title: Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses.
abstract: BACKGROUND
  Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV) and enteroviruses (HEV) which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking.
  
  
  RESULTS
  Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV), which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu). The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level.
  
  
  CONCLUSIONS
  This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.
authors.affiliation: Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA. zheng.wang@nrl.navy.mil
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Anthony P
authors.initials: AP
authors.lastname: Malanoski
authors.forename: Baochuan
authors.initials: B
authors.lastname: Lin
authors.forename: Carolyn
authors.initials: C
authors.lastname: Kidd
authors.forename: Nina C
authors.initials: NC
authors.lastname: Long
authors.forename: Kate M
authors.initials: KM
authors.lastname: Blaney
authors.forename: Dzung C
authors.initials: DC
authors.lastname: Thach
authors.forename: Clark
authors.initials: C
authors.lastname: Tibbetts
authors.forename: David A
authors.initials: DA
authors.lastname: Stenger
mesh_terms: D001483:Base Sequence; D003937:Diagnosis, Differential; D004770:Enterovirus / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D015347:RNA Probes; D012328:RNA Viruses; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000821:virology; D012229:Rhinovirus / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D015347:RNA Probes