Non-instrumented incubation of a recombinase polymerase amplification assay for the rapid and sensitive detection of proviral hiv-1 dna

PLoS ONE

Volumn 9, Issue 9, 2014, Pages

  Lillis, Lorraine ^a   Lehman, Dara ^b   Singhal, Mitra C ^a   Cantera, Jason ^a   Singleton, Jered ^a   Labarre, Paul ^c   Toyama, Anthony ^a   Piepenburg, Olaf ^c   Parker, Mathew ^c   Wood, Robert ^d   Overbaugh, Julie ^b   Boyle, David S ^a  

^a PATH   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c TWISTDX LIMITED   (United Kingdom)

^d UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA; RECOMBINASE;

AFRICA SOUTH OF THE SAHARA; ARTICLE; CIRCADIAN RHYTHM; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; ENVIRONMENTAL TEMPERATURE; GENE AMPLIFICATION; HEALTH CARE COST; HEATING; HUMAN IMMUNODEFICIENCY VIRUS 1; LOW TEMPERATURE; NONHUMAN; POINT OF CARE TESTING; PROCESS DEVELOPMENT; RECOMBINASE POLYMERASE AMPLIFICATION ASSAY; RELIABILITY; SENSITIVITY ANALYSIS; VIRUS DETECTION; CELL LINE; CLIMATE; DEVICES; GENETICS; HIV INFECTIONS; HUMAN; INFANT; METABOLISM; MOLECULAR DIAGNOSIS; NUCLEIC ACID AMPLIFICATION; PROCEDURES; TEMPERATURE;

AFRICA SOUTH OF THE SAHARA; CELL LINE; CLIMATE; DNA, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; INFANT; MOLECULAR DIAGNOSTIC TECHNIQUES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; RECOMBINASES; TEMPERATURE;

EID: 84907482392     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108189     Document Type: Article

References (33)

1. Niemz A, Ferguson TM, Boyle DS (2011) Point-of-care nucleic acid testing for infectious diseases. Trends Biotechnol 29: 240-250
2. World Health Organization (2007) Early detection of HIV infection in infants and children. Guidance note on the selection of technology for the early diagnosis of HIV in infants and children. 1-11
3. Ciaranello AL, Park JE, Ramirez-Avila L, Freedberg KA, Walensky RP, et al. (2011) Early infant HIV-1 diagnosis programs in resource-limited settings: opportunities for improved outcomes and more cost-effective interventions. BMC Med 9: 59
4. Newell ML, Coovadia H, Cortina-Borja M, Rollins N, Gaillard P, et al. (2004) Mortality of infected and uninfected infants born to HIV-infected mothers in Africa: A pooled analysis. Lancet 364: 1236-1243
5. Persaud D, Gay H, Ziemniak C, Chen YH, Piatak M Jr, et al. (2013) Absence of detectable HIV-1 viremia after treatment cessation in an infant. N Engl J Med 369: 1828-1835
6. Almassian DR, Cockrell LM, Nelson WM (2013) Portable nucleic acid thermocyclers. Chem Soc Rev 42: 8769-8798
7. Byrnes S, Fan A, Trueb J, Jareczek F, Mazzochette M, et al. (2013) A Portable, Pressure Driven, Room Temperature Nucleic Acid Extraction and Storage System for Point of Care Molecular Diagnostics. Anal Methods 5: 3177-3184
8. Pai NP, Pai M (2012) Point-of-care diagnostics for HIV and tuberculosis: landscape, pipeline, and unmet needs. Discov Med 13: 35-45
9. Roskos K, Hickerson AI, Lu HW, Ferguson TM, Shinde DN, et al. (2013) Simple system for isothermal DNA amplification coupled to lateral flow detection. PLoS One 8: E69355
10. LaBarre P, Gerlach J, Wilmoth J, Beddoe A, Singleton J, et al. (2010) Noninstrumented nucleic acid amplification (NINA): instrument-free molecular malaria diagnostics for low-resource settings. Conf Proc IEEE Eng Med Biol Soc 2010: 1097-1099
11. LaBarre P, Hawkins KR, Gerlach J, Wilmoth J, Beddoe A, et al. (2011) A simple, inexpensive device for nucleic acid amplification without electricitytoward instrument-free molecular diagnostics in low-resource settings. PLoS One 6: E19738
12. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, et al.(2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28: E63
13. Compton J (1991) Nucleic acid sequence-based amplification. Nature 350: 91-92
14. Fang R, Li X, Hu L, You Q, Li J, et al. (2009) Cross-priming amplification for rapid detection of Mycobacterium tuberculosis in sputum specimens. J Clin Microbiol 47: 845-847
15. Vincent M, Xu Y, Kong H (2004) Helicase-dependent isothermal DNA amplification. EMBO Rep 5: 795-800
16. Piepenburg O, Williams CH, Stemple DL, Armes NA (2006) DNA detection using recombination proteins. PLoS Biol 4: E204
17. Boyle DS, Lehman DA, Lillis L, Peterson D, Singhal M, et al. (2013) Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. MBio 4. 2013 Apr 2; 4(2). pii: E00135-13
18. McElgunn CJ, Pereira CR, Parham NJ, Smythe JE, Wigglesworth MJ, et al. (2014) A low complexity rapid molecular method for detection of Clostridium difficile in stool. PLoS One 9: E83808
19. Mitarai S, Okumura M, Toyota E, Yoshiyama T, Aono A, et al. (2011) Evaluation of a simple loop-mediated isothermal amplification test kit for the diagnosis of tuberculosis. Int J Tuberc Lung Dis 15: 1211-1217
20. Niemz A, Boyle DS (2012) Nucleic acid testing for tuberculosis at the point-ofcare in high burden countries. Expert Reviews in Microbiology. Sep; 12(7): 687-701
21. Ratliff AE, Duffy LB, Waites KB (2014) Comparison of the illumigene Mycoplasma DNA Amplification Assay and Culture for Detection of Mycoplasma pneumoniae. J Clin Microbiol 52: 1060-1063
22. Surabattula R, Vejandla MP, Mallepaddi PC, Faulstich K, Polavarapu R (2013) Simple, rapid, inexpensive platform for the diagnosis of malaria by loop mediated isothermal amplification (LAMP). Exp Parasitol 134: 333-340
23. Curtis KA, Rudolph DL, Nejad I, Singleton J, Beddoe A, et al. (2012) Isothermal amplification using a chemical heating device for point-of-care detection of HIV- 1. PLoS One 7: E31432
24. Hatano B, Maki T, Obara T, Fukumoto H, Hagisawa K, et al. (2010) LAMP using a disposable pocket warmer for anthrax detection, a highly mobile and reliable method for anti-bioterrorism. Jpn J Infect Dis 63: 36-40
25. Huang S, Do J, Mahalanabis M, Fan A, Zhao L, et al. (2013) Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis. PLoS One 8: E60059
26. Chow WH, McCloskey C, Tong Y, Hu L, You Q, et al.(2008) Application of isothermal helicase-dependent amplification with a disposable detection device in a simple sensitive stool test for toxigenic Clostridium difficile. J Mol Diagn 10: 452-458
27. Mohon AN, Elahi R, Khan WA, Haque R, Sullivan DJ, et al. (2014) A new visually improved and sensitive loop mediated isothermal amplification (LAMP) for diagnosis of symptomatic falciparum malaria. Acta Trop 134C: 52-57
28. Tomita 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
29. Kersting S, Rausch V, Bier FF, von Nickisch-Rosenegk M (2014) Rapid detection of Plasmodium falciparum with isothermal recombinase polymerase amplification and lateral flow analysis. Malar J 13: 99
30. Clouse KA, Powell D, Washington I, Poli G, Strebel K, et al. (1989) Monokine regulation of human immunodeficiency virus-1 expression in a chronically infected human T cell clone. J Immunol 142: 431-438
31. Kim HJ, Tong Y, Tang W, Quimson L, Cope VA, et al. (2011) A rapid and simple isothermal nucleic acid amplification test for detection of herpes simplex virus types 1 and 2. J Clin Virol 50: 26-30
32. Sheffield J, Goteti G, Wood EF (2006) Development of a 50-yr high-resolution global dataset of meteorological forcings for land surface modeling. Journal of Climate 19: 3088-3111
33. Kalnay E, Kanamitsu M, Kistler R, Collins W, Deaven D, et al. (1996) The NCEP/NCAR 40-Year Reanalysis Project. Bulletin of the American Meteorlogical Society 437-471