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PLoS ONE. Rapid Detection and Subtyping of Human Influenza A Viruses and Reassortants by Pyrosequencing
[Source: PLoS ONE, full text: (LINK). Abstract, edited.]
Rapid Detection and Subtyping of Human Influenza A Viruses and Reassortants by Pyrosequencing
Yi-Mo Deng<SUP>1</SUP><SUP>*</SUP>, Natalie Caldwell<SUP>1</SUP>, Ian G. Barr<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP>
1 WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Disease Reference Laboratory (VIDRL), Melbourne, Victoria, Australia, 2 School of Applied Sciences, Monash University, Churchill, Victoria, Australia
Abstract
Background
Given the continuing co-circulation of the 2009 H1N1 pandemic influenza A viruses with seasonal H3N2 viruses, rapid and reliable detection of newly emerging influenza reassortant viruses is important to enhance our influenza surveillance.
Methodology/Principal Findings
A novel pyrosequencing assay was developed for the rapid identification and subtyping of potential human influenza A virus reassortants based on all eight gene segments of the virus. Except for HA and NA genes, one universal set of primers was used to amplify and subtype each of the six internal genes. With this method, all eight gene segments of 57 laboratory isolates and 17 original specimens of seasonal H1N1, H3N2 and 2009 H1N1 pandemic viruses were correctly matched with their corresponding subtypes. In addition, this method was shown to be capable of detecting reassortant viruses by correctly identifying the source of all 8 gene segments from three vaccine production reassortant viruses and three H1N2 viruses.
Conclusions/Significance
In summary, this pyrosequencing assay is a sensitive and specific procedure for screening large numbers of viruses for reassortment events amongst the commonly circulating human influenza A viruses, which is more rapid and cheaper than using conventional sequencing approaches.
Citation: Deng Y-M, Caldwell N, Barr IG (2011) Rapid Detection and Subtyping of Human Influenza A Viruses and Reassortants by Pyrosequencing. PLoS ONE 6(8): e23400. doi:10.1371/journal.pone.0023400
Editor: Volker Thiel, Kantonal Hospital St. Gallen, Switzerland
Received: June 6, 2011; Accepted: July 15, 2011; Published: August 19, 2011
Copyright: ? 2011 Deng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The Melbourne WHO Collaborating Centre for Reference and Research on Influenza is supported by the Australian Government Department of Health and Ageing. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: yi-mo.deng@influenzacentre.org
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Yi-Mo Deng<SUP>1</SUP><SUP>*</SUP>, Natalie Caldwell<SUP>1</SUP>, Ian G. Barr<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP>
1 WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Disease Reference Laboratory (VIDRL), Melbourne, Victoria, Australia, 2 School of Applied Sciences, Monash University, Churchill, Victoria, Australia
Abstract
Background
Given the continuing co-circulation of the 2009 H1N1 pandemic influenza A viruses with seasonal H3N2 viruses, rapid and reliable detection of newly emerging influenza reassortant viruses is important to enhance our influenza surveillance.
Methodology/Principal Findings
A novel pyrosequencing assay was developed for the rapid identification and subtyping of potential human influenza A virus reassortants based on all eight gene segments of the virus. Except for HA and NA genes, one universal set of primers was used to amplify and subtype each of the six internal genes. With this method, all eight gene segments of 57 laboratory isolates and 17 original specimens of seasonal H1N1, H3N2 and 2009 H1N1 pandemic viruses were correctly matched with their corresponding subtypes. In addition, this method was shown to be capable of detecting reassortant viruses by correctly identifying the source of all 8 gene segments from three vaccine production reassortant viruses and three H1N2 viruses.
Conclusions/Significance
In summary, this pyrosequencing assay is a sensitive and specific procedure for screening large numbers of viruses for reassortment events amongst the commonly circulating human influenza A viruses, which is more rapid and cheaper than using conventional sequencing approaches.
Citation: Deng Y-M, Caldwell N, Barr IG (2011) Rapid Detection and Subtyping of Human Influenza A Viruses and Reassortants by Pyrosequencing. PLoS ONE 6(8): e23400. doi:10.1371/journal.pone.0023400
Editor: Volker Thiel, Kantonal Hospital St. Gallen, Switzerland
Received: June 6, 2011; Accepted: July 15, 2011; Published: August 19, 2011
Copyright: ? 2011 Deng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The Melbourne WHO Collaborating Centre for Reference and Research on Influenza is supported by the Australian Government Department of Health and Ageing. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: yi-mo.deng@influenzacentre.org