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Using a Pan-Viral Microarray Assay (Virochip) to Screen Clinical Samples for Viral Pathogens

By Eunice C. Chen, Steve A. Miller, Joseph L. DeRisi and Charles Y. Chiu

Abstract

The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence of novel viral pathogens, such as SARS coronavirus and 2009 pandemic H1N1 influenza virus, that are not detectable by traditional methods. To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology1. Using the Virochip, we have identified the full spectrum of viruses associated with respiratory infections, including cases of unexplained critical illness in hospitalized patients, with a sensitivity equivalent to or superior to conventional clinical testing2-5. The Virochip has also been used to identify novel viruses, including the SARS coronavirus6,7, a novel rhinovirus clade5, XMRV (a retrovirus linked to prostate cancer)8, avian bornavirus (the cause of a wasting disease in parrots)9, and a novel cardiovirus in children with respiratory and diarrheal illness10. The current version of the Virochip has been ported to an Agilent microarray platform and consists of ~36,000 probes derived from over ~1,500 viruses in GenBank as of December of 2009. Here we demonstrate the steps involved in processing a Virochip assay from start to finish (~24 hour turnaround time), including sample nucleic acid extraction, PCR amplification using random primers, fluorescent dye incorporation, and microarray hybridization, scanning, and analysis

Topics: Immunology
Publisher: MyJove Corporation
OAI identifier: oai:pubmedcentral.nih.gov:3169278
Provided by: PubMed Central

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Citations

  1. (2003). Characterization of a novel coronavirus associated with severe acute respiratory syndrome.
  2. (2007). Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray.
  3. (2005). E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.
  4. (2006). Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog 2,
  5. (2008). Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections.
  6. (2006). Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult.
  7. (2002). Microarray-based detection and genotyping of viral pathogens.
  8. (2007). Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity.
  9. (2011). Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent.
  10. (2008). Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children.
  11. (2003). Viral discovery and sequence recovery using DNA microarrays.

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