Recombinase polymerase amplification assay for rapid diagnostics of dengue infection

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Abd El Wahed, Ahmed ^a,b   Patel, Pranav ^c   Faye, Oumar ^d   Thaloengsok, Sasikanya ^e   Heidenreich, Doris ^f   Matangkasombut, Ponpan ^e   Manopwisedjaroen, Khajohnpong ^e   Sakuntabhai, Anavaj ^g   Sall, Amadou A ^d   Hufert, Frank T ^h   Weidmann, Manfred ⁱ  

^a GERMAN PRIMATE CENTER   (Germany)

^b MANSOURA UNIVERSITY   (Egypt)

^c ROBERT KOCH INSTITUTE   (Germany)

^d INSTITUT PASTEUR DE DAKAR   (Senegal)

^e Mahidol University ^*  (Thailand)

^f UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

^g INSTITUT PASTEUR   (France)

^h BRANDENBURG MEDICAL SCHOOL THEODOR FONTANE   (Germany)

ⁱ UNIVERSITY OF STIRLING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DENGUE; DENGUE RAPID TEST; DENGUE VIRUS 1; DENGUE VIRUS 2; DENGUE VIRUS 3; DENGUE VIRUS 4; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; GENE AMPLIFICATION; HUMAN; POINT OF CARE TESTING; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION RECOMBINASE POLYMERASE AMPLIFICATION ASSAY; RNA EXTRACTION; SENEGAL; SENSITIVITY AND SPECIFICITY; THAILAND; VIRUS DETECTION; CLASSIFICATION; DENGUE VIRUS; GENETICS; NUCLEIC ACID AMPLIFICATION; PROCEDURES; VIROLOGY;

DENGUE VIRUS;

VIRUS RNA;

DENGUE; DENGUE VIRUS; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; REPRODUCIBILITY OF RESULTS; RNA, VIRAL; SENEGAL; SENSITIVITY AND SPECIFICITY; THAILAND;

EID: 84937013070     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0129682     Document Type: Article

References (50)

1. Gan VC, Lye DC, Thein TL, Dimatatac F, Tan AS, Leo YS. Implications of discordance in world health organization 1997 and 2009 dengue classifications in adult dengue. PloS one. 2013; 8(4):e60946. doi: 10.1371/journal.pone.0060946 PMID: 23573291; PubMed Central PMCID: PMC3613419.
2. Daep CA, Munoz-Jordan JL, Eugenin EA. Flaviviruses, an expanding threat in public health: focus on dengue, West Nile, and Japanese encephalitis virus. Journal of neurovirology. 2014. doi: 10.1007/s13365-014-0285-z PMID: 25287260.
3. Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013; 496(7446):504-7. doi: 10.1038/nature12060 PMID: 23563266; PubMed Central PMCID: PMC3651993.
4. WHO. Dengue fact sheets. Available: http://wwwwprowhoint/mediacentre/factsheets/fs-09032012-Dengue/en/. 2014.
5. Thisyakorn U, Thisyakorn C. Latest developments and future directions in dengue vaccines. Therapeutic advances in vaccines. 2014; 2(1):3-9. doi: 10.1177/2051013613507862 PMID: 24757522; PubMed Central PMCID: PMC3991153.
6. Stewart Ibarra AM, Luzadis VA, Borbor Cordova MJ, Silva M, Ordonez T, Beltran Ayala E, et al. A social-ecological analysis of community perceptions of dengue fever and Aedes aegypti in Machala, Ecuador. BMC public health. 2014; 14:1135. doi: 10.1186/1471-2458-14-1135 PMID: 25370883; PubMed Central PMCID: PMC4240812.
7. Blacksell SD. Commercial dengue rapid diagnostic tests for point-of-care application: recent evaluations and future needs? Journal of biomedicine & biotechnology. 2012; 2012:151967. doi: 10.1155/2012/151967 PMID: 22654479; PubMed Central PMCID: PMC3357944.
8. Peeling RW, Artsob H, Pelegrino JL, Buchy P, Cardosa MJ, Devi S, et al. Evaluation of diagnostic tests: dengue. Nature reviews Microbiology. 2010; 8(12 Suppl):S30-8. PMID: 21548185.
9. Medina F, Medina JF, Colon C, Vergne E, Santiago GA, Munoz-Jordan JL. Dengue virus: isolation, propagation, quantification, and storage. Current protocols in microbiology. 2012;Chapter 15:Unit 15D 2. doi: 10.1002/9780471729259.mc15d02s27 PMID: 23184594.
10. Yamada K, Takasaki T, Nawa M, Kurane I. Virus isolation as one of the diagnostic methods for dengue virus infection. J Clin Virol. 2002; 24(3):203-9. PMID: 11856621.
11. Paranavitane SA, Gomes L, Kamaladasa A, Adikari TN, Wickramasinghe N, Jeewandara C, et al. Dengue NS1 antigen as a marker of severe clinical disease. BMC infectious diseases. 2014; 14:570. doi: 10.1186/s12879-014-0570-8 PMID: 25366086; PubMed Central PMCID: PMC4222370.
12. Blacksell SD, Jarman RG, Gibbons RV, Tanganuchitcharnchai A, Mammen MP Jr., Nisalak A, et al. Comparison of seven commercial antigen and antibody enzyme-linked immunosorbent assays for detection of acute dengue infection. Clinical and vaccine immunology: CVI. 2012; 19(5):804-10. doi: 10.1128/CVI.05717-11 PMID: 22441389; PubMed Central PMCID: PMC3346317.
13. Felix AC, Romano CM, Centrone Cde C, Rodrigues CL, Villas-Boas L, Araujo ES, et al. Low sensitivity of NS1 protein tests evidenced during a dengue type 2 virus outbreak in Santos, Brazil, in 2010. Clinical and vaccine immunology: CVI. 2012; 19(12):1972-6. doi: 10.1128/CVI.00535-12 PMID: 23100478; PubMed Central PMCID: PMC3535870.
14. Hue KD, Tuan TV, Thi HT, Bich CT, Anh HH, Wills BA, et al. Validation of an internally controlled one-step real-time multiplex RT-PCR assay for the detection and quantitation of dengue virus RNA in plasma. J Virol Methods. 2011; 177(2):168-73. doi: 10.1016/j.jviromet.2011.08.002 PMID: 21843553.
15. Johnson BW, Russell BJ, Lanciotti RS. Serotype-specific detection of dengue viruses in a fourplex real-time reverse transcriptase PCR assay. J Clin Microbiol. 2005; 43(10):4977-83. doi: 10.1128/JCM.43.10.4977-4983.2005 PMID: 16207951; PubMed Central PMCID: PMC1248506.
16. Lai YL, Chung YK, Tan HC, Yap HF, Yap G, Ooi EE, et al. Cost-effective real-time reverse transcriptase PCR (RT-PCR) to screen for Dengue virus followed by rapid single-tube multiplex RT-PCR for serotyping of the virus. J Clin Microbiol. 2007; 45(3):935-41. doi: 10.1128/JCM.01258-06 PMID: 17215345; PubMed Central PMCID: PMC1829098.
17. Najioullah F, Viron F, Cesaire R. Evaluation of four commercial real-time RT-PCR kits for the detection of dengue viruses in clinical samples. Virology journal. 2014; 11:164. doi: 10.1186/1743-422X-11-164 PMID: 25219286; PubMed Central PMCID: PMC4177702.
18. Pongsiri P, Praianantathavorn K, Theamboonlers A, Payungporn S, Poovorawan Y. Multiplex real-time RT-PCR for detecting chikungunya virus and dengue virus. Asian Pacific journal of tropical medicine. 2012; 5(5):342-6. doi: 10.1016/S1995-7645(12)60055-8 PMID: 22546647.
19. Wu SJ, Lee EM, Putvatana R, Shurtliff RN, Porter KR, Suharyono W, et al. Detection of dengue viral RNA using a nucleic acid sequence-based amplification assay. J Clin Microbiol. 2001; 39(8):2794-8. doi: 10.1128/JCM.39.8.2794-2798.2001 PMID: 11473994; PubMed Central PMCID: PMC88241.
20. Li S, Fang M, Zhou B, Ni H, Shen Q, Zhang H, et al. Simultaneous detection and differentiation of dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus by a combined reverse-transcription loop-mediated isothermal amplification assay. Virology journal. 2011; 8:360. doi: 10.1186/1743-422X-8-360 PMID: 21777455; PubMed Central PMCID: PMC3149006.
21. Parida M, Horioke K, Ishida H, Dash PK, Saxena P, Jana AM, et al. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay. J Clin Microbiol. 2005; 43(6):2895-903. doi: 10.1128/JCM.43.6.2895-2903.2005 PMID: 15956414; PubMed Central PMCID: PMC1151941.
22. Sahni AK, Grover N, Sharma A, Khan ID, Kishore J. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for diagnosis of dengue. Medical journal, Armed Forces India. 2013; 69(3):246-53. doi: 10.1016/j.mjafi.2012.07.017 PMID: 24600118; PubMed Central PMCID: PMC3862550.
23. Teoh BT, Sam SS, Tan KK, Johari J, Danlami MB, Hooi PS, et al. Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification. BMC infectious diseases. 2013; 13:387. doi: 10.1186/1471-2334-13-387 PMID: 23964963; PubMed Central PMCID: PMC3846474.
24. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, et al. Loop-mediated isothermal amplification of DNA. Nucleic acids research. 2000; 28(12):E63. PMID: 10871386; PubMed Central PMCID: PMC102748.
25. Piepenburg O, Williams CH, Stemple DL, Armes NA. DNA detection using recombination proteins. PLoS Biol. 2006; 4(7):e204. Epub 2006/06/08. doi: 10.1371/journal.pbio.0040204 PMID: 16756388; PubMed Central PMCID: PMC1475771.
26. Abd El Wahed A, El-Deeb A, El-Tholoth M, Abd El Kader H, Ahmed A, Hassan S, et al. A portable reverse transcription recombinase polymerase amplification assay for rapid detection of foot-and-mouth disease virus. PloS one. 2013; 8(8):e71642. doi: 10.1371/journal.pone.0071642 PMID: 23977101; PubMed Central PMCID: PMC3748043.
27. Weidmann M, Meyer-Konig U, Hufert FT. Rapid detection of herpes simplex virus and varicella-zoster virus infections by real-time PCR. J Clin Microbiol. 2003; 41(4):1565-8. Epub 2003/04/12. PMID: 12682146.
28. Wagner D, de With K, Huzly D, Hufert F, Weidmann M, Breisinger S, et al. Nosocomial acquisition of dengue. Emerging infectious diseases. 2004; 10(10):1872-3. doi: 10.3201/eid1010.031037 PMID: 15504282; PubMed Central PMCID: PMC3323263.
29. Euler M, Wang Y, Heidenreich D, Patel P, Strohmeier O, Hakenberg S, et al. Development of a panel of recombinase polymerase amplification assays for detection of biothreat agents. J Clin Microbiol. 2013; 51(4):1110-7. doi: 10.1128/JCM.02704-12 PMID: 23345286; PubMed Central PMCID: PMC3666764.
30. Euler M, Wang Y, Nentwich O, Piepenburg O, Hufert FT, Weidmann M. Recombinase polymerase amplification assay for rapid detection of Rift Valley fever virus. J Clin Virol. 2012. Epub 2012/06/12. doi: 10.1016/j.jcv.2012.05.006 PMID: 22683006.
31. Abd El Wahed A, Patel P, Heidenreich D, Hufert FT, Weidmann M. Reverse transcription recombinase polymerase amplification assay for the detection of middle East respiratory syndrome coronavirus. PLoS currents. 2013;5. doi: 10.1371/currents.outbreaks.62df1c7c75ffc96cd59034531e2e8364 PMID: 24459611; PubMed Central PMCID: PMC3871419.
32. Amer HM, Abd El Wahed A, Shalaby MA, Almajhdi FN, Hufert FT, Weidmann M. A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay. J Virol Methods. 2013; 193(2):337-40. doi: 10.1016/j.jviromet.2013.06.027 PMID: 23811231.
33. Boyle DS, Lehman DA, Lillis L, Peterson D, Singhal M, Armes N, et al. Rapid Detection of HIV-1 Proviral DNA for Early Infant Diagnosis Using Recombinase Polymerase Amplification. mBio. 2013; 4(2). Epub 2013/04/04. doi: 10.1128/mBio.00135-13 PMID: 23549916.
34. Escadafal C, Faye O, Sall AA, Faye O, Weidmann M, Strohmeier O, et al. Rapid molecular assays for the detection of yellow fever virus in low-resource settings. PLoS neglected tropical diseases. 2014; 8(3):e2730. doi: 10.1371/journal.pntd.0002730 PMID: 24603874; PubMed Central PMCID: PMC3945292.
35. Euler M, Wang Y, Otto P, Tomaso H, Escudero R, Anda P, et al. Recombinase Polymerase Amplification Assay for Rapid Detection of Francisella tularensis. J Clin Microbiol. 2012; 50(7):2234-8. Epub 2012/04/21. doi: 10.1128/JCM.06504-11 PMID: 22518861.
36. Compton J. Nucleic acid sequence-based amplification. Nature. 1991; 350(6313):91-2. doi: 10.1038/350091a0 PMID: 1706072.
37. Van Ness J, Van Ness LK, Galas DJ. Isothermal reactions for the amplification of oligonucleotides. Proceedings of the National Academy of Sciences of the United States of America. 2003; 100(8):4504-9. doi: 10.1073/pnas.0730811100 PMID: 12679520; PubMed Central PMCID: PMC404692.
38. Gusev Y, Sparkowski J, Raghunathan A, Ferguson H Jr., Montano J, Bogdan N, et al. Rolling circle amplification: a new approach to increase sensitivity for immunohistochemistry and flow cytometry. The American journal of pathology. 2001; 159(1):63-9. doi: 10.1016/S0002-9440(10)61674-4 PMID: 11438455; PubMed Central PMCID: PMC1850404.
39. Vincent M, Xu Y, Kong H. Helicase-dependent isothermal DNA amplification. EMBO reports. 2004; 5(8):795-800. doi: 10.1038/sj.embor.7400200 PMID: 15247927; PubMed Central PMCID: PMC1249482.
40. Torres C, Vitalis EA, Baker BR, Gardner SN, Torres MW, Dzenitis JM. LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures. BMC bioinformatics. 2011; 12:240. doi: 10.1186/1471-2105-12-240 PMID: 21679460; PubMed Central PMCID: PMC3213686.
41. SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences of the United States of America. 1998; 95(4):1460-5. PMID: 9465037; PubMed Central PMCID: PMC19045.
42. Daher RK, Stewart G, Boissinot M, Boudreau DK, Bergeron MG. Influence of sequence mismatches on the specificity of Recombinase Polymerase Amplification technology. Mol Cell Probes. 2014. doi: 10.1016/j.mcp.2014.11.005 PMID: 25481659.
43. Whiley DM, Sloots TP. Sequence variation can affect the performance of minor groove binder TaqMan probes in viral diagnostic assays. J Clin Virol. 2006; 35(1):81-3. Epub 2005/07/09. doi: 10.1016/j.jcv.2005.05.002 PMID: 16002331.
44. Carneiro AR, Cruz AC, Vallinoto M, Melo Dde V, Ramos RT, Medeiros DB, et al. Molecular characterisation of dengue virus type 1 reveals lineage replacement during circulation in Brazilian territory. Memorias do Instituto Oswaldo Cruz. 2012; 107(6):805-12. PMID: 22990972.
45. Holmes EC. Molecular epidemiology and evolution of emerging infectious diseases. British medical bulletin. 1998; 54(3):533-43. PMID: 10326282.
46. Holmes KC. A molecular model for muscle contraction. Acta crystallographica Section A, Foundations of crystallography. 1998; 54(Pt 6 Pt 1):789-97. PMID: 9859194.
47. Messer WB, Gubler DJ, Harris E, Sivananthan K, de Silva AM. Emergence and global spread of a dengue serotype 3, subtype III virus. Emerging infectious diseases. 2003; 9(7):800-9. PMID: 12899133; PubMed Central PMCID: PMC3023445.
48. Botling J, Edlund K, Segersten U, Tahmasebpoor S, Engstrom M, Sundstrom M, et al. Impact of thawing on RNA integrity and gene expression analysis in fresh frozen tissue. Diagnostic molecular pathology: the American journal of surgical pathology, part B. 2009; 18(1):44-52. doi: 10.1097/PDM.0b013e3181857e92 PMID: 19214109.
49. Mutter GL, Zahrieh D, Liu C, Neuberg D, Finkelstein D, Baker HE, et al. Comparison of frozen and RNA-Later solid tissue storage methods for use in RNA expression microarrays. BMC genomics. 2004; 5:88. doi: 10.1186/1471-2164-5-88 PMID: 15537428; PubMed Central PMCID: PMC534099.
50. Santiago GA, Vergne E, Quiles Y, Cosme J, Vazquez J, Medina JF, et al. Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus. PLoS neglected tropical diseases. 2013; 7(7):e2311. doi: 10.1371/journal.pntd.0002311 PMID: 23875046; PubMed Central PMCID: PMC3708876.