Multiplex reverse-transcription loop-mediated isothermal amplification coupled with cascade invasive reaction and nanoparticle hybridization for subtyping of influenza a virus

Scientific Reports

Volumn 7, Issue , 2017, Pages

  Chi, Ying ^a,b   Ge, Yiyue ^b   Zhao, Kangchen ^b   Zou, Bingjie ^c   Liu, Bin ^a   Qi, Xian ^b   Bian, Qian ^b   Shi, Zhiyang ^b   Zhu, Fengcai ^b   Zhou, Minghao ^b   Cui, Lunbiao ^b   Su, Chuan ^a  

^a NANJING MEDICAL UNIVERSITY   (China)

^b BEIJING HOSPITAL   (China)

^c MEDICAL SCHOOL OF NANJING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GOLD; NANOPARTICLE; VIRUS RNA;

CLASSIFICATION; GENETICS; HUMAN; INFLUENZA; INFLUENZA A VIRUS; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID HYBRIDIZATION; PROCEDURES; REPRODUCIBILITY; REVERSE TRANSCRIPTION; SENSITIVITY AND SPECIFICITY; VIROLOGY;

GOLD; HUMANS; INFLUENZA A VIRUS; INFLUENZA, HUMAN; NANOPARTICLES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTION; RNA, VIRAL; SENSITIVITY AND SPECIFICITY;

EID: 85016039121     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep44924     Document Type: Article

References (50)

1. Simonsen, L. et al. Global mortality estimates for the 2009 Influenza Pandemic from the GLaMOR project: a modeling study. PLoS Med 10, e1001558, doi: 10.1371/journal.pmed.1001558 (2013).
2. Medina, R. A. & Garcia-Sastre, A. Influenza A viruses: new research developments. Nat Rev Microbiol 9, 590-603, doi: 10.1038/nrmicro2613 (2011).
3. Fouchier, R. A. et al. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J Virol 79, 2814-2822, doi: 10.1128/JVI.79.5.2814-2822.2005 (2005).
4. Harper, S. A. et al. Prevention and control of influenza: recommendations of the Advisory Committee on Immunization Practices (ACIP). MMWR Recomm Rep 53, 1-40 (2004).
5. Epperson, S. et al. Influenza activity -United States, 2013-14 season and composition of the 2014-15 influenza vaccines. MMWR Morb Mortal Wkly Rep 63, 483-490 (2014).
6. Uyeki, T. M. Preventing and controlling influenza with available interventions. N Engl J Med 370, 789-791, doi: 10.1056/NEJMp1400034 (2014).
7. Hien, T. T., de Jong, M. & Farrar, J. Avian influenza-a challenge to global health care structures. N Engl J Med 351, 2363-2365, doi: 10.1056/NEJMp048267 (2004).
8. Beigel, J. H. et al. Avian influenza A (H5N1) infection in humans. N Engl J Med 353, 1374-1385, doi: 10.1056/NEJMra052211 (2005).
9. Yang, Z. F., Mok, C. K., Peiris, J. S. & Zhong, N. S. Human Infection with a Novel Avian Influenza A(H5N6) Virus. N Engl J Med 373, 487-489, doi: 10.1056/NEJMc1502983 (2015).
10. Gao, R. et al. Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med 368, 1888-1897, doi: 10.1056/NEJMoa1304459 (2013).
11. Ma, X. et al. A multiplex PCR assay for the detection of five influenza viruses using a dual priming oligonucleotide system. BMC Infect Dis 15, 93, doi: 10.1186/s12879-015-0818-y (2015).
12. Chaharaein, B., Omar, A. R., Aini, I., Yusoff, K. & Hassan, S. S. Detection of H5, H7 and H9 subtypes of avian influenza viruses by multiplex reverse transcription-polymerase chain reaction. Microbiol Res 164, 174-179, doi: 10.1016/j.micres.2007.01.001 (2009).
13. Suwannakarn, K. et al. Typing (A/B) and subtyping (H1/H3/H5) of influenza A viruses by multiplex real-time RT-PCR assays. J Virol Methods 152, 25-31, doi: 10.1016/j.jviromet.2008.06.002 (2008).
14. Choi, J. H. et al. Development and evaluation of multiplex real-time RT-PCR assays for seasonal, pandemic A/H1pdm09 and avian A/H5 influenza viruses detection. J Microbiol 51, 252-257, doi: 10.1007/s12275-013-2452-y (2013).
15. Munro, S. B., Kuypers, J. & Jerome, K. R. Comparison of a multiplex real-time PCR assay with a multiplex Luminex assay for influenza virus detection. J Clin Microbiol 51, 1124-1129, doi: 10.1128/JCM.03113-12 (2013).
16. Niemz, A., Ferguson, T. M. & Boyle, D. S. Point-of-care nucleic acid testing for infectious diseases. Trends Biotechnol 29, 240-250, doi: 10.1016/j.tibtech.2011.01.007 (2011).
17. Notomi, T. et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28, E63 (2000).
18. Parida, M., Sannarangaiah, S., Dash, P. K., Rao, P. V. & Morita, K. Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Rev Med Virol 18, 407-421, doi: 10.1002/rmv.593 (2008).
19. Hong, T. C. et al. Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus. J Clin Microbiol 42, 1956-1961 (2004).
20. Imai, M. et al. Development of H5-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenza virus infection. Vaccine 24, 6679-6682, doi: 10.1016/j.vaccine.2006.05.046 (2006).
21. Curtis, K. A., Rudolph, D. L. & Owen, S. M. Rapid detection of HIV-1 by reverse-transcription, loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 151, 264-270, doi: 10.1016/j.jviromet.2008.04.011 (2008).
22. Wang, X. et al. Detection of enterovirus 71 using reverse transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 179, 330-334, doi: 10.1016/j.jviromet.2011.11.019 (2012).
23. Ge, Y. et al. Rapid and sensitive detection of novel avian-origin influenza A (H7N9) virus by reverse transcription loop-mediated isothermal amplification combined with a lateral-flow device. PLoS One 8, e69941, doi: 10.1371/journal.pone.0069941 (2013).
24. Liang, T. et al. A rapid assay for simultaneous detection of Spiroplasma eriocheiris and white spot syndrome virus in Procambarus clarkii by multiplex PCR. Lett Appl Microbiol 51, 532-538, doi: 10.1111/j.1472-765X.2010.02927.x (2010).
25. Liang, C. et al. Multiplex loop-mediated isothermal amplification detection by sequence-based barcodes coupled with nicking endonuclease-mediated pyrosequencing. Anal Chem 84, 3758-3763, doi: 10.1021/ac3003825 (2012).
26. Mahony, J. et al. Multiplex loop-mediated isothermal amplification (M-LAMP) assay for the detection of influenza A/H1, A/H3 and influenza B can provide a specimen-to-result diagnosis in 40 min with single genome copy sensitivity. J Clin Virol 58, 127-131, doi: 10.1016/j.jcv.2013.06.006 (2013).
27. Tanner, N. A., Zhang, Y. & Evans, T. C. Jr. Simultaneous multiple target detection in real-time loop-mediated isothermal amplification. Biotechniques 53, 81-89, doi: 10.2144/0000113902 (2012).
28. Wang, Y. et al. Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification: A Novel Analytically Rapid, Sensitive, Multiplex Loop-Mediated Isothermal Amplification Detection Technique. J Mol Diagn 17, 392-401, doi: 10.1016/j. jmoldx.2015.03.002 (2015).
29. Xu, W., Xue, X., Li, T., Zeng, H. & Liu, X. Ultrasensitive and selective colorimetric DNA detection by nicking endonuclease assisted nanoparticle amplification. Angew Chem Int Ed Engl 48, 6849-6852, doi: 10.1002/anie.200901772 (2009).
30. Xu, W. et al. Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA). Small 8, 1846-1850, doi: 10.1002/smll.201200263 (2012).
31. Zou, B. et al. Sensitive and specific colorimetric DNA detection by invasive reaction coupled with nicking endonuclease-assisted nanoparticles amplification. Biosens Bioelectron 66, 50-54, doi: 10.1016/j.bios.2014.10.077 (2015).
32. Lyamichev, V. I. et al. Experimental and theoretical analysis of the invasive signal amplification reaction. Biochemistry 39, 9523-9532 (2000).
33. Hall, J. G. et al. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc Natl Acad Sci USA 97, 8272-8277, doi: 10.1073/pnas.140225597 (2000).
34. Alexander, D. J. Avian influenza -diagnosis. Zoonoses Public Health 55, 16-23, doi: 10.1111/j.1863-2378.2007.01082.x (2008).
35. Mori, Y., Kitao, M., Tomita, N. & Notomi, T. Real-time turbidimetry of LAMP reaction for quantifying template DNA. J Biochem Biophys Methods 59, 145-157, doi: 10.1016/j.jbbm.2003.12.005 (2004).
36. Nyan, D. C. & Swinson, K. L. A novel multiplex isothermal amplification method for rapid detection and identification of viruses. Sci Rep 5, 17925, doi: 10.1038/srep17925 (2015).
37. Tomita, N., Mori, Y., Kanda, H. & Notomi, T. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc 3, 877-882, doi: 10.1038/nprot.2008.57 (2008).
38. Tao, Z. Y. et al. Adaptation of a visualized loop-mediated isothermal amplification technique for field detection of Plasmodium vivax infection. Parasit Vectors 4, 115, doi: 10.1186/1756-3305-4-115 (2011).
39. Dou, M. et al. Multiplexed instrument-free meningitis diagnosis on a polymer/paper hybrid microfluidic biochip. Biosens Bioelectron 87, 865-873, doi: 10.1016/j.bios.2016.09.033 (2016).
40. Osman, H. A. et al. Development and evaluation of loop-mediated isothermal amplification assay for detection of Crimean Congo hemorrhagic fever virus in Sudan. J Virol Methods 190, 4-10, doi: 10.1016/j.jviromet.2013.03.004 (2013).
41. Wang, C., Shen, X., Lu, J. & Zhang, L. Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) system for rapid detection of HDV genotype 1. Lett Appl Microbiol 56, 229-235, doi: 10.1111/lam.12039 (2013).
42. Kaneko, H., Kawana, T., Fukushima, E. & Suzutani, T. Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances. J Biochem Biophys Methods 70, 499-501, doi: 10.1016/j.jbbm.2006.08.008 (2007).
43. Nakauchi, M., Takayama, I., Takahashi, H., Tashiro, M. & Kageyama, T. Development of a reverse transcription loop-mediated isothermal amplification assay for the rapid diagnosis of avian influenza A (H7N9) virus infection. J Virol Methods 204, 101-104, doi: 10.1016/j.jviromet.2014.03.028 (2014).
44. Lee, M. S. et al. M-specific reverse transcription loop-mediated isothermal amplification for detection of pandemic (H1N1) 2009 virus. Eur J Clin Invest 41, 434-441, doi: 10.1111/j.1365-2362.2010.02427.x (2011).
45. Ma, X. J. et al. Visual detection of pandemic influenza A H1N1 Virus 2009 by reverse-transcription loop-mediated isothermal amplification with hydroxynaphthol blue dye. J Virol Methods 167, 214-217, doi: 10.1016/j.jviromet.2010.03.027 (2010).
46. Hill, H. D. & Mirkin, C. A. The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange. Nat Protoc 1, 324-336, doi: 10.1038/nprot.2006.51 (2006).
47. Song, Q. et al. Invader Assisted Enzyme-Linked Immunosorbent Assay for Colorimetric Detection of Disease Biomarkers Using Oligonucleotide Probe-Modified Gold Nanoparticles. J Biomed Nanotechnol 12, 831-839 (2016).
48. WHO. Real-time RT-PCR Protocol for the Detection of Avian Influenza A(H7N9) Virus. Available http://www.who.int/influenza/gisrs-laboratory/cnic-realtime-rt-pcr-protocol-a-h7n9.pdf. Accessed 2016 October 10 (2013).
49. WHO. CDC protocol of realtime RTPCR for influenza A(H1N1). Available: http://www.who.int/csr/resources/publications/swineflu/CDCRealtimeRTPCR-SwineH1Assay-2009-20090430.pdf. Accessed 2016 October 10 (2009).
50. WHO. Recommendations and laboratory procedures for detection of avian influenza A(H5N1) virus in specimens from suspected human cases. Available: http://www.who.int/influenza/resources/documents/RecAIlabtestsAug07.pdf. Accessed 2016 October 10 (2007).