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SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.
During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monito...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Authors. Published by Elsevier B.V.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8487099/ https://www.ncbi.nlm.nih.gov/pubmed/34619382 http://dx.doi.org/10.1016/j.jcv.2021.104993 |
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author | Coolen, Jordy P.M. Wolters, Femke Tostmann, Alma van Groningen, Lenneke F.J. Bleeker-Rovers, Chantal P. Tan, Edward C.T.H. van der Geest-Blankert, Nannet Hautvast, Jeannine L.A. Hopman, Joost Wertheim, Heiman F.L. Rahamat-Langendoen, Janette C. Storch, Marko Melchers, Willem J.G. |
author_facet | Coolen, Jordy P.M. Wolters, Femke Tostmann, Alma van Groningen, Lenneke F.J. Bleeker-Rovers, Chantal P. Tan, Edward C.T.H. van der Geest-Blankert, Nannet Hautvast, Jeannine L.A. Hopman, Joost Wertheim, Heiman F.L. Rahamat-Langendoen, Janette C. Storch, Marko Melchers, Willem J.G. |
author_sort | Coolen, Jordy P.M. |
collection | PubMed |
description | During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. By applying a reverse complement polymerase chain reaction (RC-PCR), an Illumina library preparation is obtained in a single PCR, thereby saving time, resources and facilitating high-throughput screening. Using this WGS technique, we evaluated SARS-CoV-2 diversity and possible transmission within a group of 173 patients and healthcare workers (HCW) of the Radboud university medical center during 2020. Due to the emergence of variants of concern, we screened SARS-CoV-2 positive samples in 2021 for identification of mutations and lineages. With use of EasySeq™ RC-PCR SARS-CoV-2 WGS kit we were able to obtain reliable results to confirm outbreak clusters and additionally identify new previously unassociated links in a considerably easier workaround compared to current methods. Furthermore, various SARS-CoV-2 variants of interest were detected among samples and validated against an Oxford Nanopore sequencing amplicon strategy which illustrates this technique is suitable for surveillance and monitoring current circulating variants. |
format | Online Article Text |
id | pubmed-8487099 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Authors. Published by Elsevier B.V. |
record_format | MEDLINE/PubMed |
spelling | pubmed-84870992021-10-04 SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. Coolen, Jordy P.M. Wolters, Femke Tostmann, Alma van Groningen, Lenneke F.J. Bleeker-Rovers, Chantal P. Tan, Edward C.T.H. van der Geest-Blankert, Nannet Hautvast, Jeannine L.A. Hopman, Joost Wertheim, Heiman F.L. Rahamat-Langendoen, Janette C. Storch, Marko Melchers, Willem J.G. J Clin Virol Article During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. By applying a reverse complement polymerase chain reaction (RC-PCR), an Illumina library preparation is obtained in a single PCR, thereby saving time, resources and facilitating high-throughput screening. Using this WGS technique, we evaluated SARS-CoV-2 diversity and possible transmission within a group of 173 patients and healthcare workers (HCW) of the Radboud university medical center during 2020. Due to the emergence of variants of concern, we screened SARS-CoV-2 positive samples in 2021 for identification of mutations and lineages. With use of EasySeq™ RC-PCR SARS-CoV-2 WGS kit we were able to obtain reliable results to confirm outbreak clusters and additionally identify new previously unassociated links in a considerably easier workaround compared to current methods. Furthermore, various SARS-CoV-2 variants of interest were detected among samples and validated against an Oxford Nanopore sequencing amplicon strategy which illustrates this technique is suitable for surveillance and monitoring current circulating variants. The Authors. Published by Elsevier B.V. 2021-11 2021-10-02 /pmc/articles/PMC8487099/ /pubmed/34619382 http://dx.doi.org/10.1016/j.jcv.2021.104993 Text en © 2021 The Authors. Published by Elsevier B.V. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Coolen, Jordy P.M. Wolters, Femke Tostmann, Alma van Groningen, Lenneke F.J. Bleeker-Rovers, Chantal P. Tan, Edward C.T.H. van der Geest-Blankert, Nannet Hautvast, Jeannine L.A. Hopman, Joost Wertheim, Heiman F.L. Rahamat-Langendoen, Janette C. Storch, Marko Melchers, Willem J.G. SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. |
title | SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. |
title_full | SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. |
title_fullStr | SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. |
title_full_unstemmed | SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. |
title_short | SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. |
title_sort | sars-cov-2 whole-genome sequencing using reverse complement pcr: for easy, fast and accurate outbreak and variant analysis. |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8487099/ https://www.ncbi.nlm.nih.gov/pubmed/34619382 http://dx.doi.org/10.1016/j.jcv.2021.104993 |
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