Comparison of an in-house real-time RT-PCR assay with a commercial assay for detection of enterovirus RNA in clinical samples

Molecular detection of enterovirus (EV) RNA based on PCR methods is a quicker and more sensitive approach than culture methods. At present, different PCR-based methods for EV RNA detection are available, but comparisons of results obtained according to the different approaches are limited. We evaluated an in-house real-time RT-PCR assay with a commercialized TaqMan real-time RT-PCR kit for detection of EV. Consecutive clinical specimens from paediatric patients less than 6 years old with clinical suspicion of EV infection were analyzed between July and November 2010. After RNA extraction, samples were amplified both by the real-time RT-PCR commercial assay and the in-house assay. A total of 19 of 132 patients (14.4%) involving 20 samples (14 plasma samples and 6 CSF) were positive in at least one of the two assays. The sensitivity of the in-house assay when the MutaPLATE® assay was used as a reference was 90% (IC 95%; 74.35–100) and the specificity was 100% (IC 95%; 99.63–100). Cts results of two methods were statistically correlated (r?=?0.774; P?=?0.01). In conclusion, these two real-time RT-PCR assays are rapid and easy methods for detection of EV.     

Development and evaluation of a real-time RT-PCR assay on the LightCycler for the rapid detection of enterovirus in cerebrospinal fluid specimens.

BACKGROUND: Detection of enteroviral nucleic acid in cerebrospinal fluid (CSF) specimens has been demonstrated to improve the management of patients with aseptic meningitis. OBJECTIVE: To develop on the LightCycler (LC) instrument a real-time RT-PCR assay based on TaqMan technology for the detection of enteroviruses (EV) in cerebrospinal fluid (CSF) specimens. STUDY DESIGN: After evaluation of the analytical performances, seventy-four CSF samples collected prospectively from patients who have been suspected for a clinical diagnosis of meningitis were evaluated by two LC real-time RT-PCR assays and one conventional RT-PCR assay. RESULTS: Our assay detected all 30 different EV species tested, whereas no reactivity was observed with other neurotropic viruses. The analytical sensitivity of both LC RT-PCR real-time assays was 1 TCID50 for LC one-step and two-step RT-PCR assays. Results for LC one-step and LC two-step RT-PCR were compared to results of the conventional RT-PCR: of the 74 CSF specimens tested, 11 were positive and 56 were negative by all methods. Four other specimens were positive for EV by at least two of the methods (including the LC two-step RT-PCR and the conventional RT-PCR), two other CSF specimens were positive by the LC two-step RT-PCR assay only, and another one CSF specimen was positive by the LC one-step RT-PCR assay only. No CSF specimens were negative by the LC two-step RT-PCR assay and positive by the conventional RT-PCR assay. The sensitivity, specificity, positive and negative predictive values of both LC RT-PCR assays by using conventional RT-PCR as the "gold standard" were, respectively, 73.3, 98.3, 91.7, 93.5% for the LC one-step RT-PCR and 100, 96.6, 88.2, 100% for the LC two-step RT-PCR. There was substantial agreement between the three assays (k=0.80). CONCLUSIONS: The LC two-step RT-PCR assay is a rapid, sensitive and reliable method which can be routinely performed with CSF samples for diagnosis of EV infection and is an important improvement for optimal patient management.     

Evidence-Based Diagnosis of Toxoplasma Infection

 The aim of this study was to compare the performance of one in-house and four commercially available toxoplasma assays with the Sabin-Feldman dye test. One hundred fifty-seven routine sera and 20 potentially cross-reactive sera were tested blindly using four commercial assays: Abbott AxSym IgG (Abbott Laboratories, UK), Captia Select Toxo-G (Trinity Biotech, UK), Toxreagent 'Eiken' (Eiken Chemical, Japan) and Toxolatex Fumouze (Fumouze Laboratoires, France); an in-house IgG and IgM enzyme immunoassay (EIA); and the gold standard Sabin-Feldman dye test. The sensitivity, specificity and the values using the formulae for numbers needed to diagnose (NND) and the cost per positive diagnosis (CPPD) were calculated for each assay. These formulae use the sensitivity and specificity of the assay to allow for evidence-based comparisons between assays. The NND values for the in-house IgG EIA, AxSym, Eiken and Fumouze latex kits were similar (1.21–1.24), whereas the Captia yielded the poorest value (1.33). The in-house EIA IgG had the lowest CPPD value (￡0.57/$0.91), and the Fumouze and Eiken latex kits had the lowest CPPD values for commercial assays (￡1.42/$2.27 and ￡1.81/$2.90, respectively). Both assays were simple and straightforward to use. Specialist laboratories should opt to use in-house assays, as they were most cost-effective. Although nonspecialist laboratories could use commercial assays, specimens from immunocompromised patients and patients with ocular disease should be forwarded to specialist laboratories without prior testing.     

Evaluation of commercial enzyme immunoassays for detection of hepatitis delta antigen and anti-hepatitis delta virus (HDV) and immunoglobulin M anti-HDV antibodies.

Panels of hepatitis B virus surface antigen-positive sera from drug abusers were used to evaluate 14 commercial enzyme immunoassays from six companies for detecting hepatitis delta virus (HDV) markers. For detecting hepatitis delta virus antigen (HDAg), the Wellcome, Pasteur and Noctech assays had 100% sensitivity for all 42 HDAg-positive serum specimens that were confirmed in-house; the Organon reagents gave 59.5% sensitivity without detergent and 64.3% sensitivity with detergent, but there were 14 discrepant results with and without detergent. The Sorin assay detected HDAg in only 10 of the positive samples (23.8% sensitivity). For the detection of antibody to HDV (anti-HDV) all six commercial enzyme immunoassays were reactive with all 36 anti-HDV-positive specimens that were confirmed in-house. There were no false-positive results with the Wellcome, Noctech, or Sorin assay, but one specimen was false positive by the Organon assay. One HDAg-positive specimen gave a false anti-HDV-positive result in the Abbott assay and an equivocal result in the Pasteur assay (97.8% specificity). For the detection of immunoglobulin M anti-HDV, the Wellcome, Noctech, and Sorin assays agreed for the 38 positives confirmed in-house, except for one false negative with the Sorin test. We conclude that there has been a substantial improvement over previously evaluated assays in sensitivity and specificity of commercial assays for anti-HDV detection, and the sensitivities of immunoglobulin M anti-HDV assays are also comparable. However, there are still major differences in sensitivity among some assays for HDAg detection.     

Rapid detection of enterovirus infection by automated RNA extraction and real-time fluorescence PCR.

BACKGROUND: Molecular detection has been shown to be superior to tissue culture for the detection of enteroviruses in cerebrospinal fluid (CSF) specimens. OBJECTIVES: In this study, a qualitative molecular assay based on automated RNA extraction with the MagNA Pure LC and real-time PCR on the LightCycler (LC) instrument was evaluated and compared with an in-house molecular assay. STUDY DESIGN: A total of 109 CSF specimens were investigated for the comparative study. The detection limit of the new molecular assay was determined with 10-fold dilutions of two enterovirus strains and with the Third European Union Concerted Action Enterovirus Proficiency Panel. RESULTS: With the enterovirus strains, the detection limit of the LC assay was found to be 0.1 TCID(50) (50% tissue culture infective dose). When samples of the Third European Union Concerted Action Enterovirus Proficiency Panel were tested, both molecular assays gave identical results to the expected results, which were based upon the results of three reference laboratories using a total of four different molecular methods before distribution of the panel. When clinical specimens were tested, there was a correlation between the LC assay and the in-house assay in 105 of 109 cerebrospinal fluids. CONCLUSIONS: The new molecular assay allows rapid detection of enterovirus RNA in CSF. It was found to be labor saving and showed sufficient sensitivity.     

Evaluation of real-time RT-PCR Rhino&EV/Cc r-gene® (bioMérieux) kit versions 1 and 2 for rhinovirus detection

BackgroundHuman rhinoviruses (HRVs) are frequent etiologic agents of tract infections, ranging from benign upper to potentially life-threatening lower respiratory tract infections. Diagnosis is based on molecular methods. 169 HRV types, belonging to species A, B and C, have been identified. This high genetic diversity makes it difficult to accurately detect circulating HRVs and to diagnose severe infection.ObjectivesTo comparatively assess the ability to detect HRV clinical isolates of the first version (V1) of the commercial real-time RT-PCR Rhino&EV/Cc r-gene^® (bioMérieux) kit, of an in-house RT-PCR followed by genotyping, considered as the reference method, and of the second version of this commercial test (V2).Study designFrom September 2011 to April 2013, HRVs were prospectively detected in 2525 respiratory specimens, using V1 in combination with the in-house reference RT-PCR. In November 2013, 85 specimens that had given initially false negative results with V1 were retested simultaneously with V1 and V2 and the in-house RT-PCR. In addition, 421 negative specimens with the in-house assay were prospectively tested with V2.ResultsAmong the 2525 specimens, V1 detected 80.7% (502/622) of in-house RT-PCR positive isolates: 85.3% (220/258) of HRV-A, 84.4% (27/32) of HRV-B and 74.9% (176/235) of HRV-C. Among the 85 respiratory samples tested with V1, V2 and the in-house RT-PCR, V2 was more efficient than V1 in detecting 16 HRV isolates: 11/33 (33.3%) of HRV-A and 5/47 (10.6%) of HRV-C tested. The analytical sensitivity of V2 was greater for 8/18 HRV-A genotypes and 2/22 HRV-C genotypes. Relative to the in-house assay, the specificity of V2 was 100% (421/421).ConclusionsThis study showed a slightly higher sensitivity of V2. However, diverse genotypes, especially HRV-C, were undetected.     

Early diagnosis of SARS coronavirus infection by real time RT-PCR.

BACKGROUND: A novel coronavirus was recently identified as the aetiological agent of Severe Acute Respiratory Syndrome (SARS). Molecular assays currently available for detection of SARS-coronavirus (SARS-CoV) have low sensitivity during the early stage of the illness. OBJECTIVE: To develop and evaluate a sensitive diagnostic test for SARS by optimizing the viral RNA extraction methods and by applying real-time quantitative RT-PCR technology. STUDY DESIGN: 50 nasopharyngeal aspirate (NPA) samples collected from days 1-3 of disease onset from SARS patients in whom SARS CoV infections was subsequently serologically confirmed and 30 negative control samples were studied. Samples were tested by: (1) our first generation conventional RT-PCR assay with a routine RNA extraction method (Lancet 361 (2003) 1319), (2) our first generation conventional RT-PCR assay with a modified RNA extraction method, (3) a real-time quantitative RT-PCR assay with a modified RNA extraction method. RESULTS: Of 50 NPA specimens collected during the first 3 days of illness, 11 (22%) were positive in our first generation RT-PCR assay. With a modification in the RNA extraction protocol, 22 (44%) samples were positive in the conventional RT-PCR assay. By combining the modified RNA extraction method and real-time quantitative PCR technology, 40 (80%) of these samples were positive in the real-time RT-PCR assay. No positive signal was observed in the negative controls. CONCLUSION: By optimizing RNA extraction methods and applying quantitative real time RT-PCR technologies, the sensitivity of tests for early diagnosis of SARS can be greatly enhanced.     

Clinical performance of different SARS-CoV-2 IgG antibody tests

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays are urgently needed for rapid diagnosis, contact tracing, and for epidemiological studies. So far, there is limited data on how commercially available tests perform with real patient samples, and if positive tested samples show neutralizing abilities. Focusing on IgG antibodies, we demonstrate the performance of two enzyme-linked immunosorbent assay (ELISA) assays (Euroimmun SARS-CoV-2 IgG and Vircell COVID-19 ELISA IgG) in comparison to one lateral flow assay (FaStep COVID-19 IgG/IgM Rapid Test Device) and two in-house developed assays (immunofluorescence assay [IFA] and plaque reduction neutralization test [PRNT]). We tested follow up serum/plasma samples of individuals polymerase chain reaction-diagnosed with COVID-19. Most of the SARS-CoV-2 samples were from individuals with moderate to the severe clinical course, who required an in-patient hospital stay. For all examined assays, the sensitivity ranged from 58.8 to 76.5% for the early phase of infection (days 5-9) and from 93.8% to 100% for the later period (days 10-18).     

Development and evaluation of an efficient 3'-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections

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.     

Evaluation of real-time polymerase chain reaction assays for the detection of herpes simplex virus in swab specimens

An in-house herpes simplex virus (HSV) real-time polymerase chain reaction (PCR) hydrolysis probe assay and three commercial real-time HSV assays were evaluated for the detection of HSV from genital, oral, ocular and dermal clinical samples. Five hundred and sixty samples from patients displaying signs and symptoms of HSV infection were used to evaluate the in-house HSV assay. A representative 151 samples were processed using the artus(R) HSV-1/2 TM PCR Kit, SmartCycler(R) Non-typing and SmartCycler(R) Typing ASR kits. The in-house PCR assay demonstrated an overall positivity rate of 38% (211/560), equating to a 14% increase in HSV detection compared to 24% for culture (135/560). All 76 culture-negative, in-house PCR-positive samples were confirmed using at least one HSV commercial kit. The in-house, SmartCycler(R) Non-typing, artus(R) and SmartCycler(R) Typing assays showed improved sensitivity (100%, 100%, 98% and 99%, respectively) compared to culture (37%), and all real-time assays were highly specific (100%). The in-house and commercial real-time HSV PCR assays performed well and, combined with careful clinical interpretation, should improve the detection, differentiation and quantification of HSV from mucocutaneous swab samples.     

Evaluation of analytical and preliminary clinical performance of Myconostica MycAssay Aspergillus when testing serum specimens for diagnosis of invasive Aspergillosis

Diagnosis of invasive aspergillosis remains a significant problem. PCR testing may aid diagnosis but is not yet included in disease-defining criteria due to a lack of standardization of assays and methodologies. This study investigated the analytical performance and the clinical sensitivity and specificity of the Myconostica MycAssay Aspergillus PCR (MAP) assay compared to those of a validated in-house Aspergillus PCR (IHP) test when testing serum specimens. Serum specimens spiked with Aspergillus genomic DNA had a limit of detection equivalent to 5 genomes and a linear dynamic range of 5 to >5 × 10(4) genomes for both assays. When testing clinical specimens (n = 170), the MAP assay had a sensitivity of 60 to 70% and a specificity of 90.5 to 100%. The IHP assay had a sensitivity of 50 to 80% and a specificity of 100%. A commercially available Aspergillus PCR assay provides a methodology that is standardized and reagents that are quality controlled. This facilitates multicenter evaluation of the clinical utility of PCR diagnosis. The performance of the MAP assay is comparable to that of the IHP assay and to those in previously reported studies evaluating commercial tests (galactomannan enzyme-linked immunosorbent assay).     

Evaluation of a new NASBA assay for the qualitative detection of hepatitis C virus based on the NucliSens Basic Kit reagents.

BACKGROUND: Direct detection of HCV RNA by nucleic acid amplification methods is an essential tool in the diagnosis of HCV infections. In-house developed methods based on reverse transcribed polymerase chain reaction (RT-PCR) are widely used but they are laborious and usually lack the standardization required by clinical laboratories. OBJECTIVES: To evaluate the sensitivity and the clinical performance of an HCV specific nucleic acid sequence based amplification (NASBA) assay based on the commercially available, NucliSens Basic Kit (bioMérieux) reagents. STUDY DESIGN: The analytical sensitivity of the Basic Kit-based HCV assay (BK-HCV) was determined using dilutions of the First World Health Organization International Standard for HCV RNA. The performance of the BK-HCV was evaluated at two study sites in comparison with in-house RT-nested PCR (RT-nPCR) by testing a total of 77 plasma specimens. Additional HCV laboratory tests such as Amplicor HCV v2.0 (Roche Diagnostics) and genotype were also included in the comparative analysis. RESULTS: The sensitivity of the BK-HCV was 100-150 IU/ml HCV RNA (85-100% hit rate). When evaluating the clinical performance, we found 96-100% correlation between BK-HCV and RT-nPCR, and 85-91% correlation between BK-HCV and Amplicor. The level of efficiency of the BK-HCV for detecting prevalent HCV genotypes was equal to in house RT-nPCR and Amplicor. CONCLUSIONS: The BK-HCV offers adequate sensitivity for diagnostic purposes and equivalent clinical performance to in-house RT-nPCR assays. The BK-HCV could become a suitable alternative to the in-house amplification methods, providing standardized reagents and procedures, plus rapid results to clinical laboratories.     

Comparison of Test Specificities of Commercial Antigen-Based Assays and In-House PCR Methods for Detection of Rotavirus in Stool Specimens

Seven commercial rotavirus antigen assays were compared with in-house PCR methods for detecting rotavirus in stool specimens. The assay sensitivities were 80% to 100%, while the specificities were 54.3% for one commercial immunochromatographic (ICT) method and 99.4% to 100% for other assays. Thus, except for one commercial ICT, all the assays were generally reliable for rotavirus detection.