title: Performance and Cost evaluation of one commercial and six in-house conventional and real-time reverse transcription-pcr assays for detection of severe acute respiratory syndrome coronavirus.
abstract: We evaluated seven reverse transcription-PCR (RT-PCR) assays, including six in-house assays and one commercial assay for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV) RNA in clinical specimens. RT-PCR assays targeted different genomic regions and included three conventional assays (one nested and two non-nested) run on a conventional heat block and four real-time assays performed in a LightCycler (LC; Roche Diagnostics). All in-house assays were optimized for assay parameters, including MgCl2, primer, and probe concentrations. The commercial assay was the RealArt HPA CoV RT-PCR assay (Artus), which was run in the LC. Testing serial dilutions of cultured SARS-CoV showed that the analytical sensitivity of the assays ranged from 10(-8) to 10(-6), corresponding to 1 and 100 copies of viral RNA, respectively. Significant differences in analytical sensitivities were observed between assays (P < 0.01, probit regression analysis for 50% sensitivity levels for the top two assays versus the others). Testing 68 clinical specimens (including 17 respiratory tract specimens, 29 urine samples, and 22 stools or rectal swabs) demonstrated that six of the seven assays detected at least 17 of 18 positives (defined as positive in at least two assays), and two of the assays had a sensitivity of 100%. There were no significant differences in sensitivity between the assays (P = 0.5 [Cochrance Q test, least sensitive 15 of 18 versus 18 of 18]). The specificities of the assays ranged from 94.0 to 100% without significant differences (P = 0.25 to 0.5 [McNemar test]). The reagent and technologist cost of performing the in-house PCR assays ranged from $5.46 to $9.81 Canadian dollars (CDN) per test. The commercial assay cost was considerably higher at $40.37 per test. The results demonstrated good performance for all assays, providing laboratories that need to do SARS RNA testing with a choice of assay formats.
authors.affiliation: McMaster University, Toronto, Ontario L8N 4A6, Canada. mahonyj@mcmaster.ca
authors.forename: James B
authors.initials: JB
authors.lastname: Mahony
authors.forename: Astrid
authors.initials: A
authors.lastname: Petrich
authors.forename: Lisa
authors.initials: L
authors.lastname: Louie
authors.forename: Xinyu
authors.initials: X
authors.lastname: Song
authors.forename: Sylvia
authors.initials: S
authors.lastname: Chong
authors.forename: Marek
authors.initials: M
authors.lastname: Smieja
authors.forename: Max
authors.initials: M
authors.lastname: Chernesky
authors.forename: Mark
authors.initials: M
authors.lastname: Loeb
authors.forename: Susan
authors.initials: S
authors.lastname: Richardson
mesh_terms: D003365:Costs and Cost Analysis; D006801:Humans; D012367:RNA, Viral / Q000032:analysis; D011933:Reagent Kits, Diagnostic / Q000191:economics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000191:economics* / Q000379:methods*; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D045169:Severe Acute Respiratory Syndrome / Q000821:virology*
chemical_list: D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic