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Towards reliable whole genome sequencing for outbreak preparedness and response

BACKGROUND: To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- a...

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Autores principales: Nieuwenhuijse, David F., van der Linden, Anne, Kohl, Robert H. G., Sikkema, Reina S., Koopmans, Marion P. G., Oude Munnink, Bas B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9361258/
https://www.ncbi.nlm.nih.gov/pubmed/35945497
http://dx.doi.org/10.1186/s12864-022-08749-5
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author Nieuwenhuijse, David F.
van der Linden, Anne
Kohl, Robert H. G.
Sikkema, Reina S.
Koopmans, Marion P. G.
Oude Munnink, Bas B.
author_facet Nieuwenhuijse, David F.
van der Linden, Anne
Kohl, Robert H. G.
Sikkema, Reina S.
Koopmans, Marion P. G.
Oude Munnink, Bas B.
author_sort Nieuwenhuijse, David F.
collection PubMed
description BACKGROUND: To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus. RESULTS: We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination. CONCLUSIONS: The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08749-5.
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spelling pubmed-93612582022-08-09 Towards reliable whole genome sequencing for outbreak preparedness and response Nieuwenhuijse, David F. van der Linden, Anne Kohl, Robert H. G. Sikkema, Reina S. Koopmans, Marion P. G. Oude Munnink, Bas B. BMC Genomics Research Article BACKGROUND: To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus. RESULTS: We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination. CONCLUSIONS: The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08749-5. BioMed Central 2022-08-09 /pmc/articles/PMC9361258/ /pubmed/35945497 http://dx.doi.org/10.1186/s12864-022-08749-5 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Nieuwenhuijse, David F.
van der Linden, Anne
Kohl, Robert H. G.
Sikkema, Reina S.
Koopmans, Marion P. G.
Oude Munnink, Bas B.
Towards reliable whole genome sequencing for outbreak preparedness and response
title Towards reliable whole genome sequencing for outbreak preparedness and response
title_full Towards reliable whole genome sequencing for outbreak preparedness and response
title_fullStr Towards reliable whole genome sequencing for outbreak preparedness and response
title_full_unstemmed Towards reliable whole genome sequencing for outbreak preparedness and response
title_short Towards reliable whole genome sequencing for outbreak preparedness and response
title_sort towards reliable whole genome sequencing for outbreak preparedness and response
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9361258/
https://www.ncbi.nlm.nih.gov/pubmed/35945497
http://dx.doi.org/10.1186/s12864-022-08749-5
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