Typing of enteroviruses by use of microwell oligonucleotide arrays

Petri Susi, Liisa Hattara, Matti Waris, Tiina Luoma-aho, Harri Siitari, Timo Hyypiä, Petri Saviranta (Corresponding Author)

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Abstract

We have developed a straightforward assay for the rapid typing of enteroviruses using oligonucleotide arrays in microtiter wells. The viral nucleic acids are concomitantly amplified and labeled during reverse transcription-PCR, and unpurified PCR products are used for hybridization. DNA strands are separated by alkaline denaturation, and hybridization is started by neutralization. The microarray hybridization reactions and the subsequent washes are performed in standard 96-well microtiter plates, which makes the method easily adaptable to high-throughput analysis. We describe here the assay principle and its potential in clinical laboratory use by correctly identifying 10 different enterovirus reference strains. Furthermore, we explore the detection of unknown sequence variants using serotype consensus oligonucleotide probes. With just two consensus probes for the coxsackievirus A9 (CVA9) serotype, we detected 23 out of 25 highly diverse CVA9 isolates. Overall, the assay involves several features aiming at ease of performance, robustness, and applicability to large-scale studies.
Original languageEnglish
Pages (from-to)1863-1870
Number of pages8
JournalJournal of Clinical Microbiology
Volume47
Issue number6
DOIs
Publication statusPublished - 2009
MoE publication typeA1 Journal article-refereed

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Susi, P., Hattara, L., Waris, M., Luoma-aho, T., Siitari, H., Hyypiä, T., & Saviranta, P. (2009). Typing of enteroviruses by use of microwell oligonucleotide arrays. Journal of Clinical Microbiology, 47(6), 1863-1870. https://doi.org/10.1128/JCM.02226-08