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Taguchi array optimization of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for sensitive and rapid detection of dengue virus serotype 2

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Abstract

Objectives

Serotype 2 of dengue virus (DENV-2) is the most prevalent cause of dengue fevers. In this study, the C-prM gene was used for specific detection of DENV-2 by RT-LAMP assay. The RT-LAMP assay was optimized using the Taguchi design of experiments.

Results

The efficiency of the assay in such optimal conditions resulted in 100% sensitivity, 100% specificity, and 100% overall accuracy for detection of 4 copies/μL of the genome of DENV-2. In addition, the detection of 2 copies/μL of the genome of DENV-2 was feasible, although the sensitivity was 50%. Considering the importance of the specific detection of the dengue virus serotypes, the cost-effective RT-LAMP approach can be used for rapid, specific, and sensitive detection of DENV-2.

Conclusion

RT-LAMP, as a cost-effective method, was optimized using Taguchi array approach for specific and rapid detection of DENV-2. Such methods can facilitate the diagnosis procedure in remote regions.

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Data availability

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Abbreviations

DENV:

Dengue virus

RT-LAMP:

Reverse transcription loop-mediated isothermal amplification

DF:

Dengue fever

DHF:

Dengue hemorrhagic fever

DSS:

Dengue shock syndrome

DENV-2:

Serotype 2 of dengue virus

RT-RPA:

Reverse transcription recombinase polymerase amplification

Bst :

Bacillus stearothermophilus

DoE:

Design of experiment

FIP:

Forward inner primer

F3:

Forward outer primer

FL:

Forward loop primer

BIP:

Backward inner primer

B3:

Backward outer primer

BL:

Backward loop primer

References

  • Abd El Wahed A, Patel P, Faye O, Thaloengsok S, Heidenreich D, Matangkasombut P, Manopwisedjaroen K, Sakuntabhai A, Sall AA, Hufert FT (2015) Recombinase polymerase amplification assay for rapid diagnostics of dengue infection. PloS One 10:e0129682

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • AbuBakar S, Wong P-F, Chan Y-F (2002) Emergence of dengue virus type 4 genotype IIA in Malaysia. J Gen Virol 83:2437–2442

    Article  CAS  PubMed  Google Scholar 

  • Baniasadi V, Salehi-Vaziri M, Jalali T, Azad-Manjiri S, Mohammadi T, Khakifirouz S, Fazlalipour M (2016) An imported case of dengue fever in Iran, 2015. Iran J Virol 10:31–34

    Article  Google Scholar 

  • Bhat A, Siljo A, Deeshma K (2013) Rapid detection of Piper yellow mottle virus and Cucumber mosaic virus infecting black pepper (Piper nigrum) by loop-mediated isothermal amplification (LAMP). J Virol Methods 193:190–196

    Article  CAS  PubMed  Google Scholar 

  • Boubourakas I, Fukuta S, Kyriakopoulou P (2009) Sensitive and rapid detection of peach latent mosaic viroid by the reverse transcription loop-mediated isothermal amplification. J Virol Methods 160:63–68

    Article  CAS  PubMed  Google Scholar 

  • Burch GJ, Ferguson CH, Cartwright G, Kwong FY (1995) Application of Taguchi experimental design to the optimisation of a baculovirus expression system. Biochem Soc Trans 23:107S

  • Caetano-Anollés G, Schlarbaum S, Trigiano R (1999) DNA amplification fingerprinting and marker screening for pseudo-testcross mapping of flowering dogwood (Cornus florida L.). Euphytica 106:209–222

    Article  Google Scholar 

  • Cobb BD, CIarkson JM (1994) A simple procedure for optimising the polymerase chain reaction (PCR) using modified Taguchi methods. Nucleic Acids Res 22:3801–3805

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Den Boon JA, Ahlquist P (2010) Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories. Annu Rev Microbiol 64:241–256

    Article  CAS  Google Scholar 

  • Drosten C, Göttig S, Schilling S, Asper M, Panning M, Schmitz H, Günther S (2002) Rapid detection and quantification of RNA of Ebola and Marburg viruses, Lassa virus, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, dengue virus, and yellow fever virus by real-time reverse transcription-PCR. J Clin Microbiol 40:2323–2330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Euler M, Wang Y, Nentwich O, Piepenburg O, Hufert FT, Weidmann M (2012) Recombinase polymerase amplification assay for rapid detection of Rift Valley fever virus. J Clin Virol 54:308–312

    Article  CAS  PubMed  Google Scholar 

  • Ghani JA, Choudhury I, Hassan H (2004) Application of Taguchi method in the optimization of end milling parameters. J Mater Process Technol 145:84–92

    Article  CAS  Google Scholar 

  • Guo X-G, Zhou Y-Z, Li Q, Wang W, Wen J-Z, Zheng L, Wang Q (2018) Rapid and reliable diagnostic method to detect Zika virus by real-time fluorescence reverse transcription loop-mediated isothermal amplification. AMB Express 8:1–8

    Article  CAS  Google Scholar 

  • Guzman MG, Alvarez M, Halstead SB (2013) Secondary infection as a risk factor for dengue hemorrhagic fever/dengue shock syndrome: an historical perspective and role of antibody-dependent enhancement of infection. Arch Virol 158:1445–1459

    Article  CAS  PubMed  Google Scholar 

  • Hunsperger E, Kroeger A, Margolis H, Martnez E, Nathan M, Pelegrino J, Simmons C, Yoksan S, Peeling R (2010) Dengue: a continuing global threat. Nat Rev Microbiol 8:S7–S16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jittmittraphap A, Thammapalo S, Ratanasetyuth N, Wongba N, Mammen MP, Jampangern W (2006) Rapid detection of dengue viral RNA in mosquitoes by nucleic acid-sequence based amplification (NASBA). SE Asian J Trop Med 37:1117

    CAS  Google Scholar 

  • Kaarj K, Akarapipad P, Yoon J-Y (2018) Simpler, faster, and sensitive Zika virus assay using smartphone detection of loop-mediated isothermal amplification on paper microfluidic chips. Sci Rep 8:1–11

    Article  CAS  Google Scholar 

  • Khoudoli GA, Porter IM, Blow JJ, Swedlow JR (2004) Optimisation of the two-dimensional gel electrophoresis protocol using the Taguchi approach. Proteome Sci 2:1–12

    Article  CAS  Google Scholar 

  • Lanciotti RS, Calisher CH, Gubler DJ, Chang G-J, Vorndam AV (1992) Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J Clin Microbiol 30:545–551

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lo S-J, Yang S-C, Yao D-J, Chen J-H, Cheng C-M (2012) Molecular-level dengue fever diagnostics: developing a combination of RT-LAMP and paper-based devices. IEEE Nanotechnol Mag 6:26–30

    Article  Google Scholar 

  • Lopez-Jimena B, Bekaert M, Bakheit M, Frischmann S, Patel P, Simon-Loriere E, Lambrechts L, Duong V, Dussart P, Harold G (2018) Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype. PLOS Negl Trop Dis 12:e0006381

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lu X, Li X, Mo Z, Jin F, Wang B, Zhao H, Shan X, Shi L (2012) Rapid identification of Chikungunya and Dengue virus by a real-time reverse transcription-loop-mediated isothermal amplification method. Am J Trop Med Hyg 87:947–953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mendes GM, Oliveira KG, Borba JC, Oliveira TS, Fiaccadori FS, Nogueira ML, Bailão AM, Soares CMA, Carrilho E, Duarte GR (2019) Molecular diagnostics of dengue by reverse transcription-loop mediated isothermal amplification (RT-LAMP) in disposable polyester-toner microdevices. J Braz Chem Soc 30:1841–1849

    CAS  Google Scholar 

  • Minero GAS, Nogueira C, Rizzi G, Tian B, Fock J, Donolato M, Strömberg M, Hansen MF (2017) Sequence-specific validation of LAMP amplicons in real-time optomagnetic detection of Dengue serotype 2 synthetic DNA. Analyst 142:3441–3450

    Article  CAS  PubMed  Google Scholar 

  • Monazah A, Zeinoddini M, Saeedinia AR, Xodadadi N (2018) Detection of Coxsackievirus B3 using RT-LAMP assay: optimization by Taguchi method and comparison of one and two step RT-LAMP. J Bionanosci 12:515–520

    Article  CAS  Google Scholar 

  • Mori Y, Nagamine K, Tomita N, Notomi T (2001) Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun 289:150–154

    Article  CAS  PubMed  Google Scholar 

  • Neeraja M, Lakshmi V, Lavanya V, Priyanka E, Parida M, Dash P, Sharma S, Rao PL, Reddy G (2015) Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India. J Virol Methods 211:22–31

    Article  CAS  PubMed  Google Scholar 

  • Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:e63–e63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • World Health Organization, Special Programme for Research, Training in Tropical Diseases, World Health Organization. Department of Control of Neglected Tropical Diseases, World Health Organization. Epidemic, & Pandemic Alert (2009) Dengue: guidelines for diagnosis, treatment, prevention and control. World Health Organization

  • Parida M, Horioke K, Ishida H, Dash PK, Saxena P, Jana AM, Islam MA, Inoue S, Hosaka N, Morita K (2005) Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay. J Clin Microbiol 43:2895–2903

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Phadungsombat J, Lin MY-C, Srimark N, Yamanaka A, Nakayama EE, Moolasart V, Suttha P, Shioda T, Uttayamakul S (2018) Emergence of genotype Cosmopolitan of dengue virus type 2 and genotype III of dengue virus type 3 in Thailand. PloS One 13:e0207220

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Prasad KK, Mohan SV, Bhaskar YV, Ramanaiah S, Babu VL, Pati B, Sarma P (2005) Laccase production using Pleurotus ostreatus 1804 immobilized on PUF cubes in batch and packed bed reactors: influence of culture conditions. J Microbiol 43:301–307

    CAS  PubMed  Google Scholar 

  • Pyke AT, Huang B, Warrilow D, Moore PR, McMahon J, Harrower B (2017) Complete genome sequence of a highly divergent dengue virus type 2 strain, imported into Australia from Sabah, Malaysia. Genome Announc 5:00546–e00517

    Article  PubMed  PubMed Central  Google Scholar 

  • Raheel U, Faheem M, Riaz MN, Kanwal N, Javed F, Qadri I (2011) Dengue fever in the Indian subcontinent: an overview. J Infect Dev Ctries 5:239–247

    Article  PubMed  Google Scholar 

  • Ranjan R, Kangayan M, Subramaniam S, Mohapatra JK, Biswal JK, Sharma GK, Sanyal A, Pattnaik B (2014) Development and evaluation of a one step reverse transcription-loop mediated isothermal amplification assay (RT-LAMP) for rapid detection of foot and mouth disease virus in India. VirusDisease 25:358–364

    Article  PubMed  PubMed Central  Google Scholar 

  • Sahni AK, Grover N, Sharma A, Khan ID, Kishore J (2013) Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for diagnosis of dengue. Med J Armed Forces India 69:246–253

    Article  PubMed  Google Scholar 

  • Saxena P, Dash PK, Santhosh S, Shrivastava A, Parida M, Rao PL (2008) Development and evaluation of one step single tube multiplex RT-PCR for rapid detection and typing of dengue viruses. Virol J 5:1–5

    Article  CAS  Google Scholar 

  • Silva SJRd, Pardee K, Pena L (2020) Loop-mediated isothermal amplification (LAMP) for the diagnosis of Zika virus: a review. Viruses 12:19

    Article  CAS  Google Scholar 

  • Teoh B-T, Sam S-S, Tan K-K, Johari J, Danlami MB, Hooi P-S, Md-Esa R, AbuBakar S (2013) Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification. BMC Infect Dis 13:1–9

    Article  Google Scholar 

  • Tian B, Qiu Z, Ma J, de la Torre TZG, Johansson C, Svedlindh P, Strömberg M (2016) Attomolar Zika virus oligonucleotide detection based on loop-mediated isothermal amplification and AC susceptometry. Biosens Bioelectron 86:420–425

    Article  CAS  PubMed  Google Scholar 

  • Tomito N, Mori Y, Kanda H, Notomi T (2008) Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc 3:877–882

    Article  CAS  Google Scholar 

  • Vashishtha AK, Konigsberg WH (2016) Effect of different divalent cations on the kinetics and fidelity of RB69 DNA polymerase. Biochemistry 55:2661–2670

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Yin F, Bi Y, Cheng G, Li J, Hou L, Li Y, Yang B, Liu W, Yang L (2016) Rapid and sensitive detection of Zika virus by reverse transcription loop-mediated isothermal amplification. J Virol Methods 238:86–93

    Article  CAS  PubMed  Google Scholar 

  • Wu S-JL, Lee EM, Putvatana R, Shurtliff RN, Porter KR, Suharyono W, Watts DM, King C-C, Murphy GS, Hayes CG (2001) Detection of dengue viral RNA using a nucleic acid sequence-based amplification assay. J Clin Microbiol 39:2794–2798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Xie Z, Fletcher JD, Wang Y, Wang R, Guo Z, He Y (2020) Rapid and sensitive detection of lettuce necrotic yellows virus and cucumber mosaic virus infecting lettuce (Lactuca sativa L.) by reverse transcription loop-mediated isothermal amplification. Plant Pathol J 36:76

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This research covers a part of a PhD program. The authors would like to thank the Molecular Virology department and Arboviruses and Viral Hemorrhagic Fevers Department of Pasteur Institute of Iran, Tehran. Great Thanks to Moslem Papizadeh for helping us to improve the manuscript.

Supplementary Information

Results for job clustalo-E20200221-153418-0969-15241688-p1m.

Funding

The study, as a PhD program (TP-9356), was financially supported by Pasteur Institute of Iran.

Author information

Authors and Affiliations

  1. Department of Virology, Pasteur Institute of Iran, Tehran, Iran

    Mohammad Shoushtari, Farzin Roohvand, Arash Arashkia & Kayhan Azadmanesh

  2. Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran

    Mostafa Salehi-Vaziri & Tahmineh Jalali

  3. Department of Biology, Shahed University, Tehran, Iran

    Tahmineh Jalali

  4. Department of Virology, Research Center for Emerging and Re-Emerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran

    Kayhan Azadmanesh

Authors
  1. Mohammad Shoushtari
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  2. Mostafa Salehi-Vaziri
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  3. Farzin Roohvand
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  4. Arash Arashkia
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  5. Tahmineh Jalali
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Contributions

MS: designed and performed experiments, analyzed data and co-wrote the manuscript. KA, MS, FR, and AA: designed experiments, supervised the research and co-wrote the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Kayhan Azadmanesh.

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Conflict of interest

The authors declare no competing interests financial or otherwise related to this project.

Ethical approval

The present study was performed on serum sample of suspected cases with Arboviral infections at the National Reference Laboratory for Arboviruses and Viral Hemorrhagic Fever (Pasteur Institute of Iran) in the context of the national surveillance program.

Consent to participate

Personal identifiers were removed from the samples before performing the experiments related to this study. Because of the retrospective design of the study, we did not have access to patients; thus, we could not obtain informed consent from subjects.

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Not applicable.

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Shoushtari, M., Salehi-Vaziri, M., Roohvand, F. et al. Taguchi array optimization of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for sensitive and rapid detection of dengue virus serotype 2. Biotechnol Lett 43, 2149–2160 (2021). https://doi.org/10.1007/s10529-021-03175-1

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  • DOI: https://doi.org/10.1007/s10529-021-03175-1

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