title: SYBR green-based real-time quantitative PCR assay for detection of West Nile Virus circumvents false-negative results due to strain variability.
abstract: Real-time quantitative PCR is used routinely for the high-throughput diagnosis of viral pathogens, such as West Nile virus (WNV). Rapidly evolving RNA viruses present a challenge for diagnosis because they accumulate mutations that may render them undetectable. To explore the effect of sequence variations on assay performance, we generated every possible single point mutation within the target region of the widely used TaqMan assay for WNV and found that the TaqMan assay failed to detect 47% of possible single nucleotide variations in the probe-binding site and was unable to detect any targets with more than two mutations. In response, we developed and validated a less expensive assay with the intercalating dye SYBR green. The SYBR green-based assay was as sensitive as the TaqMan assay for WNV. Importantly, it detected 100% of possible WNV target region variants. The assay developed here adds an additional layer of protection to guard against false-negative results that result from natural variations or drug-directed selection and provides a rapid means to identify such variants for subsequent detailed analysis.
authors.affiliation: Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.
authors.forename: James F
authors.initials: JF
authors.lastname: Papin
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Vahrson
authors.forename: Dirk P
authors.initials: DP
authors.lastname: Dittmer
mesh_terms: D000818:Animals; D001483:Base Sequence; D052160:Benzothiazoles; D002522:Chlorocebus aethiops; D003959:Diamines; D005188:False Negative Reactions; D005456:Fluorescent Dyes; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000235:genetics; D009930:Organic Chemicals; D017354:Point Mutation; D011804:Quinolines; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D014709:Vero Cells; D014901:West Nile Fever / Q000821:virology; D014902:West Nile virus / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D052160:Benzothiazoles; D003959:Diamines; D005456:Fluorescent Dyes; D009841:Oligonucleotides; D009930:Organic Chemicals; D011804:Quinolines; C098022:SYBR Green I