogile Adelabu, Olusesan Bester, Philip Armand Goedhals, Dominique Nyaga, Martin Arch Virol Brief Report Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) amplicon contamination was discovered due to next-generation sequencing (NGS) reads mapping in the negative controls. Environmental screening was undertaken to determine the source of contamination, which was suspected to be evaporation during polymerase chain reaction (PCR) assays while using the coronavirus disease 2019 (COVID-19) ARTIC protocol. A decontamination strategy is hereby documented to assist laboratories that may experience similar amplicon contamination. Routine molecular laboratory environmental screening as a quality control is highly recommended. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-022-05411-z. Springer Vienna 2022-03-17 2022 /pmc/articles/PMC8926888/ /pubmed/35298714 http://dx.doi.org/10.1007/s00705-022-05411-z Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Brief Report
Mwangi, Peter
Mogotsi, Milton
Ogunbayo, Ayodeji
Mooko, Teboho
Maringa, Wairimu
Sondlane, Hlengiwe
Nkwadipo, Kelebogile
Adelabu, Olusesan
Bester, Philip Armand
Goedhals, Dominique
Nyaga, Martin
A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory
title A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory
title_full A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory
title_fullStr A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory
title_full_unstemmed A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory
title_short A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory
title_sort decontamination strategy for resolving sars-cov-2 amplicon contamination in a next-generation sequencing laboratory
topic Brief Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8926888/
https://www.ncbi.nlm.nih.gov/pubmed/35298714
http://dx.doi.org/10.1007/s00705-022-05411-z
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