Identifying Influenza Viruses with Resequencing Microarrays

Wang, Zheng; Daum, Luke T.; Vora, Gary J.; Metzgar, David; Walter, Elizabeth; Canas, Linda C.; Malanoski, Anthony P.; Lin, Baochuan; Stenger, David A.

doi:10.3201/eid1204.051441

Cited by 73 publications

(75 citation statements)

References 28 publications

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“…Among the several microarrays reported for the typing and subtyping of influenza viruses (9,13,14,19,21,22,27), a majority used at least 55 oligonucleotides as primers and detecting probes. On the other hand, the eMA influenza virus genotyping assay requires a total of 41 oligonucleotides: 16 PCR primers, 10 capture oligonucleotides, 13 bifunctional discriminator oligonucleotides, and 2 fluorescently labeled universal reporter oligonucleotides.…”

Section: Discussionmentioning

confidence: 99%

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Multiplex Assay for Simultaneously Typing and Subtyping Influenza Viruses by Use of an Electronic Microarray

et al. 2009

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We report on the use of an electronic microarray to simultaneously type influenza A and B viruses and to distinguish influenza A virus subtypes H1N1 and H3N2 from the potentially pandemic avian virus subtype H5N1. The assay targets seven genes: the H1, H3, H5, N1, and N2 genes of influenza A virus; the matrix protein M1 gene of influenza A virus; and the nonstructural protein (NS) gene of influenza B virus. By combining a two-step reverse transcription-multiplex PCR with typing and subtyping on the electronic microarray, the assay achieved an analytical sensitivity of 10 2 to 10 3 copies of transcripts per reaction for each of the genes. The assay correctly typed and subtyped 15 different influenza virus isolates, including two influenza B virus, five A/H1N1, six A/H3N2, and two A/H5N1 isolates. In addition, the assay correctly identified 8 out of 10 diluted, archived avian influenza virus specimens with complete typing and subtyping information and 2 specimens with partial subtyping information. In a study of 146 human clinical specimens that had previously been shown to be positive for influenza virus or another respiratory virus, the assay showed a clinical sensitivity of 96% and a clinical specificity of 100%. The assay is a rapid, accurate, user-friendly method for simultaneously typing and subtyping influenza viruses.

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Section: Discussionmentioning

confidence: 99%

“…However, analysis of different amplification products from multiplex RT-PCR using traditional agarose gel electrophoresis can be problematic and slow (26). Recently, different types of microarrays in combination with multiplex amplification have been reported for the typing and subtyping of influenza viruses (9,13,14,19,21,22,27).…”

mentioning

confidence: 99%

Multiplex Assay for Simultaneously Typing and Subtyping Influenza Viruses by Use of an Electronic Microarray

et al. 2009

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“…Microarray technologies have become a tool of choice for multiparametric diagnostic assays and for gene expression profiling (7,14,21,24). The ability to perform sensitive and reproducible microarray hybridizations depends to a great extent on the quality of the microarray substrate.…”

Section: Discussionmentioning

confidence: 99%

Plastic Polymers for Efficient DNA Microarray Hybridization: Application to Microbiological Diagnostics

et al. 2008

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Fabrication of microarray devices using traditional glass slides is not easily adaptable to integration into microfluidic systems. There is thus a need for the development of polymeric materials showing a high hybridization signal-to-background ratio, enabling sensitive detection of microbial pathogens. We have developed such plastic supports suitable for highly sensitive DNA microarray hybridizations. The proof of concept of this microarray technology was done through the detection of four human respiratory viruses that were amplified and labeled with a fluorescent dye via a sensitive reverse transcriptase PCR (RT-PCR) assay. The performance of the microarray hybridization with plastic supports made of PMMA [poly(methylmethacrylate)]-VSUVT or Zeonor 1060R was compared to that with high-quality glass slide microarrays by using both passive and microfluidic hybridization systems. Specific hybridization signal-to-background ratios comparable to that obtained with high-quality commercial glass slides were achieved with both polymeric substrates. Microarray hybridizations demonstrated an analytical sensitivity equivalent to approximately 100 viral genome copies per RT-PCR, which is at least 100-fold higher than the sensitivities of previously reported DNA hybridizations on plastic supports. Testing of these plastic polymers using a microfluidic microarray hybridization platform also showed results that were comparable to those with glass supports. In conclusion, PMMA-VSUVT and Zeonor 1060R are both suitable for highly sensitive microarray hybridizations.

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“…In addition, nucleic acid microarrays have demonstrated higher sensitivity than traditional antibody-based assays, making the detection of pathogens down to 10 cfu/mL or 10 pfu/mL possible (Lin et al 2007). Indeed, several studies have shown the utility of DNA microarrays for pathogen detection (Call et al 2003a, b;Chizhikov et al 2001Chizhikov et al , 2002Davignon et al 2005;Gingeras et al 1998;Lin et al 2007;Roth et al 2004;Troesch et al 1999;Wang et al 2002Wang et al , 2003Wang et al , 2006Wilson et al 2002a, b).…”

Section: Introductionmentioning

confidence: 99%

Automated module for hybridization and staining of commercially produced nucleic acid microarrays

Erickson¹,

Anderson³

et al. 2007

Microfluid Nanofluid

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Nucleic acid microarrays are a rapidly expanding technology that enables the detection of pathogens at the genetic level. Currently, the processing of commercially produced microarrays requires cumbersome, expensive, and time-consuming benchtop equipment, which is not practical for point-of-care diagnostic applications. We demonstrate a portable module that can perform the hybridization, wash, and stain steps required for processing a nucleic acid microarray; and it performs these steps in a timeline significantly shorter than the standard commercial protocol. This device is automated, has a small footprint, and serves as a replacement for two commercial pieces of benchtop equipment. Furthermore, our device is designed to serve as a module in a portable biosensor that performs automated sample preparation and nucleic acid amplification. Results with Affymetrix GeneChips show that our device performs as well as non-portable equipment specifically manufactured to process these microarrays.

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Identifying Influenza Viruses with Resequencing Microarrays

Abstract: Resequencing microarrays rapidly identify influenza viruses.

Cited by 73 publications

References 28 publications

Multiplex Assay for Simultaneously Typing and Subtyping Influenza Viruses by Use of an Electronic Microarray

Multiplex Assay for Simultaneously Typing and Subtyping Influenza Viruses by Use of an Electronic Microarray

Plastic Polymers for Efficient DNA Microarray Hybridization: Application to Microbiological Diagnostics

Automated module for hybridization and staining of commercially produced nucleic acid microarrays

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