title: Development and evaluation of an efficient 3'-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections.
abstract: The severe acute respiratory syndrome (SARS) epidemic originating from China in 2002 was caused by a previously uncharacterized coronavirus that could be identified by specific RT-PCR amplification. Efforts to control future SARS outbreaks depend on the accurate and early identification of SARS-CoV infected patients. A real-time fluorogenic RT-PCR assay based on the 3'-noncoding region (3'-NCR) of SARS-CoV genome was developed as a quantitative SARS diagnostic tool. The ideal amplification efficiency of a sensitive SARS-CoV RT-PCR assay should yield an E value (PCR product concentration increase per amplification cycle) equal to 2.0. It was demonstrated that the 3'-NCR SARS-CoV based RT-PCR reactions could be formulated to reach excellent E values of 1.81, or 91% amplification efficacy. The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The viral genomic copy (or genomic equivalences, GE) per infectious unit (GE/pfu) of SARS-CoV used in this study was also established to be approximate 1200-1600:1. The assay's detection sensitivity could reach 0.005 pfu or 6-8 GE per assay. It was preliminarily demonstrated that the assay could efficiently detect SARS-CoV from clinical specimens of SARS probable and suspected patients identified in Taiwan. The 3'-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region.
authors.affiliation: Department of Virus Diseases, Walter Reed Army Institute of Research, Silver Spring, MD 20910-7500, USA. huo-shu.houng@na.amedd.army.mil
authors.forename: Huo-Shu H
authors.initials: HS
authors.lastname: Houng
authors.forename: David
authors.initials: D
authors.lastname: Norwood
authors.forename: George V
authors.initials: GV
authors.lastname: Ludwig
authors.forename: Wellington
authors.initials: W
authors.lastname: Sun
authors.forename: Minta
authors.initials: M
authors.lastname: Lin
authors.forename: David W
authors.initials: DW
authors.lastname: Vaughn
mesh_terms: D020413:3' Untranslated Regions; D018076:DNA, Complementary; D016679:Genome, Viral; D006801:Humans; D010614:Pharynx / Q000821:virology; D012367:RNA, Viral / Q000032:analysis* / Q000235:genetics / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics* / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D045169:Severe Acute Respiratory Syndrome / Q000175:diagnosis*; D013624:Taiwan; D010948:Viral Plaque Assay
chemical_list: D020413:3' Untranslated Regions; D018076:DNA, Complementary; D012367:RNA, Viral