tetano
Editor, Senior Moderator
PLoS One. 2016 Sep 22;11(9):e0163175. doi: 10.1371/journal.pone.0163175.
[h=1]Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics.[/h] Zhao J[SUP]1[/SUP], Liu J[SUP]1[/SUP], Vemula SV[SUP]1[/SUP], Lin C[SUP]1[/SUP], Tan J[SUP]1[/SUP], Ragupathy V[SUP]1[/SUP], Wang X[SUP]1[/SUP], Mbondji-Wonje C[SUP]1[/SUP], Ye Z[SUP]2[/SUP], Landry ML[SUP]3[/SUP], Hewlett I[SUP]1[/SUP].
[h=3]Author information[/h]
[h=3]Abstract[/h] Reassortment of 2009 (H1N1) pandemic influenza virus (pdH1N1) with other strains may produce more virulent and pathogenic forms, detection and their rapid characterization is critical. In this study, we reported a "one-size-fits-all" approach using a next-generation sequencing (NGS) detection platform to extensively identify influenza viral genomes for diagnosis and determination of novel virulence and drug resistance markers. A de novo module and other bioinformatics tools were used to generate contiguous sequence and identify influenza types/subtypes. Of 162 archived influenza-positive patient specimens, 161(99.4%) were positive for either influenza A or B viruses determined using the NGS assay. Among these, 135(83.3%) were A(H3N2), 14(8.6%) were A(pdH1N1), 2(1.2%) were A(H3N2) and A(pdH1N1) virus co-infections and 10(6.2%) were influenza B viruses. Of the influenza A viruses, 66.7% of A(H3N2) viruses tested had a E627K mutation in the PB2 protein, and 87.8% of the influenza A viruses contained the S31N mutation in the M2 protein. Further studies demonstrated that the NGS assay could achieve a high level of sensitivity and reveal adequate genetic information for final laboratory confirmation. The current diagnostic platform allows for simultaneous identification of a broad range of influenza viruses, monitoring emerging influenza strains with pandemic potential that facilitating diagnostics and antiviral treatment in the clinical setting and protection of the public health.
PMID: 27658193 DOI: 10.1371/journal.pone.0163175
[PubMed - as supplied by publisher]
[h=1]Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics.[/h] Zhao J[SUP]1[/SUP], Liu J[SUP]1[/SUP], Vemula SV[SUP]1[/SUP], Lin C[SUP]1[/SUP], Tan J[SUP]1[/SUP], Ragupathy V[SUP]1[/SUP], Wang X[SUP]1[/SUP], Mbondji-Wonje C[SUP]1[/SUP], Ye Z[SUP]2[/SUP], Landry ML[SUP]3[/SUP], Hewlett I[SUP]1[/SUP].
[h=3]Author information[/h]
[h=3]Abstract[/h] Reassortment of 2009 (H1N1) pandemic influenza virus (pdH1N1) with other strains may produce more virulent and pathogenic forms, detection and their rapid characterization is critical. In this study, we reported a "one-size-fits-all" approach using a next-generation sequencing (NGS) detection platform to extensively identify influenza viral genomes for diagnosis and determination of novel virulence and drug resistance markers. A de novo module and other bioinformatics tools were used to generate contiguous sequence and identify influenza types/subtypes. Of 162 archived influenza-positive patient specimens, 161(99.4%) were positive for either influenza A or B viruses determined using the NGS assay. Among these, 135(83.3%) were A(H3N2), 14(8.6%) were A(pdH1N1), 2(1.2%) were A(H3N2) and A(pdH1N1) virus co-infections and 10(6.2%) were influenza B viruses. Of the influenza A viruses, 66.7% of A(H3N2) viruses tested had a E627K mutation in the PB2 protein, and 87.8% of the influenza A viruses contained the S31N mutation in the M2 protein. Further studies demonstrated that the NGS assay could achieve a high level of sensitivity and reveal adequate genetic information for final laboratory confirmation. The current diagnostic platform allows for simultaneous identification of a broad range of influenza viruses, monitoring emerging influenza strains with pandemic potential that facilitating diagnostics and antiviral treatment in the clinical setting and protection of the public health.
PMID: 27658193 DOI: 10.1371/journal.pone.0163175
[PubMed - as supplied by publisher]