Progress in the Development of a Universal Plant Virus Microarray for the Detection and Identification of Viruses

J. Hammond, D. C. Henderson, B. Bagewadi, R. L. Jordan, K. L. Perry, U. Melcher, D. Wang, K. F. Fischer, C. M. Fauquet

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Microarrays based on oligonucleotides representing sequences conserved at the level of viral species, genera, and families are able to detect and identify both characterized and previously uncharacterized viruses infecting mammals and birds. Software initially developed for these animal virus microarrays has been further refined for both design and analysis of a Universal Plant Virus Microarray (UPVM). The UPVM is based on 9,600 60-mer oligonucleotides, including at least four genuslevel and four family-level probes per taxonomic group, and 44 control probes for highly conserved plant genes. These probes together represent all characterized plant viruses for which significant genomic sequence was publically available in GenBank as of January 2010, and additional sequences made available to us prior to public GenBank release. Associated methods have been developed for high quality total nucleic acid extraction, applicable to a broad range of plant tissues containing metabolites such as phenolics, polysaccharides, latex, and resins that can interfere with nucleic acid extraction or subsequent amplification. Validation of the UPVM with a broad range of DNA and RNA plant viruses is in progress. Many high-titer viruses can be detected by direct labeling of total RNA extracts. Amplification and subtractive hybridization protocols to increase the sensitivity of detection of low titer viruses are being examined.

Original languageEnglish
Title of host publicationXIII International Symposium on Virus Diseases of Ornamental Plants
EditorsD.-R. Blystad, E. Floistad, C. Spetz
PublisherInternational Society for Horticultural Science
Pages149-156
Number of pages8
ISBN (Electronic)9789462610644
DOIs
StatePublished - Feb 20 2015

Publication series

NameActa Horticulturae
Volume1072
ISSN (Print)0567-7572

Keywords

  • Hybridization
  • Nucleic acid extraction
  • T-predict
  • Unbiased amplification
  • Uncharacterized virus

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  • Cite this

    Hammond, J., Henderson, D. C., Bagewadi, B., Jordan, R. L., Perry, K. L., Melcher, U., Wang, D., Fischer, K. F., & Fauquet, C. M. (2015). Progress in the Development of a Universal Plant Virus Microarray for the Detection and Identification of Viruses. In D-R. Blystad, E. Floistad, & C. Spetz (Eds.), XIII International Symposium on Virus Diseases of Ornamental Plants (pp. 149-156). (Acta Horticulturae; Vol. 1072). International Society for Horticultural Science. https://doi.org/10.17660/ActaHortic.2015.1072.18