Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics

References

• Accessible quality-assured diagnostics. 2009 annual report. Available from: www.who.int/tdr/publications/about-tdr/annual-reports/bl7-annual-report/en/
   Google Scholar
• Low-cost tools for diagnosing and monitoring HIV infection in low-resource settings. Available from: www.who.int/bulletin/volumes/90/12/12-102780/en/
   Google Scholar
• Li Y, Kumar N, Gopalakrishnan A, et al. Detection and species identification of malaria parasites by isothermal tHDA amplification directly from human blood without sample preparation. J Mol Diagn 2013;15(5):634-41
   PubMed Web of Science ®Google Scholar
• Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. Lab Chip 2012;12(14):2469-86
   PubMed Web of Science ®Google Scholar
• Asiello PJ, Baeumner AJ. Miniaturized isothermal nucleic acid amplification, a review. Lab Chip 2011;11(8):1420-30
   PubMed Web of Science ®Google Scholar
• Compton J. Nucleic acid sequence-based amplification. Nature 1991;350(6313):91-2
   PubMed Web of Science ®Google Scholar
• Pasternack R, Vuorinen P, Miettinen A. Evaluation of the Gen-Probe Chlamydia trachomatis transcription-mediated amplification assay with urine specimens from women. J Clin Microbiol 1997;35(3):676-8
   PubMedGoogle Scholar
• Gingeras TR, Whitfield KM, Kwoh DY. Unique features of the self-sustained sequence replication (3SR) reaction in the in vitro amplification of nucleic acids. Ann Biol Clin 1990;48(7):498-501
   PubMed Web of Science ®Google Scholar
• van Gemen B, Kievits T, Nara P, et al. Qualitative and quantitative detection of HIV-1 RNA by nucleic acid sequence-based amplification. AIDS 1993;7(Suppl 2)):S107-10
   Google Scholar
• Dimov IK, Garcia-Cordero JL, O’Grady J, et al. Integrated microfluidic tmRNA purification and real-time NASBA device for molecular diagnostics. Lab Chip 2008;8(12):2071-8
   PubMed Web of Science ®Google Scholar
• Gulliksen A, Keegan H, Martin C, et al. Towards a "Sample-In, Answer-Out" Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System. J Oncol 2012; 905024
   PubMedGoogle Scholar
• Walker GT, Fraiser MS, Schram JL, et al. Strand displacement amplification–an isothermal, in vitro DNA amplification technique. Nucleic Acids Res 1992;20(7):1691-6
   PubMed Web of Science ®Google Scholar
• Yang JM, Bell J, Huang Y, et al. An integrated, stacked microlaboratory for biological agent detection with DNA and immunoassays. Biosens Bioelectron 2002;17(6-7):605-18
   PubMedGoogle Scholar
• Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 2000;28(12)):E63
   PubMedGoogle Scholar
• Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes 2002;16(3):223-9
   PubMed Web of Science ®Google Scholar
• Lalande V, Barrault L, Wadel S, et al. Evaluation of a loop-mediated isothermal amplification assay for diagnosis of Clostridium difficile infections. J Clin Microbiol 2011;49(7):2714-16
   PubMed Web of Science ®Google Scholar
• Yoneda A, Taniguchi K, Torashima Y, et al. The detection of gastric cancer cells in intraoperative peritoneal lavage using the reverse transcription-loop-mediated isothermal amplification method. J Surg Res 2013;187(1)):E1-6
   PubMedGoogle Scholar
• Zhang J, Zhu J, Ren H, et al. Rapid visual detection of highly pathogenic Streptococcus suis serotype 2 isolates by use of loop-mediated isothermal amplification. J Clin Microbiol 2013;51(10):3250-6
   PubMedGoogle Scholar
• Soli KW, Kas M, Maure T, et al. Evaluation of colorimetric detection methods for Shigella, Salmonella, and Vibrio cholerae by loop-mediated isothermal amplification. Diagn Microbiol Infect Dis 2013;77(4):321-3
   PubMedGoogle Scholar
• Kaewphinit T, Arunrut N, Kiatpathomchai W, et al. Detection of Mycobacterium tuberculosis by using loop-mediated isothermal amplification combined with a lateral flow dipstick in clinical samples. Biomed Res Int 2013;2013:926230
   PubMed Web of Science ®Google Scholar
• McElgunn CJ, Pereira CR, Parham NJ, et al. A low complexity rapid molecular method for detection of clostridium difficile in stool. PLoS One 2014;9(1)):e83808
   Google Scholar
• Liu C, Jiang DN, Xiang GM, et al. DNA detection of Clostridium difficile infection based on real-time resistance measurement. Genet Mol Res 2013;12(3):3296-304
   PubMedGoogle Scholar
• Tomita N, Mori Y, Kanda H, Notomi T. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc 2008;3(5):877-82
   PubMed Web of Science ®Google Scholar
• Tanner NA, Zhang Y, Evans TC. Simultaneous multiple target detection in real-time loop-mediated isothermal amplification. Biotechniques 2012;53(2):81-9
   PubMed Web of Science ®Google Scholar
• Mahony J, Chong S, Bulir D, 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 2013;58(1):127-31
   PubMed Web of Science ®Google Scholar
• Suzuki R, Ihira M, Enomoto Y, et al. Heat denaturation increases the sensitivity of the cytomegalovirus loop-mediated isothermal amplification method. Microbiol Immunol 2010;54(8):466-70
   PubMed Web of Science ®Google Scholar
• Pyrc K, Milewska A, Potempa J. Development of loop-mediated isothermal amplification assay for detection of human coronavirus-NL63. J Virol Methods 2011;175(1):133-6
   PubMed Web of Science ®Google Scholar
• Francois P, Tangomo M, Hibbs J, et al. Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications. FEMS Immunol Med Microbiol 2011;62(1):41-8
   PubMedGoogle Scholar
• Ihira M, Sugiyama H, Enomoto Y, et al. Direct detection of human herpes virus 6 DNA in serum by variant specific loop-mediated isothermal amplification in hematopoietic stem cell transplant recipients. J Virol Methods 2010;167(1):103-6
   PubMedGoogle Scholar
• Kim DW, Kilgore PE, Kim EJ, et al. Loop-mediated isothermal amplification assay for detection of Haemophilus influenzae type b in cerebrospinal fluid. J Clin Microbiol 2011;49(10):3621-6
   PubMed Web of Science ®Google Scholar
• Gotoh K, Nishimura N, Takeuchi S, et al. Assessment of the loop-mediated isothermal amplification assay for rapid diagnosis of Mycoplasma pneumoniae in pediatric community-acquired pneumonia. Jpn J Infect Dis 2013;66(6):539-42
   PubMed Web of Science ®Google Scholar
• Koizumi N, Nakajima C, Harunari T, et al. A new loop-mediated isothermal amplification method for rapid, simple, and sensitive detection of Leptospira spp. in urine. J Clin Microbiol 2012;50(6):2072-4
   PubMed Web of Science ®Google Scholar
• Malik YS, Sharma K, Kumar N, et al. Rapid detection of human rotavirus using NSP4 gene specific reverse transcription loop-mediated isothermal amplification assay. Indian J Virol 2013;24(2):265-71
   PubMed Web of Science ®Google Scholar
• Moradi A, Almasi MA, Jafary H, Mercado-Blanco J. A novel and rapid loop-mediated isothermal amplification assay for the specific detection of Verticillium dahliae. J Appl Microbiol 2014;116(4):942-54
   PubMedGoogle Scholar
• Verma S, Avishek K, Sharma V, et al. Application of loop-mediated isothermal amplification assay for the sensitive and rapid diagnosis of visceral leishmaniasis and post-kala-azar dermal leishmaniasis. Diagn Microbiol Infect Dis 2013;75(4):390-5
   PubMedGoogle Scholar
• Hopkins H, Gonzalez IJ, Polley SD, et al. Highly sensitive detection of malaria parasitemia in a malaria-endemic setting: performance of a new loop-mediated isothermal amplification kit in a remote clinic in Uganda. J Infect Dis 2013;208(4):645-52
   PubMed Web of Science ®Google Scholar
• Polley SD, Gonzalez IJ, Mohamed D, et al. Clinical evaluation of a loop-mediated amplification kit for diagnosis of imported malaria. J Infect Dis 2013;208(4):637-44
   PubMed Web of Science ®Google Scholar
• Lee SY, Lee CN, Mark H, et al. Efficient, specific, compact hepatitis B diagnostic device: optical detection of the hepatitis B virus by isothermal amplification. Sens Actuators B Chem 2007;127(2):598-605
   Web of Science ®Google Scholar
• Fang X, Liu Y, Kong J, Jiang X. Loop-mediated isothermal amplification integrated on microfluidic chips for point-of-care quantitative detection of pathogens. Anal Chem 2010;82(7):3002-6
   PubMed Web of Science ®Google Scholar
• Fang X, Chen H, Yu S, et al. Predicting viruses accurately by a multiplex microfluidic loop-mediated isothermal amplification chip. Anal Chem 2011;83(3):690-5
   PubMedGoogle Scholar
• Chen Q, Yuan L, Wan J, et al. Colorimetric detection of hepatitis E virus based on reverse transcription loop mediated isothermal amplification (RT-LAMP) assay. J Virol Methods 2014;197:29-33
   PubMed Web of Science ®Google Scholar
• Myers FB, Henrikson RH, Bone J, Lee LP. A handheld point-of-care genomic diagnostic system. PLoS One 2013;8(8)):e70266
   Google Scholar
• Vincent M, Xu Y, Kong H. Helicase-dependent isothermal DNA amplification. EMBO Rep 2004;5(8):795-800
   PubMed Web of Science ®Google Scholar
• An L, Tang W, Ranalli TA, et al. Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification. J Biol Chem 2005;280(32):28952-8
   PubMed Web of Science ®Google Scholar
• Tong Y, Lemieux B, Kong H. Multiple strategies to improve sensitivity, speed and robustness of isothermal nucleic acid amplification for rapid pathogen detection. BMC Biotechnol 2011;11:50
   PubMed Web of Science ®Google Scholar
• Andresen D, von Nickisch-Rosenegk M, Bier FF. Helicase dependent OnChip-amplification and its use in multiplex pathogen detection. Clin Chim Acta 2009;403(1-2):244-8
   PubMed Web of Science ®Google Scholar
• Doseeva V, Forbes T, Wolff J, et al. Multiplex isothermal helicase-dependent amplification assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. Diagn Microbiol Infect Dis 2011;71(4):354-65
   PubMed Web of Science ®Google Scholar
• Ramalingam N, Liu HB, Dai CC, et al. Real-time PCR array chip with capillary-driven sample loading and reactor sealing for point-of-care applications. Biomed Microdevices 2009;11(5):1007-20
   PubMedGoogle Scholar
• Torres-Chavolla E, Alocilja EC. Nanoparticle based DNA biosensor for tuberculosis detection using thermophilic helicase-dependent isothermal amplification. Biosens Bioelectron 2011;26(11):4614-18
   PubMed Web of Science ®Google Scholar
• Mahalanabis M, Do J, ALMuayad H, et al. An integrated disposable device for DNA extraction and helicase dependent amplification. Biomed Microdevices 2010;12(2):353-9
   PubMed Web of Science ®Google Scholar
• Tang W, Chow WH, Li Y, et al. Nucleic acid assay system for tier II laboratories and moderately complex clinics to detect HIV in low-resource settings. J Infect Dis 2010;201(Suppl 1):S46-51
   PubMedGoogle Scholar
• Frech GC, Munns D, Jenison RD, Hicke BJ. Direct detection of nasal Staphylococcus aureus carriage via helicase-dependent isothermal amplification and chip hybridization. BMC Res Notes 2012;5:430
   PubMedGoogle Scholar
• Ramalingam N. Microfluidic devices harboring unsealed reactors for real-time isothermal helicase-dependent amplification. Microfluid Nanofluid 2009;7(3):325-36
   PubMedGoogle Scholar
• Zhang Y, Park S, Liu K, et al. A surface topography assisted droplet manipulation platform for biomarker detection and pathogen identification. Lab Chip 2011;11(3):398-406
   PubMed Web of Science ®Google Scholar
• Huang S, Do J, Mahalanabis M, et al. Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis. PLoS ONE 2013;8(3):e60059
   PubMed Web of Science ®Google Scholar
• Piepenburg O, Williams CH, Stemple DL, Armes NA. DNA detection using recombination proteins. PLoS Biol 2006;4(7):e204
   PubMed Web of Science ®Google Scholar
• Boyle DS, Lehman DA, Lillis L, et al. Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. MBio 2013;4(2):e00135-13
   PubMed Web of Science ®Google Scholar
• Abd El Wahed A, El-Deeb A, El-Tholoth M, 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
   PubMed Web of Science ®Google Scholar
• Amer HM, Abd El Wahed A, Shalaby MA, et al. A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay. J Virol Methods 2013;193(2):337-40
   PubMed Web of Science ®Google Scholar
• Euler M, Wang Y, Heidenreich D, et al. Development of a panel of recombinase polymerase amplification assays for detection of biothreat agents. J Clin Microbiol 2013;51(4):1110-17
   PubMed Web of Science ®Google Scholar
• Lutz S, Weber P, Focke M, et al. Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA). Lab Chip 2010;10(7):887-93
   PubMed Web of Science ®Google Scholar
• Shen F, Davydova EK, Du W, et al. Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip. Anal Chem 2011;83(9):3533-40
   PubMed Web of Science ®Google Scholar
• Van Ness J, Van Ness LK, Galas DJ. Isothermal reactions for the amplification of oligonucleotides. Proc Natl Acad Sci USA 2003;100(8):4504-9
   PubMed Web of Science ®Google Scholar
• Jia H, Li Z, Liu C, Cheng Y. Ultrasensitive detection of microRNAs by exponential isothermal amplification. Angew Chem Int Ed Engl 2010;49(32):5498-501
   PubMed Web of Science ®Google Scholar
• Roth U, Richard B. Rapid isothermal nucleic acid assays for the detection of pathogens. Lab Automation; San Diego, CA, USA; 2008
   Google Scholar
• Spenlinahauer TR, Estock ML, McFadd T, et al. Nicking Enzyme Amplification Reaction (NEAR), an Isothermal Nucleic Acid Based Technology for Point-of-Testing of Plant Pathogens. American Phytopathological Society Annual meeting; 1 – 5 August 2009; Portland, Oregon, USA
   Google Scholar
• Liu D, Daubendiek SL, Zillman MA, et al. Rolling Circle DNA Synthesis: small Circular Oligonucleotides as Efficient Templates for DNA Polymerases. J Am Chem Soc 1996;118(7):1587-94
   PubMed Web of Science ®Google Scholar
• Henriksson S, Blomström AL, Fuxler L, et al. Development of an in situ assay for simultaneous detection of the genomic and replicative form of PCV2 using padlock probes and rolling circle amplification. Virol J 2011;8:37
   PubMed Web of Science ®Google Scholar
• Yan J, Song S, Li B, et al. An on-nanoparticle rolling-circle amplification platform for ultrasensitive protein detection in biological fluids. Small 2012;6(22):2520-5
   Google Scholar
• Sato K, Tachihara A, Renberg B, et al. Microbead-based rolling circle amplification in a microchip for sensitive DNA detection. Lab Chip 2010;10(10):1262-6
   PubMedGoogle Scholar
• Mahmoudian L, Melin J, Mohamadi MR, et al. Microchip electrophoresis for specific gene detection of the pathogenic bacteria V. cholerae by circle-to-circle amplification. Anal Sci 2008;24(3):327-32
   PubMedGoogle Scholar
• Reiss E, Hölzel R, Bier FF. Synthesis and stretching of rolling circle amplification products in a flow-through system. Small 2009;5(20):2316-22
   PubMedGoogle Scholar
• Mitani Y, Lezhava A, Kawai Y, et al. Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology. Nat Methods 2007;4(3):257-62
   PubMed Web of Science ®Google Scholar
• Azuma K, Lezhava A, Shimizu M, et al. Direct genotyping of Cytochrome P450 2A6 whole gene deletion from human blood samples by the SmartAmp method. Clin Chim Acta 2011;412(13-14):249-51
   PubMedGoogle Scholar
• Kimura Y, de Hoon MJ, Aoki S, et al. Optimization of turn-back primers in isothermal amplification. Nucleic Acids Res 2011;39(9):e59-2011
   PubMed Web of Science ®Google Scholar
• Kimura Y, Oguchi-Katayama A, Kawai Y, et al. Tail variation of the folding primer affects the SmartAmp2 process differently. Biochem Biophys Res Commun 2009;383(4):455-9
   PubMedGoogle Scholar
• Kawai Y, Kimura Y, Lezhava A, et al. One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation. PLoS One 2012;7(1)):e30236
   Google Scholar
• Shimada M, Hino F, Sagawa H, et al. Development of the detection system for Mycobacterium tuberculosis DNA by using the isothermal DNA amplification method ICAN. Rinsho Byori 2002;50(5):528-32
   PubMedGoogle Scholar
• Urasaki N, Kawano S, Mukai H, et al. Rapid and sensitive detection of “Candidatus Liberibacter asiaticus” by cycleave isothermal and chimeric primer-initiated amplification of nucleic acids. J Gen Plant Pathol 2008;74(2):5
   Google Scholar
• Shimada M, Hino F, Yamamoto J, et al. Evaluation of the simultaneous detection system for Chlamydia trachomatis/Neisseria gonorrhoeae DNA by the isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN). Rinsho Byori 2003;51(11):1061-7
   PubMedGoogle Scholar
• Inami H, Tsuge K, Matsuzawa M, et al. Semi-automated bacterial spore detection system with micro-fluidic chips for aerosol collection, spore treatment and ICAN DNA detection. Biosens Bioelectron 2009;24(11):3299-305
   PubMedGoogle Scholar
• Isogai E, Makungu C, Yabe J, et al. Detection of Salmonella invA by isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) in Zambia. Comp Immunol Microbiol Infect Dis 2005;28(5-6):363-70
   PubMedGoogle Scholar
• Jani IV, Peter TF. How point-of-care testing could drive innovation in global health. N Engl J Med 2013;368(24):2319-24
   PubMed Web of Science ®Google Scholar
• Chin CD, Linder V, Sia SK. Commercialization of microfluidic point-of-care diagnostic devices. Lab Chip 2012;12(12):2118-34
   PubMed Web of Science ®Google Scholar
• Brian K Maples, Rebecca C Holmberg, Andrew P Miller, et al. Nicking and extension amplification reaction for the exponential amplification of nucleic acids. US20090017453; 2007
   Google Scholar
• The global burden of disease. 2004 Update. Available from: www.who.int/healthinfo/global_burden_disease/GBD_report_2004update_full.pdf
   Google Scholar