Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

BMC Genomics
Silvie Van den HoeckeXavier Saelens

Abstract

Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequencing technique and data analysis pipeline. We compared the suitability of two benchtop next-generation sequencers for whole genome influenza A quasispecies analysis: the Illumina MiSeq sequencing-by-synthesis and the Ion Torrent PGM semiconductor sequencing technique. We first compared the accuracy and sensitivity of both sequencers using plasmid DNA and different ratios of wild type and mutant plasmid. Illumina MiSeq sequencing reads were one and a half times more accurate than those of the Ion Torrent PGM. The majority of sequencing errors were substitutions on the Illumina MiSeq and insertions and deletions, mostly in homopolymer regions, on the Ion Torrent PGM. To evaluate the suitability of the two techniques for determining the genome diversity of influenza A virus, we generated plasmid-derived PR8 virus and grew this virus in vitro. We also optimized an RT-PCR protocol to obtain uniform coverage of all eight genomic RNA segments. The sequencing reads obtained with both sequencers could successfully be assembled de nov...Continue Reading

References

Jan 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·J J Skehel, M D Waterfield
Jul 1, 1993·Scientific American·M Eigen
Jun 1, 1996·Trends in Microbiology·M Eigen
Jun 17, 1998·Journal of Virology·S K BiswasD P Nayak
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·I Y GoryshinW S Reznikoff
May 10, 2000·Proceedings of the National Academy of Sciences of the United States of America·E HoffmannR G Webster
Aug 7, 2002·Vaccine·Erich HoffmannRobert G Webster
May 28, 2004·Virus Research·Emmie de WitRon A M Fouchier
Mar 16, 2006·Journal of Virology·Eri Nobusawa, Katsuhiko Sato
Nov 17, 2006·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Mariana BazGuy Boivin
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
Aug 22, 2008·Journal of Virology·Xiaojin XuIan A Wilson
Feb 20, 2009·Journal of Virology·Zejun LiYoshihiro Kawaoka
Jun 12, 2009·Protein Science : a Publication of the Protein Society·Mathias DregerTao Deng
Aug 19, 2009·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Munir IqbalJohn W McCauley
Oct 20, 2009·Vaccine·A H Ellebedy, R J Webby
Oct 21, 2009·Vaccine·Guus F RimmelzwaanAlbert D M E Osterhaus
Nov 11, 2009·Science·Scott E HensleyJonathan W Yewdell
May 7, 2010·Journal of Virology·Pablo R MurciaJames L N Wood
May 21, 2010·Cellular Microbiology·Mirco Schmolke, Adolfo García-Sastre
Jul 28, 2010·Journal of Virology·Rafael SanjuánRobert Belshaw
Jul 28, 2010·PLoS Pathogens·Adam S Lauring, Raul Andino
Apr 1, 1992·Trends in Ecology & Evolution·M A Nowak
May 18, 2011·Nucleic Acids Research·Kensuke NakamuraShigehiko Kanaya
May 20, 2011·Molecular Ecology Resources·Travis C Glenn

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Citations

Jan 19, 2016·Transfusion clinique et biologique : journal de la Société française de transfusion sanguine·V Sauvage, M Eloit
Jul 26, 2015·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Fiona ThorburnPablo R Murcia
Jun 1, 2016·The Veterinary Journal·Masatoshi OkamatsuYoshihiro Sakoda
May 20, 2016·Scientific Reports·Silvie Van den HoeckeXavier Saelens
Jul 4, 2016·Applied Microbiology and Biotechnology·Genyan YangC Todd Davis
Nov 12, 2015·BMC Bioinformatics·Koen Van der BorghtJeroen Aerssens
May 18, 2016·PloS One·Claudia CagliotiMaria Rosaria Capobianchi
Jan 2, 2018·Virusdisease·Mageshbabu RamamurthyGopalan Sridharan
Jul 24, 2015·Journal of Clinical Microbiology·Malaya K SahooBenjamin A Pinsky
Jan 24, 2020·Journal of Virology·Nancy BeerensBen Peeters
Apr 7, 2017·PloS One·Jose Carlos Mancera GraciaKristien Van Reeth
Apr 10, 2019·Transboundary and Emerging Diseases·Saskia A BergervoetNancy Beerens
Apr 20, 2021·JHEP Reports : Innovation in Hepatology·Su-Ru LinJia-Horng Kao
May 10, 2016·Journal of Microbiology & Biology Education·Boriana Marintcheva

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Datasets Mentioned

BETA
SRP052608
SRP052225

Methods Mentioned

BETA
amplicon sequencing
PCR
bronchoalveolar lavage
chip
mechanical
mechanical shearing
electrophoresis

Software Mentioned

Covaris
CLC Genomics Workbench
Ion Torrent Suite
Genstat
PyMol
Ion Torrent PGM

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