Towards reliable whole genome sequencing for outbreak preparedness and response

David F. Nieuwenhuijse; Anne van der Linden; Robert H.G. Kohl; Reina S. Sikkema; Marion P.G. Koopmans; Bas B. Oude Munnink

doi:10.1186/s12864-022-08749-5

Towards reliable whole genome sequencing for outbreak preparedness and response

David F. Nieuwenhuijse, Anne van der Linden, Robert H.G. Kohl, Reina S. Sikkema, Marion P.G. Koopmans, Bas B. Oude Munnink^*

^*Corresponding author for this work

Virology

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

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.

Original language	English
Article number	569
Journal	BMC Genomics
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s12864-022-08749-5
Publication status	Published - Dec 2022

Bibliographical note

Funding
COMPARE, VEO. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Publisher Copyright: © 2022. The Author(s).

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s12864-022-08749-5Final published version, 13 MBLicence: CC BY

Cite this

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title = "Towards reliable whole genome sequencing for outbreak preparedness and response",

abstract = "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.",

author = "Nieuwenhuijse, {David F.} and {van der Linden}, Anne and Kohl, {Robert H.G.} and Sikkema, {Reina S.} and Koopmans, {Marion P.G.} and {Oude Munnink}, {Bas B.}",

note = "Funding COMPARE, VEO. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Publisher Copyright: {\textcopyright} 2022. The Author(s).",

year = "2022",

month = dec,

doi = "10.1186/s12864-022-08749-5",

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AU - Nieuwenhuijse, David F.

AU - van der Linden, Anne

AU - Kohl, Robert H.G.

AU - Sikkema, Reina S.

AU - Koopmans, Marion P.G.

AU - Oude Munnink, Bas B.

N1 - Funding COMPARE, VEO. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Publisher Copyright: © 2022. The Author(s).

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

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Towards reliable whole genome sequencing for outbreak preparedness and response

Abstract

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