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Viro -chip Microarray

Viro -chip Microarray. Using a Pan-Viral Microarray Assay ( Viro -chip) to Screen Clinical Samples for Viral Pathogens. Introduction. Microarray for simultaneous screening of ALL known viruses “ Virochip ”  Detection of novel variants on the basis of conserved sequence homology.

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Viro -chip Microarray

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  1. Viro-chip Microarray Using a Pan-Viral Microarray Assay (Viro-chip) to Screen Clinical Samples for Viral Pathogens

  2. Introduction • Microarray for simultaneous screening of ALL known viruses “Virochip” •  Detection of novel variants on the basis of conserved sequence homology. • 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.

  3. Purpose • Detection of those viruses that cannot be detected by conventional methods, •  such as SARS coronavirus and 2009 pandemic H1N1 influenza virus, can be detected through virochip microarray • Novel rhinovirus clade • XMRV (a retrovirus linked to prostate cancer)8, • avian bornavirus (the cause of a wasting disease in parrots) • Novel cardiovirus in children with respiratory and diarrheal illness

  4. Protocol (steps of viro-chip assay) • Nucleic acid extraction from clinical samples • Reverse transcription of extracted RNA and 2nd-strand cDNA synthesis. • PCR amplification of randomly primed cDNA • Cy3 fluorescent dye incorporation • Hybridization of labeled material to the Virochip microarray • scanning and analysis

  5. Protocol

  6. Analysis and results • Scan Cy3-labeled array at 5 μm or 2 μm according to the instrument's standard scanning protocol (Figure 2B). • Analyze Virochip microarrays by visual inspection, cluster analysis, or the automated Virochip analysis program, E-Predict. • By each of these three methods, influenza virus is readily detected in the nasal swab sample (from a child with influenza-like illness)

  7. Analysis and results

  8. Discussion • The Virochip protocol as described here is complex and requires skilled research technician. • reagent concentrations and conditions for PCR, labeling, and hybridization are critical. • "Some applications of the Virochip assay currently under development include broad-spectrum viral diagnostics in the clinical laboratory, outbreak investigation, purity screening of drugs and vaccines, and novel viral pathogen discovery.

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