title: Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray.
abstract: Pan viral DNA microarrays, which can detect known, novel and multiple viral infections, are major laboratory assets contributing to the control of infectious diseases. The large quantity of ribosomal RNA (rRNA) found in tissue samples is thought to be a major factor contributing to the comparatively lower sensitivity of detecting RNA viruses, as a sequence-independent PCR is used to amplify unknown samples for microarray analysis. This study aimed to determine whether depletion or exclusion of rRNA can improve microarray detection and simplify its analysis. Therefore, two different rRNA depletion and exclusion protocols, RiboMinus™ technology and non-rRNA binding hexanucleotides, were applied to the microarray sample processing and the outcome was compared with those of the sequence-independent amplification protocol. This study concludes that the two procedures, described to deplete or exclude rRNA, have negligible effect on the microarrays detection and analysis and might only in combination with further techniques result in a significant enhancement of sensitivity. Currently, existing protocols of random amplification and background adjustment are pertinent for the purpose of sample processing for microarray analysis.
authors.affiliation: Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; Royal Veterinary College, Royal College Street, London NW1 0TU, UK.
authors.forename: Sarah
authors.initials: S
authors.lastname: McGowan
authors.affiliation: Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, UK.
authors.forename: Javier
authors.initials: J
authors.lastname: Nunez-Garcia
authors.affiliation: Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, UK.
authors.forename: Falko
authors.initials: F
authors.lastname: Steinbach
authors.affiliation: Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, UK.
authors.forename: Anna
authors.initials: A
authors.lastname: La Rocca
authors.affiliation: Royal Veterinary College, Royal College Street, London NW1 0TU, UK.
authors.forename: Damer
authors.initials: D
authors.lastname: Blake
authors.affiliation: Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey KT15 3NB, UK. Electronic address: akbar.dastjerdi@ahvla.gsi.gov.uk.
authors.forename: Akbar
authors.initials: A
authors.lastname: Dastjerdi
mesh_terms: D000818:Animals; D046228:Microarray Analysis / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012328:RNA Viruses / Q000235:genetics / Q000302:isolation & purification*; D012335:RNA, Ribosomal / Q000302:isolation & purification* / Q000378:metabolism; D012680:Sensitivity and Specificity; D013048:Specimen Handling / Q000379:methods*; D014773:Virology / Q000379:methods*
chemical_list: D012335:RNA, Ribosomal
keywords: Hexanucleotide; Microarray; RiboMinus™; Ribosomal RNA depletion; Virus discovery