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.
Highlights
The control of viral diseases is reliant on identifying the causative agent in order to help devise and implement appropriate control measures
Microarray has proven to be a successful tool in detecting novel viruses and viral co-infections establishing itself as a front-line diagnostic tool for investigation of emerging infectious diseases
This study looked at implementing two different ribosomal RNA (rRNA) depletion or exclusion methods to assess whether an improvement to microarray detection of RNA viruses from tissue samples could be made
Summary
The control of viral diseases is reliant on identifying the causative agent in order to help devise and implement appropriate control measures. Infectious diseases are emerging continuously in new species and geographical locations due to factors such as pathogen mutations, genetic reassortment, animal and human movement and climate change (Weiss and Mcmichael, 2004; Butler, 2012). In this regard, RNA viruses are of particular concern, as they mutate at a higher rate than DNA viruses and lack proofreading enzymes to prevent errors during RNA replication (Holland et al, 1982). The constant threat of new infectious diseases reiterates the need for rapid and multiplex detection assays such as microarrays, which can probe thousands of viruses simultaneously.
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