A simple method for the parallel deep sequencing of full influenza A genomes

Marie-Louise Kampmann; Sarah Louise Fordyce; Maria del Carmen Avila Arcos; Morten Rasmussen; Eske Willerslev; Lars Peter  Nielsen; Tom Gilbert

doi:10.1016/j.jviromet.2011.09.001

A simple method for the parallel deep sequencing of full influenza A genomes

Marie-Louise Kampmann, Sarah Louise Fordyce, Maria del Carmen Avila Arcos, Morten Rasmussen, Eske Willerslev, Lars Peter Nielsen, Tom Gilbert

32 Citations (Scopus)

Abstract

Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool. This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus from human and H1N1 virus from swine, on a single lane of a GAIIx flow cell to an average depth of 122-fold. This technique can be applied to cultivated and uncultivated virus.

Original language	English
Journal	Journal of Virological Methods
Volume	178
Issue number	1-2
Pages (from-to)	243-248
Number of pages	6
ISSN	0166-0934
DOIs	https://doi.org/10.1016/j.jviromet.2011.09.001
Publication status	Published - Dec 2011

Keywords

Faculty of Science

Access to Document

10.1016/j.jviromet.2011.09.001

Cite this

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title = "A simple method for the parallel deep sequencing of full influenza A genomes",

abstract = "Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool. This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus from human and H1N1 virus from swine, on a single lane of a GAIIx flow cell to an average depth of 122-fold. This technique can be applied to cultivated and uncultivated virus.",

keywords = "Faculty of Science, Influenza A , Full genome sequencing, High-throughput sequencing ",

author = "Marie-Louise Kampmann and Fordyce, {Sarah Louise} and {Avila Arcos}, {Maria del Carmen} and Morten Rasmussen and Eske Willerslev and Nielsen, {Lars Peter} and Tom Gilbert",

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language = "English",

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T1 - A simple method for the parallel deep sequencing of full influenza A genomes

AU - Kampmann, Marie-Louise

AU - Fordyce, Sarah Louise

AU - Avila Arcos, Maria del Carmen

AU - Rasmussen, Morten

AU - Willerslev, Eske

AU - Nielsen, Lars Peter

AU - Gilbert, Tom

PY - 2011/12

Y1 - 2011/12

N2 - Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool. This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus from human and H1N1 virus from swine, on a single lane of a GAIIx flow cell to an average depth of 122-fold. This technique can be applied to cultivated and uncultivated virus.

AB - Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool. This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus from human and H1N1 virus from swine, on a single lane of a GAIIx flow cell to an average depth of 122-fold. This technique can be applied to cultivated and uncultivated virus.

KW - Faculty of Science

KW - Influenza A

KW - Full genome sequencing

KW - High-throughput sequencing

U2 - 10.1016/j.jviromet.2011.09.001

DO - 10.1016/j.jviromet.2011.09.001

M3 - Letter

SN - 0166-0934

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