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Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses
Zheng Wang1, Anthony P Malanoski, Baochuan Lin
1Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA. zheng.wang@nrl.navy.mil
BMC Genomics
|December 3, 2008
Summary
A new microarray design strategy effectively detects and serotypes diverse human rhinoviruses (HRV) and enteroviruses (HEV) causing febrile respiratory illness. This method uses minimal probes for simultaneous pathogen identification, improving diagnostic capabilities.
Area of Science:
- Virology
- Molecular Diagnostics
- Bioinformatics
Background:
- Febrile respiratory illness (FRI) presents diagnostic challenges due to genetically diverse pathogens like human rhinoviruses (HRV) and enteroviruses (HEV).
- Current methods struggle with simultaneous detection and differentiation of these varied viral strains.
- Resequencing Pathogen Microarray (RPM) technology shows promise but lacks a robust design strategy for diverse viral targets.
Purpose of the Study:
- To develop and evaluate a general design strategy for detecting and serotyping genetically diverse viruses using a minimal set of probe sequences.
- To assess the efficacy of this strategy for human rhinoviruses (HRV) and enteroviruses (HEV) as model pathogens.
- To implement and validate the designed probes on the Resequencing Pathogen Microarray RPM-Flu v.30/31.
Main Methods:
- Determined a minimal set of probe sequences for HRV (26) and HEV (13) capable of detecting all serotypes.
- Implemented these probes on the Resequencing Pathogen Microarray RPM-Flu v.30/31.
- Validated probe specificity using 34 HRV and 28 HEV strains.
Main Results:
- All tested HRV and HEV strains were successfully detected and identified to at least the species level.
- The newly designed probes differentiated 33 out of 34 HRV strains and 16 out of 28 HEV strains to the serotype level.
- The RPM-Flu v.30/31 demonstrated comprehensive and specific analysis of HRV and HEV samples.
Conclusions:
- The study provides a fundamental evaluation of simultaneous detection and differential identification of diverse RNA viruses using minimal prototype sequences.
- The developed RPM-Flu v.30/31 design strategy is effective for HRV and HEV.
- This strategy is likely applicable to other genetically diverse viral pathogens, advancing diagnostic capabilities.
