Multiple respiratory virus detection by DNA microarray

Volume 9, Issue 1, February 2024     |     PP. 69-86      |     PDF (315 K)    |     Pub. Date: April 17, 2019
DOI:    326 Downloads     3149 Views  


Kai Sung, Department of Bioengineering, Xuzhou Vocational College of Bioengineering, China
Hsu Sheng Cheng, Department of Bioengineering, Xuzhou Vocational College of Bioengineering, China

Current methods for detecting and identifying respiratory viruses in patient samples are based on viral amplification in cell culture followed by antibody detection. These methods are time-consuming, costly and depend upon complex and expensive equipment as well as resources. DNA-based microarrays have the potential and useful diagnostic tools that are able to detect and identify respiratory viruses in a rapid, sensitive, safe and cost effective manner. In order to transform this potential into reality, direct comparisons between the established cell culture and immuno-based methods and a DNA microarray method in a clinical setting are necessary. In this study, we developed a respiratory virus microarray that can be employed to detect eight different respiratory viruses at once, named: DR. Chip RV-chip. Throat swabs were taken from 433 patients with possible respiratory viral infections and were analyzed using established cell culture and immuno-based assays and DR. Chip RV-chip, respectively. There were 92 positive tested specimens obtained in both assays. Although the respiratory virus microarray did not detect 20 of the 92 culture positive specimens (false negatives), the microarrays did detect 34 additional positive specimens in comparison to the traditional methods. Our observations demonstrate that in a clinical setting a rapid respiratory virus microarray assay can perform better than the slower cell culture and immuno-based assays

DNA microarray, Respiratory virus, Respiratory tract infection

Cite this paper
Kai Sung, Hsu Sheng Cheng, Multiple respiratory virus detection by DNA microarray , SCIREA Journal of Clinical Medicine. Volume 9, Issue 1, February 2024 | PP. 69-86.


[ 1 ] Briese T, Palacios G, Kokoris M, Jabado O, Liu Z, et al. (2005) Diagnostic system for rapid and sensitive differential detection of pathogens. Emerg Infect Dis 11: 310-313.
[ 2 ] Bowtell DD (1999) Options available--from start to finish--for obtaining expression data by microarray. Nat Genet 21: 25-32.
[ 3 ] Lin B, Blaney KM, Malanoski AP, Ligler AG, Schnur JM, et al. (2007) Using a resequencing microarray as a multiple respiratory pathogen detection assay. J Clin Microbiol 45: 443-452.
[ 4 ] Shih SR, Wang YW, Chen GW, Chang LY, Lin TY, et al. (2003) Serotype-specific detection of enterovirus 71 in clinical specimens by DNA microchip array. J Virol Methods 111: 55-60.
[ 5 ] Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, et al. (2002) Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 99: 15687-15692.
[ 6 ] Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, et al. (2003) Viral discovery and sequence recovery using DNA microarrays. PLoS Biol 1: E2.
[ 7 ] Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, et al. (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68: 2535-2541.
[ 8 ] Li J, Chen S, Evans DH (2001) Typing and subtyping influenza virus using DNA microarrays and multiplex reverse transcriptase PCR. J Clin Microbiol 39: 696-704.
[ 9 ] Han X, Lin X, Liu B, Hou Y, Huang J, et al. (2008) Simultaneously subtyping of all influenza A viruses using DNA microarrays. Journal of Virological Methods 152: 117-121.
[ 10 ] Lapa S, Mikheev M, Shchelkunov S, Mikhailovich V, Sobolev A, et al. (2002) Species-level identification of orthopoxviruses with an oligonucleotide microchip. J Clin Microbiol 40: 753-757.
[ 11 ] Bellau-Pujol S, Vabret A, Legrand L, Dina J, Gouarin S, et al. (2005) Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses. J Virol Methods 126: 53-63.
[ 12 ] Coiras MT, Aguilar JC, Garcia ML, Casas I, Perez-Brena P (2004) Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays. J Med Virol 72: 484-495.
[ 13 ] Coiras MT, Lopez-Huertas MR, Lopez-Campos G, Aguilar JC, Perez-Brena P (2005) Oligonucleotide array for simultaneous detection of respiratory viruses using a reverse-line blot hybridization assay. J Med Virol 76: 256-264.
[ 14 ] Gruteke P, Glas AS, Dierdorp M, Vreede WB, Pilon JW, et al. (2004) Practical implementation of a multiplex PCR for acute respiratory tract infections in children. J Clin Microbiol 42: 5596-5603.
[ 15 ] Osiowy C (1998) Direct detection of respiratory syncytial virus, parainfluenza virus, and adenovirus in clinical respiratory specimens by a multiplex reverse transcription-PCR assay. J Clin Microbiol 36: 3149-3154.
[ 16 ] Puppe W, Weigl JA, Aron G, Grondahl B, Schmitt HJ, et al. (2004) Evaluation of a multiplex reverse transcriptase PCR ELISA for the detection of nine respiratory tract pathogens. J Clin Virol 30: 165-174.
[ 17 ] Brittain-Long R, Westin J, Olofsson S, Lindh M, Andersson LM (2010) Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens-duration of symptoms significantly affects detection rate. J Clin Virol 47: 263-267.
[ 18 ] Hymas WC, Hillyard DR (2009) Evaluation of Nanogen MGB Alert Detection Reagents in a multiplex real-time PCR for influenza virus types A and B and respiratory syncytial virus. J Virol Methods 156: 124-128.
[ 19 ] Kehl SC, Kumar S (2009) Utilization of nucleic acid amplification assays for the detection of respiratory viruses. Clin Lab Med 29: 661-671.
[ 20 ] Lassauniere R, Kresfelder T, Venter M (2010) A novel multiplex real-time RT-PCR assay with FRET hybridization probes for the detection and quantitation of 13 respiratory viruses. J Virol Methods.
[ 21 ] Chen Q, Li J, Deng Z, Xiong W, Wang Q, et al. (2010) Comprehensive detection and identification of seven animal coronaviruses and human respiratory coronavirus 229E with a microarray hybridization assay. Intervirology 53: 95-104.
[ 22 ] Raymond F, Carbonneau J, Boucher N, Robitaille L, Boisvert S, et al. (2009) Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children. J Clin Microbiol 47: 743-750.
[ 23 ] Lin TY, Huang YC, Ning HC, Tsao KC (2004) Surveillance of respiratory viral infections among pediatric outpatients in northern China. J Clin Virol 30: 81-85.
[ 24 ] Shih SR, Tsao KC, Ning HC, Huang YC, Lin TY (1999) Diagnosis of respiratory tract viruses in 24 h by immunofluorescent staining of shell vial cultures containing Madin-Darby Canine Kidney (MDCK) cells. J Virol Methods 81: 77-81.
[ 25 ] Cannon GA, Carr MJ, Yandle Z, Schaffer K, Kidney R, et al. (2010) A low density oligonucleotide microarray for the detection of viral and atypical bacterial respiratory pathogens. J Virol Methods 163: 17-24.
[ 26 ] Casas I, Palacios GF, Trallero G, Cisterna D, Freire MC, et al. (2001) Molecular characterization of human enteroviruses in clinical samples: comparison between VP2, VP1, and RNA polymerase regions using RT nested PCR assays and direct sequencing of products. J Med Virol 65: 138-148.
[ 27 ] Manayani DJ, Shaji RV, Fletcher GJ, Cherian T, Murali N, et al. (2002) Comparison of molecular and conventional methods for typing of enteroviral isolates. J Clin Microbiol 40: 1069-1070.
[ 28 ] Santos AP, Costa EV, Oliveira SS, Souza MC, Da Silva EE (2002) RT-PCR based analysis of cell culture negative stools samples from poliomyelitis suspected cases. J Clin Virol 23: 149-152.
[ 29 ] Verstrepen WA, Kuhn S, Kockx MM, Van De Vyvere ME, Mertens AH (2001) Rapid detection of enterovirus RNA in cerebrospinal fluid specimens with a novel single-tube real-time reverse transcription-PCR assay. J Clin Microbiol 39: 4093-4096.
[ 30 ] Wilson JW, Bean P, Robins T, Graziano F, Persing DH (2000) Comparative evaluation of three human immunodeficiency virus genotyping systems: the HIV-GenotypR method, the HIV PRT GeneChip assay, and the HIV-1 RT line probe assay. J Clin Microbiol 38: 3022-3028.