ArticleJournal of medical virology2011
Improvement of the specificity of a pan-viral microarray by using genus-specific oligonucleotides and reduction of interference by host genomes.
Article in Journal of medical virology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Flavivirus Persistence in Wildlife Populations.Viruses · 2021Review
- Article
- A Novel Pan-BioMed research international · 2017Article
- Propidium monoazide (PMA) and ethidium bromide monoazide (EMA) improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification.Journal of virological methods · 2015Article
- Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray.Journal of virological methods · 2014Article
- Mosquito cellular factors and functions in mediating the infectious entry of chikungunya virus.PLoS neglected tropical diseases · 2013Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid detection of viral pathogens is crucial for antiviral therapy. High-density 60-70-mer oligonucleotide microarrays have been explored for broad detection of many viruses. However, relatively low specificity and the complex analytical processes are the major limitations when pan-viral oligonucleotide microarrays are used to detect viral pathogens. In this study, genus-specific oligonucleotides were used as probes and modified sample preparations were carried out to improve the specificity and accuracy of the pan-viral oligonucleotide microarray. Genus-specific 63-mer oligonucleotide probes were used for screening human pathogenic RNA viruses. A total of 628 oligonucleotide probes covering 32 RNA viral genera from 14 viral families were used. The number of oligonucleotide probes was decreased to simplify the analytical process of hybridization and to minimize cross-hybridization. Host genomes were removed by DNase I/RNase T1 digestion before viral nucleic acid extraction, and non-ribosomal hexanucleotides were used for reverse transcription to minimize interference of host genomes. Cultured viruses were used for microarray validation. The microarray was validated by cultured isolates that belonged to five viral genera. By using DNase I/RNase T1 digestion before viral nucleic acid extraction and non-ribosomal hexanucleotides for reverse transcription, the specificity of the microarray was improved. Furthermore, the analytical process of hybridization results was simplified. The specificity of pan-viral microarray could be improved by using genus-specific oligonucleotides as probes and by using non-ribosomal hexanucleotides for reverse transcription. Combined with subsequent degenerate reverse transcriptase-polymerase chain reaction and sequencing processes, this improved genus-specific oligonucleotides microarray provides a relatively flexible strategy for diagnosis of RNA virus diseases.
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