Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children - PubMed (original) (raw)

Comparative Study

Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children

Frédéric Raymond et al. J Clin Microbiol. 2009 Mar.

Abstract

Respiratory virus infections are a major health concern and represent the primary cause of testing consultation and hospitalization for young children. We developed and compared two assays that allow the detection of up to 23 different respiratory viruses that frequently infect children. The first method consisted of single TaqMan quantitative real-time PCR assays in a 96-well-plate format. The second consisted of a multiplex PCR followed by primer extension and microarray hybridization in an integrated molecular diagnostic device, the Infiniti analyzer. Both of our assays can detect adenoviruses of groups A, B, C, and E; coronaviruses HKU1, 229E, NL63, and OC43; enteroviruses A, B, C, and D; rhinoviruses of genotypes A and B; influenza viruses A and B; human metapneumoviruses (HMPV) A and B, human respiratory syncytial viruses (HRSV) A and B; and parainfluenza viruses of types 1, 2, and 3. These tests were used to identify viruses in 221 nasopharyngeal aspirates obtained from children hospitalized for respiratory tract infections. Respiratory viruses were detected with at least one of the two methods in 81.4% of the 221 specimens: 10.0% were positive for HRSV A, 38.0% for HRSV B, 13.1% for influenzavirus A, 8.6% for any coronaviruses, 13.1% for rhinoviruses or enteroviruses, 7.2% for adenoviruses, 4.1% for HMPV, and 1.5% for parainfluenzaviruses. Multiple viral infections were found in 13.1% of the specimens. The two methods yielded concordant results for 94.1% of specimens. These tests allowed a thorough etiological assessment of respiratory viruses infecting children in hospital settings and would assist public health interventions.

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Figures

FIG. 1.

FIG. 1.

Flowchart comparing the protocols for the real-time PCR assay and for the microarray assay. RNA extraction and reverse transcription steps are common to both methods. The real-time PCR assay has only one setup step, while the microarray assay has three. However, the time required to perform the real-time PCR assay increased for each four samples tested. The time required for the automated microarray assay is increased for each 24 samples. Overall, the qRT-PCR assay requires 60 min of setup time and a total of 120 min of reaction time for 4 specimens, while the microarray assay requires 60 min of setup time and 17 h of reaction time for 24 specimens.

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