Toward universal Flavivirus identification by mass cataloging

Journal of Molecular Diagnostics

Volumn 10, Issue 2, 2008, Pages 135-141

  Jackson, George W ^a,c   McNichols, Roger J ^c   Fox, George E ^a,b   Willson, Richard C ^a,b   Jackson, Bill ^c  

^a University of Houston   (United States)

^b University of Houston   (United States)

^c BIOTEX INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DENGUE VIRUS; DOCUMENTATION; FLAVIVIRUS; GENOTYPE; HIGH THROUGHPUT SCREENING; JAPANESE ENCEPHALITIS VIRUS; MASS SPECTROMETRY; NONHUMAN; SEROTYPING; VIRUS IDENTIFICATION; VIRUS STRAIN; WEST NILE FLAVIVIRUS; YELLOW FEVER FLAVIVIRUS;

DENGUE VIRUS; FLAVIVIRUS; JAPANESE ENCEPHALITIS VIRUS;

EID: 41149127407     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2008.070130     Document Type: Article

References (30)

1. Scaramozzino N, Crance JM, Jouan A, Debriel Da, Stoll F, Garin D: Comparison of flavivirus universal primer pairs and development of a rapid, highly sensitive heminested reverse transcription-PCR assay for detection of flaviviruses targeted to a conserved region of the NS5 gene sequences. J Clin Microbiol 2001, 39:1922-1927
2. Kao CL KC, Chao DY, Wu HL, Chang GJJ: Laboratory diagnosis of dengue virus infection: current and future perspectives in clinical diagnosis and public health. J Microbiol Immunol Infect 2005, 38:5-16
3. Monath TP: Dengue: the risk to developed and developing countries. Proc Natl Acad Sci USA 1994, 91:2395-2400
4. Shu PY, Chen LK, Chang SF, Su CL, Chien LJ, Chin C, Lin TH, Huang JH: Dengue virus serotyping based on envelope and membrane and nonstructural protein NS1 serotype-specific capture immunoglobulin M enzyme-linked immunosorbent assays. J Clin Microbiol 2004, 42:2489-2494
5. Halstead SB: Pathogenesis of dengue: challenge to molecular biology. Science 1988, 239:476-481
6. Teles FR, Prazeres DM, Lima-Filho JL: Trends in dengue diagnosis. Rev Med Viral 2005, 15:287-302
7. Putonti C, Chumakov S, Mitra R, Fox GE, Willson RC, Fofanov Y: Human-blind probes and primers for dengue virus identification: exhaustive analysis of subsequences present in the human and 83 dengue genome sequences. FEBS J 2006, 273:398-408
8. De Paula SO, da Fonseca BAL: Dengue: a review of the laboratory tests a clinician must know to achieve a correct diagnosis. Brazil J Infect Dis 2004, 8:390-398
9. Lanciotti RS CC, Gubler DJ, Chang GJ, Vorndam AV: Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J Clin Microbiol 1992, 30:545-551
10. Harris ERT, Smith L, Selle J, Krammer LD, Valle S, Sandoval E, Balmaseda A: Typing of dengue viruses in clinical specimens and mosquitoes by single-tube multiplex reverse transcriptase PCR. J Clin Microbiol 1998, 36:2634-2639
11. Wang WK ST, Tsai YC, Kao CL, Chang SM, King CC: Detection of dengue virus replication in peripheral blood mononuclear cells from dengue virus type 2-infected patients by a reverse transcription-real-time PCR assay. J Clin Microbiol 2002, 40:4472-4478
12. De Paula SOD LC, Torres MP, Pereira MR, da Fonseca BAL: One-step RT-PCR protocols improve the rate of dengue diagnosis compared to two-step RT-PCR approaches. J Clin Virol 2004, 30:297-301
13. Drosten CGS, Schilling S, Asper M, Panning M, Schmitz H, Gunther S: 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 2002, 40:2323-2330
14. de Morais Bronzoni R, Baleotti FG, Nogueira RMR, Nunes, M, Figueiredo: LTM duplex reverse transcription-PCR followed by nested PCR assays for detection and identification of Brazilian alpha-viruses and flaviviruses. J Clin Microbiol 2005, 43:696-702
15. Collins S: Automated MALDI mass spectrometry for rapid biological agent detection. In Abstracts of Bio-Sensors for Homeland Security Conference, October 24-28, 2005, College Station, TX
16. Jackson GW, McNichols RM, Fox GE, Willson RC: Universal bacterial identification by mass spectrometry of 16S ribosomal RNA cleavage products. Intl J Mass Spectrom 2007, 261:218-226
17. Jackson GW, McNichols RJ, Fox GE, Willson RC: Bacterial genotyping by 16S ribosomal RNA mass cataloging. BioMed Central Bioinformatics 2006, 7(321)
18. Zhang Z, Jackson GW, Fox GE, Willson RC: Microbial identification by mass cataloging. BioMed Central Bioinformatics 2006, 7(117)
19. Lefmann M, Honisch C, Bocker S, Storm N, von Wintzingerode F, Schlotelburg C, Moter A, van den Boom D, Gobel UB: Novel mass spectrometry-based tool for genotypic identification of mycobacteria. J Clin Microbiol 2004, 42:339-346
20. von Wintzingerode F, Bocker S, Schlotelburg C, Chiu NH, Storm N, Jurinke C, Cantor CR, Gobel UB, van den Boom D: Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proc Natl Acad Sci USA 2002, 99:7039-7044
21. Fulop L, Barrett ADT, Philipotts R, Martin K, Leslie D, Titball RW: Rapid identification of flaviviruses based conserved NS5 gene sequences. J Virol Methods 1993, 44:179-188
22. Thompson JD, Higgins DG, Gibson TJ: Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680
23. Kumar S, Tamura K, Nei M: MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings Bioinformatics 2004, 5:150-163
24. Trent DW, Grant JA, Monath TP, Manske CL, Corina M, Fox GE: Genetic variation and microevolution of dengue 2 virus in Southeast Asia. Virology 1989, 172:523-535
25. Stanssens P, Zabeau M, Meersseman G, Remes G, Gansemans Y, Storm N, Hartmer R, Honisch C, Rodi CP, Bocker S, van den Boom D: High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res 2004, 14:126-133
26. Woese C, Sogin M, Stahl D, Lewis BJ, Bonen L: A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: some modifications in the Sanger method for RNA sequencing. J Mol Evol 1976, 7:197-213
27. English RD, Warscheid B, Fenselau C, Cotter RJ: Bacillus spore identification via proteolytic peptide mapping with a miniaturized MALDI TOF mass spectrometer. Anal Chem 2003, 75:6886-6893
28. Gardner BD, Cotter RJ: A miniature MALDI-time-of-flight mass spectrometer using nonlinear ion optics for improved performance. In Abstracts of Papers, 225th ACS National Meeting, March 23-27, 2003, New Orleans, LA
29. Ecelberger SA, Cornish TJ, Bryden WA: The improved teeny-TOF mass spectrometer for chemical and biological sensing. In Third Harsh-Environment Mass Spectrometry Workshop and Second NASA/JPL Miniature Vacuum Pumps Workshop, March 25-28, 2002
30. Cotter RJ, Fancher C, Cornish TJ: Miniaturized time-of-flight mass spectrometer for peptide and oligonucleotide analysis. J Mass Spectrom 1999, 34:1368-1372