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Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15

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Abstract

The influenza season 2014/15 was dominated by drift variants of influenza A(H3N2), which resulted in a reduced vaccine effectiveness. It was not clear if the performance of commercial nucleic-acid-based amplification (NAT) assays for the detection of influenza was affected. The purpose of this study was to perform a real-life evaluation of two commercial NAT assays. During January-April 2015, we tested a total of 665 samples from patients with influenza-like illness using the Fast Track Diagnostics Respiratory pathogens 21, a commercial multiplex kit, (cohorts 1 and 2, n = 563 patients) and the Xpert Flu/RSV XC assay (cohort 3, n = 102 patients), a single-use cartridge system. An in-house influenza real-time RT-PCR (cohort 1) and the RealStar Influenza RT-PCR 1.0 Kit (cohort 2 and 3) served as reference tests. Compared to the reference assay, an overall agreement of 95.9 % (cohort 1), 95 % (cohort 2), and 98 % (cohort 3) was achieved. A total of 24 false-negative results were observed using the Fast Track Diagnostics Respiratory pathogens 21 kit. No false-negative results occurred using the Xpert Flu/RSV XC assay. The Fast Track Diagnostics Respiratory pathogens 21 kit and the Xpert Flu/RSV XC assay had sensitivities of 90.7 % and 100 % and specificities of 100 % and 94.1 %, respectively, compared to the RealStar 1.0 kit. Upon modification of the Fast Track Diagnostics Respiratory pathogens 21 kit, the sensitivity increased to 97.3 %. Influenza virus strains circulating during the 2014/15 season reduced the detection sensitivity of a commercial NAT assay, and continuous monitoring of test performance is therefore necessary.

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References

  1. Broberg E, Snacken R, Adlhoch C, Beauté J, Galinska M, Pereyaslov D, Brown C, Penttinen P; WHO European Region, the European Influenza Surveillance Network (2015) Start of the 2014/15 influenza season in Europe: drifted influenza A(H3N2) viruses circulate as dominant subtype. Euro Surveill 20(4)

  2. Arbeitsgemeinschaft Influenza (AGI) Bericht zur Epidemiologie der Influenza in Deutschland Saison 2014/15. Robert-Koch-Institut. https://influenza.rki.de/Saisonberichte/2014.pdf. Accessed 21 Sep 2015

  3. Pebody RG, Warburton F, Ellis J, Andrews N, Thompson C, von Wissmann B, Green HK, Cottrell S, Johnston J, de Lusignan S, Moore C, Gunson R, Robertson C, McMenamin J, Zambon M (2015) Low effectiveness of seasonal influenza vaccine in preventing laboratory-confirmed influenza in primary care in the United Kingdom: 2014/15 mid-season results. Euro Surveill: bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 20(5):21025

    Article  CAS  Google Scholar 

  4. Panning M, Eickmann M, Landt O, Monazahian M, Olschläger S, Baumgarte S, Reischl U, Wenzel JJ, Niller HH, Günther S, Hollmann B, Huzly D, Drexler JF, Helmer A, Becker S, Matz B, Eis-Hübinger A, Drosten C (2009) Detection of influenza A(H1N1)v virus by real-time RT-PCR. Euro Surveill 14(36)

  5. Drexler JF, Helmer A, Kirberg H, Reber U, Panning M, Muller M, Hofling K, Matz B, Drosten C, Eis-Hubinger AM (2009) Poor clinical sensitivity of rapid antigen test for influenza A pandemic (H1N1) 2009 virus. Emerg Infect Dis 15(10):1662–1664. doi:10.3201/eid1510.091186

    Article  PubMed  PubMed Central  Google Scholar 

  6. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature 453(7195):615–619. doi:10.1038/nature06945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Yang JR, Kuo CY, Huang HY, Wu FT, Huang YL, Cheng CY, Su YT, Chang FY, Wu HS, Liu MT (2014) Newly emerging mutations in the matrix genes of the human influenza A(H1N1)pdm09 and A(H3N2) viruses reduce the detection sensitivity of real-time reverse transcription-PCR. J Clin Microbiol 52(1):76–82. doi:10.1128/JCM.02467-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Binnicker MJ, Baddour LM, Grys TE, Espy MJ, Hata DJ, Wotton JT, Patel R (2013) Identification of an influenza A H1N1/2009 virus with mutations in the matrix gene causing a negative result by a commercial molecular assay. J Clin Microbiol 51(6):2006–2007. doi:10.1128/JCM.00446-13

    Article  PubMed  PubMed Central  Google Scholar 

  9. Bonzel L, Tenenbaum T, Schroten H, Schildgen O, Schweitzer-Krantz S, Adams O (2008) Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction. Pediatr Infect Dis J 27(7):589–594. doi:10.1097/INF.0b013e3181694fb9

    Article  PubMed  Google Scholar 

  10. Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP, Perdue ML, Lohman K, Daum LT, Suarez DL (2002) Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. J Clin Microbiol 40(9):3256–3260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Schulze M, Nitsche A, Schweiger B, Biere B (2010) Diagnostic approach for the differentiation of the pandemic influenza A(H1N1)v virus from recent human influenza viruses by real-time PCR. PLoS One 5(4):e9966. doi:10.1371/journal.pone.0009966

    Article  PubMed  PubMed Central  Google Scholar 

  12. Overmeire Y, Vanlaere E, Hombrouck A, De Beenhouwer H, Simons G, Brink A, Van den Abeele AM, Verfaillie C, Van Acker J (2016) Severe sensitivity loss in an influenza A molecular assay due to antigenic drift variants during the 2014/15 influenza season. Diagn Microbiol Infect Dis. doi:10.1016/j.diagmicrobio.2016.02.004

    PubMed  Google Scholar 

  13. Panning M, Baumgarte S, Laue T, Bierbaum S, Raith S, Drexler JF, Helmer A, Falcone-Kapper V, Kochs G, Campe H, Huzly D, Eis-Hubinger AM, Drosten C (2011) Singleplex real-time RT-PCR for detection of influenza A virus and simultaneous differentiation of A/H1N1v and evaluation of the RealStar influenza kit. J Clin Virol 50(2):171–174. doi:10.1016/j.jcv.2010.10.010

    Article  CAS  PubMed  Google Scholar 

  14. Bierbaum S, Forster J, Berner R, Rucker G, Rohde G, Neumann-Haefelin D, Panning M, CAPNETZ study group (2014) Detection of respiratory viruses using a multiplex real-time PCR assay in Germany, 2009/10. Arch Virol 159(4):669–676. doi:10.1007/s00705-013-1876-3

    Article  CAS  PubMed  Google Scholar 

  15. Salez N, Nougairede A, Ninove L, Zandotti C, de Lamballerie X, Charrel RN (2015) Prospective and retrospective evaluation of the Cepheid Xpert(R) Flu/RSV XC assay for rapid detection of influenza A, influenza B, and respiratory syncytial virus. Diagn Microbiol Infect Dis 81(4):256–258. doi:10.1016/j.diagmicrobio.2015.01.008

    Article  CAS  PubMed  Google Scholar 

  16. Popowitch EB, Miller MB (2015) Performance characteristics of Xpert Flu/RSV XC assay. J Clin Microbiol 53(8):2720–2721. doi:10.1128/JCM.00972-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Klungthong C, Chinnawirotpisan P, Hussem K, Phonpakobsin T, Manasatienkij W, Ajariyakhajorn C, Rungrojcharoenkit K, Gibbons RV, Jarman RG (2010) The impact of primer and probe-template mismatches on the sensitivity of pandemic influenza A/H1N1/2009 virus detection by real-time RT-PCR. J Clin Virol 48(2):91–95. doi:10.1016/j.jcv.2010.03.012

    Article  CAS  PubMed  Google Scholar 

  18. Sun Y, Jia T, Sun Y, Han Y, Wang L, Zhang R, Zhang K, Lin G, Xie J, Li J (2013) External quality assessment for avian influenza A (H7N9) virus detection using armored RNA. J Clin Microbiol 51(12):4055–4059. doi:10.1128/JCM.02018-13

    Article  PubMed  PubMed Central  Google Scholar 

  19. Sakthivel SK, Whitaker B, Lu X, Oliveira DB, Stockman LJ, Kamili S, Oberste MS, Erdman DD (2012) Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses. J Virol Methods 185(2):259–266. doi:10.1016/j.jviromet.2012.07.010

    Article  CAS  PubMed  Google Scholar 

  20. Zheng X, Todd KM, Yen-Lieberman B, Kaul K, Mangold K, Shulman ST (2010) Unique finding of a 2009 H1N1 influenza virus-positive clinical sample suggests matrix gene sequence variation. J Clin Microbiol 48(2):665–666. doi:10.1128/JCM.02318-09

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank the technicians of the molecular diagnostic and virus isolation unit at both study sites for expert technical assistance and support.

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    Authors and Affiliations

    1. Institute of Virology, Medical Center - University of Freiburg, Hermann-Herder-Str. 11, 79104, Freiburg, Germany

      Daniela Huzly, Sibylle Bierbaum, Björn Eberle, Valeria Falcone & Marcus Panning

    2. Institute of Clinical and Molecular Virology, University of Erlangen-Nuremberg, Erlangen, Germany

      Klaus Korn, Antje Knöll & Philipp Steininger

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    1. Daniela Huzly
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    3. Sibylle Bierbaum
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    Correspondence to Marcus Panning.

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    D. Huzly and K. Korn contributed equally to this work.

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    Huzly, D., Korn, K., Bierbaum, S. et al. Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15. Arch Virol 161, 2417–2423 (2016). https://doi.org/10.1007/s00705-016-2930-8

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    • DOI: https://doi.org/10.1007/s00705-016-2930-8

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