title: Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics.
abstract: 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.
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Jiangqin
authors.identifier: http://orcid.org/0000-0003-4672-0735
authors.initials: J
authors.lastname: Zhao
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Jikun
authors.initials: J
authors.lastname: Liu
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Sai Vikram
authors.initials: SV
authors.lastname: Vemula
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Corinna
authors.initials: C
authors.lastname: Lin
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Jiying
authors.initials: J
authors.lastname: Tan
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Viswanath
authors.initials: V
authors.lastname: Ragupathy
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Xue
authors.initials: X
authors.lastname: Wang
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Christelle
authors.initials: C
authors.lastname: Mbondji-Wonje
authors.affiliation: DVP/OVRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Ye
authors.affiliation: Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06520, United States of America.
authors.forename: Marie L
authors.initials: ML
authors.lastname: Landry
authors.affiliation: DETTD/OBRR/CBER, Food and Drug Administration, Silver Spring, MD, 20993, United States of America.
authors.forename: Indira
authors.initials: I
authors.lastname: Hewlett