sábado, 14 de febrero de 2015

Ahead of Print -Nanomicroarray and Multiplex Next-Generation Sequencing for Simultaneous Identification and Characterization of Influenza Viruses - Volume 21, Number 3—March 2015 - Emerging Infectious Disease journal - CDC

full-text ►

Ahead of Print -Nanomicroarray and Multiplex Next-Generation Sequencing for Simultaneous Identification and Characterization of Influenza Viruses - Volume 21, Number 3—March 2015 - Emerging Infectious Disease journal - CDC



CDC. Centers for Disease Control and Prevention. CDC 24/7: Saving Lives. Protecting People.



Thumbnail of Nanomicroarray layout design for testing of samples for influenza A and B viruses. The microarray internal positive control capture is listed in Technical Appendix Table 1. The negative control is the printing buffer. M, matrix protein.

Figure 1. Nanomicroarray layout design for testing of samples for influenza A and B viruses. The microarray internal positive control capture is listed in Technical Appendix[PDF - 596 KB - 8 pages] Table 1. The negative...


Volume 21, Number 3—March 2015

Research

Nanomicroarray and Multiplex Next-Generation Sequencing for Simultaneous Identification and Characterization of Influenza Viruses

Jiangqin ZhaoComments to Author , Viswanath Ragupathy, Jikun Liu, Xue Wang, Sai Vikram Vemula, Haja Sittana El Mubarak, Zhiping Ye, Marie L. Landry, and Indira HewlettComments to Author 
Author affiliations: Food and Drug Administration, Silver Spring, Maryland, USA (J. Zhao, V. Ragupathy, J. Liu, X. Wang, S.V. Vemula, H.S. El Mubarak, Z. Ye, I. Hewlett)Yale University School of Medicine, New Haven, Connecticut, USA (M.L. Landry)

Abstract

Conventional methods for detection and discrimination of influenza viruses are time consuming and labor intensive. We developed a diagnostic platform for simultaneous identification and characterization of influenza viruses that uses a combination of nanomicroarray for screening and multiplex next-generation sequencing (NGS) assays for laboratory confirmation. The nanomicroarray was developed to target hemagglutinin, neuraminidase, and matrix genes to identify influenza A and B viruses. PCR amplicons synthesized by using an adapted universal primer for all 8 gene segments of 9 influenza A subtypes were detected in the nanomicroarray and confirmed by the NGS assays. This platform can simultaneously detect and differentiate multiple influenza A subtypes in a single sample. Use of these methods as part of a new diagnostic algorithm for detection and confirmation of influenza infections may provide ongoing public health benefits by assisting with future epidemiologic studies and improving preparedness for potential influenza pandemics.
Influenza A virus consists of 8 negative, single-stranded RNA segments encoding 11 proteins: polymerase basic 1 and 2 (PB1 and PB2); polymerase acidic (PA); hemagglutinin (HA); nucleoprotein (NP); neuraminidase (NA); matrix (M1/2); and nonstructural (NS1/2). Influenza A viruses are classified into 18 HA subtypes (H1–H18) and 11 NA subtypes (N1–N11), determined on the basis of the antigenic differences in the surface glycoproteins HA and NA (14). All known HA subtypes of influenza A virus are found in aquatic birds, and some, including H1, H2, H3, H5, H7, and H9, have been reported to infect humans (1,57). Direct transmission of avian influenza A virus subtypes H5N1, H7N2, H7N3, H7N7, H9N2, and H10N7 from domestic poultry to humans has been reported (813).
In early 2009, a novel swine-origin virus, designated influenza A(H1N1)pdm09 (pH1N1), emerged in Mexico and spread rapidly around the world, causing a global influenza pandemic (14,15). This virus was generated by multiple reassortment events over 10 years (16,17) and continued to circulate in humans after the initial pandemic period, replacing the previously circulating seasonal H1N1 viruses. Influenza A(H3N2) variant virus (H3N2v) isolated from humans in the United States in 2011 was also generated through reassortment originating from swine, avian, and human viruses, including the M gene from pH1N1 virus (18,19). More recently, a novel avian-origin influenza A(H7N9) virus capable of poultry-to-human transmission was identified in China (7;http://www.who.int/influenza/human_animal_interface/influenza_h7n9/140225_H7N9RA_for_web_20140306FM.pdf). Diagnosis of infection with this virus is difficult because infection does not kill infected poultry, but the virus may post a substantial risk for a human pandemic because of a lack of immunity in the general population (7). As these viruses demonstrate, reassortment of pH1N1 virus with other circulating seasonal strains can produce virulent variants that can be transmitted to and among humans and that could emerge as a future pandemic strain (15,20,21). Therefore, it is critical to determine whether transmitted viruses have pandemic potential in humans during the influenza season.
Multiple influenza strains are usually prevalent during an influenza season. Increasing global travel results in rapid spread of novel influenza viruses from one geographic region to another (13,22). Current approaches for screening and characterizing novel influenza viruses require many steps and multiple assays. A single test has not been available for simultaneous identification of newly emerging strains from known or unknown subtypes of influenza viruses and the characterization of unique virulence factors or putative antiviral resistance markers.
We previously described a method for detection of avian influenza A(H5N1) and swine-origin pH1N1 viruses that used a nanotechnology-based, PCR-free, whole-genome microarray assay (nanomicroarray) (23,24). In this article, we describe a new diagnostic platform for identification and characterization of subtypes of influenza A virus that uses nanomicroarray for screening and multiplex next-generation sequencing (NGS) for laboratory confirmation. We demonstrate that this platform enables accurate and simultaneous identification of multiple subtypes in a single sample. We used this platform to evaluate clinical nasopharyngeal swab specimens from patients with influenza-like illness that had tested positive for influenza virus to determine influenza virus subtype.

Dr Zhao is a virologist and reviewer at the Food and Drug Administration, Silver Spring, Maryland. His research interests include new technologies and tools for diagnosis of infectious viral pathogens.

Acknowledgments

We are thankful to FDA Center for Biologics Evaluation and Research core facility staff for help with some NGS assays and oligosynthesis.
This work was funded through the FDA Center for Biologics Evaluation and Research intramural and Medical Countermeasures Initiative funds.
The findings and conclusions in this article have not been formally disseminated by the Food and Drug Administration and should not be construed to represent any Agency determination or policy.

References

  1. Webster RGBean WJGorman OTChambers TMKawaoka YEvolution and ecology of influenza A viruses. Microbiol Rev1992;56:15279.PubMed
  2. Röhm CZhou NSuss JMackenzie JWebster RGCharacterization of a novel influenza hemagglutinin, H15: criteria for determination of influenza A subtypes. Virology1996;217:50816DOIPubMed
  3. Fouchier RAMunster VWallensten ABestebroer TMHerfst SSmith DCharacterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J Virol2005;79:281422DOIPubMed
  4. Tong SZhu XLi YNew world bats harbor diverse influenza A viruses. PLoS Pathog2013;9:e1003657DOIPubMed
  5. Horimoto TKawaoka YPandemic threat posed by avian influenza A viruses. Clin Microbiol Rev2001;14:12949DOIPubMed
  6. Hilleman MRRealities and enigmas of human viral influenza: pathogenesis, epidemiology and control. Vaccine2002;20:306887DOIPubMed
  7. Gao RCao BHu YFeng ZWang DHu WHuman infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med2013;368:188897.DOIPubMed
  8. Arzey GGKirkland PDArzey KEFrost MMaywood PConaty SInfluenza virus A (H10N7) in chickens and poultry abattoir workers, Australia.Emerg Infect Dis2012;18:8146DOIPubMed
  9. Cheng VCChan JFWen XWu WLQue TLChen HInfection of immunocompromised patients by avian H9N2 influenza A virus. J Infect.2011;62:3949DOIPubMed
  10. Koopmans MWilbrink BConyn MNatrop Gvan der Nat HVennema HTransmission of H7N7 avian influenza A virus to human beings during a large outbreak in commercial poultry farms in the Netherlands. Lancet2004;363:58793DOIPubMed
  11. Ostrowsky BHuang ATerry WAnton DBrunagel BTraynor LLow pathogenic avian influenza A (H7N2) virus infection in immunocompromised adult, New York, USA, 2003. Emerg Infect Dis2012;18:112831DOIPubMed
  12. Tweed SASkowronski DMDavid STLarder APetric MLees WHuman illness from avian influenza H7N3, British Columbia. Emerg Infect Dis.2004;10:21969DOIPubMed
  13. Pabbaraju KTellier RWong SLi YBastien NTang JWFull-genome analysis of avian influenza A(H5N1) virus from a human, North America, 2013.Emerg Infect Dis2014;20:88791DOIPubMed
  14. Gallaher WRTowards a sane and rational approach to management of influenza H1N1 2009. Virol J2009;6:51DOIPubMed
  15. Vijaykrishna DPoon LLZhu HCMa SKLi OTCheung CLReassortment of pandemic H1N1/2009 influenza A virus in swine. Science.2010;328:1529DOIPubMed
  16. Smith GJVijaykrishna DBahl JLycett SJWorobey MPybus OGOrigins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature2009;459:11225DOIPubMed
  17. Garten RJDavis CTRussell CAShu BLindstrom SBalish AAntigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science2009;325:197201DOIPubMed
  18. Lindstrom SGarten RBalish AShu BEmery SBerman LHuman infections with novel reassortant influenza A(H3N2)v viruses, United States, 2011. Emerg Infect Dis2012;18:8347DOIPubMed
  19. Nelson MIVincent ALKitikoon PHolmes ECGramer MREvolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009–2011. J Virol2012;86:88728DOIPubMed
  20. Kitikoon PVincent ALGauger PCSchlink SNBayles DOGramer MRPathogenicity and transmission in pigs of the novel A(H3N2)v influenza virus isolated from humans and characterization of swine H3N2 viruses isolated in 2010–2011. J Virol2012;86:680414DOIPubMed
  21. Webby RJWebster RGEmergence of influenza A viruses. Philos Trans R Soc Lond B Biol Sci2001;356:181728DOIPubMed
  22. Chang SYLin PHTsai JCHung CCChang SCThe first case of H7N9 influenza in Taiwan. Lancet2013;381:1621DOIPubMed
  23. Zhao JWang XRagupathy VZhang PTang WYe ZRapid detection and differentiation of swine-origin influenza a virus (H1N1/2009) from other seasonal influenza A viruses. Viruses2012;4:30129DOIPubMed
  24. Zhao JTang SStorhoff JMarla SBao YPWang XMultiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay. BMC Biotechnol2010;10:74DOIPubMed
  25. Landry MLFerguson DCytospin-enhanced immunofluorescence and impact of sample quality on detection of novel swine origin (H1N1) influenza virus. J Clin Microbiol2010;48:9579DOIPubMed
  26. Zhou BDonnelly MEScholes DTSt George KHatta MKawaoka YSingle-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza a viruses. J Virol2009;83:1030913DOIPubMed
  27. Hoffmann EStech JGuan YWebster RGPerez DRUniversal primer set for the full-length amplification of all influenza A viruses. Arch Virol.2001;146:227589DOIPubMed
  28. Treangen TJSalzberg SLRepetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet.2012;13:3646.PubMed
  29. Tamura KDudley JNei MKumar SMEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol.2007;24:15969DOIPubMed
  30. Chen YLiang WYang SWu NGao HSheng JHuman infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome. Lancet2013;381:191625DOIPubMed
  31. Yurovsky AMoret BMFluReF, an automated flu virus reassortment finder based on phylogenetic trees. BMC Genomics2011;12(Suppl 2):S3.DOIPubMed
  32. Rabadan RLevine AJKrasnitz M. Non-random reassortment in human influenza A viruses. Influenza Other Respir Viruses. 2008;2:9–22.
  33. Lun ATWong JWDownard KMFluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry. BMC Bioinformatics2012;13:208DOIPubMed
  34. Jonges MMeijer AFouchier RAKoch GLi JPan JCGuiding outbreak management by the use of influenza A(H7Nx) virus sequence analysis. Euro Surveill2013;18:20460 .PubMed
  35. Munster VJde Wit Evan Riel DBeyer WERimmelzwaan GFOsterhaus ADThe molecular basis of the pathogenicity of the Dutch highly pathogenic human influenza A H7N7 viruses. J Infect Dis2007;196:25865DOIPubMed
  36. Mok CKLee HHLestra MNicholls JMChan MCSia SFAmino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts. J Virol2014;88:356876DOIPubMed
  37. Hatta MGao PHalfmann PKawaoka YMolecular basis for high virulence of Hong Kong H5N1 influenza A viruses. Science2001;293:18402.DOIPubMed
  38. Zaraket HSaito RSuzuki YSuzuki YCaperig-Dapat IDapat CGenomic events contributing to the high prevalence of amantadine-resistant influenza A/H3N2. Antivir Ther2010;15:30719DOIPubMed
  39. Liu QLu LSun ZChen GWWen YJiang SGenomic signature and protein sequence analysis of a novel influenza A (H7N9) virus that causes an outbreak in humans in China. Microbes Infect2013;15:4329DOIPubMed
  40. Chen YLiang WYang SWu NGao HSheng JHuman infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterization of viral genome. Lancet2013;381:191625DOIPubMed

Figures

Tables

Technical Appendix

Suggested citation for this article: Zhao J, Ragupathy V, Liu J, Wang X, Vemula SV, El Mubarak HS, et al. Nanomicroarray and multiplex next-generation sequencing for simultaneous identification and characterization of influenza viruses. Emerg Infect Dis [Internet]. 2015 Mar [date cited].http://dx.doi.org/10.3201/eid2103.141169
DOI: 10.3201/eid2103.141169

No hay comentarios:

Publicar un comentario