Development, Validation, and Application of Reverse Transcription Real-Time and Droplet Digital PCR Assays for the Detection of the Potyviruses Watermelon Mosaic Virus and Zucchini Yellow Mosaic Virus in Cucurbits.

Among the cucurbit-infecting viruses, watermelon mosaic virus (WMV) and zucchini yellow mosaic virus (ZYMV) (Potyvirus: Potyviridae) are responsible for severe symptoms on cucumber, melon, watermelon, and zucchini cultivations worldwide. In this study, reverse transcription real-time PCR (real-time RT-PCR) and droplet-digital PCR (RT-ddPCR) assays targeting the coat protein (CP) genes of WMV and ZYMV were developed and validated according to the international standards of plant pest diagnosis (EPPO PM 7/98 (5)). First, the diagnostic performance of WMV-CP and ZYMV-CP real-time RT-PCRs was evaluated, and the assays displayed an analytical sensitivity of 10-5 and 10-3, respectively. The tests also showed an optimal repeatability, reproducibility and analytical specificity, and were reliable for the virus detection in naturally infected samples and across a wide range of cucurbit hosts. Based on these results, the real-time RT-PCR reactions were adapted to set up RT-ddPCR assays. These were the first RT-ddPCR assays aiming at the detection and quantification of WMV and ZYMV and showed a high sensitivity, being able to detect until 9 and 8 copies/µL of WMV or ZYMV, respectively. The RT-ddPCRs allowed the direct estimation of the virus concentrations and opened to a broad range of applications in disease management, such as the evaluation of partial resistance in breeding processes, identification of antagonistic/synergistic events, and studies on the implementation of natural compounds in the integrated management strategies.

Evaluation of the artus® Prep&Amp UM RT-PCR for detection of SARS-CoV-2 from nasopharyngeal swabs without prior nucleic acid eluate extraction.

Here we describe a retrospective clinical evaluation of the QIAGEN artus® SARS-CoV-2 Prep&Amp UM RT-PCR assay that detects SARS-CoV-2 RNA without the need for a nucleic acid eluate extraction procedure. Using Roche SARS-CoV-2 RT-PCR on the cobas® 8800 platform as a reference standard, a total of 225 confirmed SARS-CoV-2 positive and 320 negative nasopharyngeal swabs in viral transport media, were used to evaluate the artus® assay. Using the RT-PCR cycle threshold as a semi-quantitative marker of viral load, an assessment of over 370,000 SARS-CoV-2 RT-PCR positive results was used in the design of the reference positive specimen cohort. The viral load of all reference positive specimens used in the evaluation was a unique and accurate representation of the range and levels of SARS-CoV-2 positivity observed over a 13-month period of the COVID-19 pandemic. The artus® RT-PCR detects the presence of SARS-CoV-2 RNA, an internal control, and the human RNase P gene to ensure specimen quality. The diagnostic sensitivity of artus® was 92.89% with a specificity of 100%. To assess the analytical sensitivity, a limit of detection was performed using the 1st WHO NIBSC SARS-CoV-2 international standard, recording a 95% LOD of 1.1 × 103 IU/ml. The total invalid rate of specimens was 7.34% due to a lack of detectable RNase P (Ct >35). The artus® SARS-CoV-2 Prep&Amp UM RT-PCR assay is a new rapid RT-PCR assay, which may be considered to produce acceptable levels of diagnostic sensitivity and specificity whilst potentially halving the laboratory processing time.

Analytic and Clinical Performance of Major Commercial Severe Acute Respiratory Syndrome Coronavirus 2 Molecular Assays in the United States.

The rapid development of commercially available molecular assays in response to the COVID-19 pandemic has been essential in identifying positive cases and guiding state and national response plans. With over 200 SARS-CoV-2 molecular tests having received emergency use authorization by the US Food and Drug Administration, numerous studies have been conducted to evaluate these methods and compare their analytical and clinical performance. By applying the lessons learned from the rapid development of molecular assays in response to the COVID-19 pandemic, the diagnostic industry will be better prepared to respond to future outbreaks of novel infectious diseases.

Multiplex Microsphere PCR (mmPCR) Allows Simultaneous Gram Typing, Detection of Fungal DNA, and Antibiotic Resistance Genes.

OBJECTIVE: To show the high analytical specificity of our multiplex microsphere polymerase chain reaction (mmPCR) method, which offers the simultaneous detection of both general (eg, Gram type) and specific (eg, Pseudomonas species) clinically relevant genetic targets in a single modular multiplex reaction. MATERIALS AND METHODS: Isolated gDNA of 16S/rRNA Sanger-sequenced and Basic Local Alignment Tool-identified bacterial and fungal isolates were selectively amplified in a custom 10-plex Luminex MagPlex-TAG microsphere-based mmPCR assay. The signal/noise ratio for each reaction was calculated from flow cytometry standard data collected on a BD LSR Fortessa II flow cytometer. Data were normalized to the no-template negative control and the signal maximum. The analytical specificity of the assay was compared to single-plex SYBR chemistry quantitative PCR. RESULTS: Both general and specific primer sets were functional in the 10-plex mmPCR. The general Gram typing and pan-fungal primers correctly identified all bacterial and fungal isolates, respectively. The species-specific and antibiotic resistance-specific primers correctly identified the species- and resistance-carrying isolates, respectively. Low-level cross-reactive signals were present in some reactions with high signal/noise primer ratios. CONCLUSION: We found that mmPCR can simultaneously detect specific and general clinically relevant genetic targets in multiplex. These results serve as a proof-of-concept advance that highlights the potential of high multiplex mmPCR diagnostics in clinical practice. Further development of specimen-specific DNA extraction techniques is required for sensitivity testing.

Review of critical factors affecting analytical characteristics of serological and molecular assays.

Analytical characteristics of diagnostic tests, encompassing estimates of repeatability, analytical specificity (ASp) and analytical sensitivity (ASe), are determined during Stage 1 of the OIE Assay Validation Pathway. Repeatability (an estimate of assay precision and robustness), ASp (measuring only what an assay is intended to measure) and ASe (synonymous with the lower limit of detection) are fundamental parameters that determine future test performance. Importantly, these parameters provide the basis for deciding whether a prototype assay progresses to the next stage of the OIE Assay Validation Pathway (determination of diagnostic characteristics) or is withdrawn in favour of alternate tests with better analytical performance characteristics. Implicit in the successful development and validation of any assay is a sound understanding of the target pathogen, the disease pathogenesis in susceptible hosts, the fundamental technical principles that underliey each test system, and its intended use. Factors that affect analytical characteristics of diagnostic assays are numerous and may vary according to each assay type. Using, as examples, development of an enzyme-linked immunosorbent assay for detection of antibodies to capripoxviruses, and the comparative assessment of three quantitative real-time polymerase chain reactions for detection of African swine fever virus DNA, the main factors affecting analytical characteristics of serological and molecular assays are considered. As reviewed within, comprehensive and well-designed experiments are required to develop and optimise assays with favourable analytical characteristics. The underlying principles are broadly applicable to all assay types and, when conducted with appropriate rigour, provide the foundations for high-quality diagnostic tests that are fit for their intended purpose(s).

Les caractéristiques de performance analytique des tests diagnostiques, qui recouvrent l'estimation de la répétabilité, de la spécificité analytique (SpA) et de la sensibilité analytique (SeA) d'un test sont déterminées lors de l'étape 1 du processus de l'OIE relatif à la validation des essais. La répétabilité (une estimation de la précision et de la robustesse de l'essai), la SpA (qui mesure uniquement ce que l'essai est destiné à mesurer) et la SeA (synonyme de limite inférieure de détection) sont des paramètres essentiels qui déterminent les futures performances du test. Il est important de noter que ces paramètres apportent les éléments essentiels pour décider si l'essai peut passer à l'étape suivante du processus de validation de l'OIE (détermination des caractéristiques diagnostiques) ou s'il doit céder la place à des tests alternatifs dotés de meilleures caractéristiques de performance analytique. Pour réussir la mise au point et la validation d'un essai, certaines conditions préalables doivent être réunies : bien connaître l'agent pathogène cible et la pathogenèse de la maladie chez les réservoirs sensibles, ainsi que les grands principes techniques sous-jacents à chaque système de test et l'emploi prévu du test. Les facteurs affectant les caractéristiques analytiques d'un essai diagnostique sont nombreux et varient suivant le type d'essai dont il s'agit. À partir d'exemples portant sur une épreuve immuno-enzymatique mise au point pour la détection des anticorps dirigés contre les capripoxvirus et sur l'évaluation comparative de trois techniques d'amplification en chaîne par polymérase quantitative en temps réel pour la détection de l'ADN viral de la peste porcine africaine, les auteurs mettent en exergue les principaux facteurs qui peuvent altérer les caractéristiques analytiques des essais sérologiques et moléculaires. Il ressort de cette évaluation que des expérimentations complètes et bien conçues sont nécessaires pour mettre au point et optimiser des essais possédant les caractéristiques analytiques souhaitées. En général, les principes sous-jacents sont applicables à tous les types d'essai, et s'ils sont appliqués de manière rigoureuse, ils fournissent la garantie de disposer de tests diagnostiques de qualité élevée et aptes à l'emploi ou aux emplois prévus.

La primera etapa del proceso de validación de ensayos de la OIE es aquella en que se determinan las características analíticas de una prueba de diagnóstico, o dicho de otro modo, en que se calculan los valores de repetibilidad (estimación de la precisión y robustez del ensayo), especificidad analítica (es decir, el hecho de que el ensayo mida únicamente lo que está destinado a medir) y sensibilidad analítica (sinónimo referido al límite inferior de detección), que son tres parámetros fundamentales para determinar el futuro rendimiento de una prueba. Un aspecto importante es que estos parámetros sientan las bases a partir de las cuales decidir si un prototipo de ensayo debe pasar a la siguiente etapa del proceso de validación de ensayos de la OIE (determinación de las características de diagnóstico) o si vale más retirarlo en beneficio de otras pruebas que presenten mejores características de rendimiento analítico. Un factor implícito en el éxito de todo proceso de desarrollo y validación de ensayos es un sólido conocimiento del patógeno en cuestión, la patogénesis de la enfermedad en los anfitriones sensibles, los principios técnicos fundamentales en que reposa cada sistema de ensayo y sus usos previstos. Los numerosos factores que influyen en las características analíticas de un ensayo de diagnóstico difieren en función del tipo de ensayo. Utilizando como ejemplo el desarrollo de un ensayo inmunoenzimático de detección de anticuerpos contra capripoxvirus y la evaluación comparativa de tres PCR cuantitativas en tiempo real para detectar ADN del virus de la peste porcina africana, los autores pasan revista a los principales factores que determinan las características analíticas de los ensayos serológicos y moleculares. Como explican, para desarrollar y optimizar ensayos que presenten características analíticas favorables se requieren experimentos completos y bien concebidos. Los principios subyacentes son válidos en general para todo tipo de ensayos y, cuando se aplican con el debido rigor, sientan las bases para obtener pruebas de diagnóstico de gran calidad y adaptadas a la(s) finalidad(es) prevista(s).

Analytical validation of two RT-qPCR tests and detection of spring viremia of carp virus (SVCV) in persistently infected koi Cyprinus carpio.

Spring viremia of carp virus (SVCV) ia a carp sprivivirus and a member of the genus Sprivivirus within the family Rhabdoviridae. The virus is the etiological agent of spring viremia of carp, a disease of cyprinid species including koi Cyprinus carpio L. and notifiable to the World Organisation for Animal Health. The goal of this study was to explore hypotheses regarding inter-genogroup (Ia to Id) SVCV infection dynamics in juvenile koi and contemporaneously create new reverse-transcription quantitative PCR (RT-qPCR) assays and validate their analytical sensitivity, specificity (ASp) and repeatability for diagnostic detection of SVCV. RT-qPCR diagnostic tests targeting the SVCV nucleoprotein (Q2N) or glycoprotein (Q1G) nucleotides were pan-specific for isolates typed to SVCV genogroups Ia to Id. The Q2N test had broader ASp than Q1G because Q1G did not detect SVCV isolate 20120450 and Q2N displayed occasional detection of pike fry sprivivirus isolate V76. Neither test cross-reacted with other rhabdoviruses, infectious pancreatic necrosis virus or co-localizing cyprinid herpesvirus 3. Both tests were sensitive with observed 50% limits of detection of 3 plasmid copies and high repeatability. Test analysis of koi immersed in SVCV showed that the virus could be detected for at least 167 d following exposure and that titer, prevalence, replicative rate and persistence in koi were correlated significantly with virus virulence. In this context, high virulence SVCV isolates were more prevalent, reached higher titers quicker and persisted in koi for longer periods of time relative to moderate and low virulence isolates.

Optimization and diagnostic evaluation of monoclonal antibody-based blocking ELISA formats for detection of neutralizing antibodies to Hendra virus in mammalian sera.

Maintenance of Hendra virus (HeV) in pteropid bat populations has been associated with spillover events in horses, humans and dogs. Experimental studies have demonstrated infections for several other species including guinea pigs, cats and ferrets. The criteria of a sensitive and specific serological test that is effective for a range of species, but which does not require use of live virus, has not been satisfactorily addressed by currently available tests. We have evaluated the use of two HeV neutralizing monoclonal antibodies (mAbs) in a blocking format enzyme-linked immunosorbent assay (bELISA) to detect serum antibody against a recombinant expressed HeV G protein (sol G) in several animal species. The human mAb m102.4 neutralises both HeV and the closely related Nipah virus (NiV); the mouse mAb 1.2 neutralises only HeV. Given these functional differences, we have investigated both antibodies using a bELISA format. Diagnostic sensitivity (DSe) and diagnostic specificity (DSp) were optimized using individual thresholds for mAb 1.2 and m102.4. For mAb 1.2 the positive threshold of >33% inhibition yielded DSe and DSp values of 100% (95% CI 95.3-100.0) and 99.5 (95% CI 98.8-99.8) respectively; for mAb m102.4 a positive threshold of >49% inhibition gave DSe and DSp values of 100 (95% CI 95.3-100.0) and 99.8 (95% CI 99.2-100.0) respectively. At these thresholds the DSe was 100% for both tests relative to the virus neutralization test. Importantly, the occurrence of false positive reactions did not overlap across the assays. Therefore, by sequential and selective application of these assays, it is possible to identify false positive reactions and achieve a DSp that approximates 100% in the test population.

Analytical validation of a reverse transcriptase droplet digital PCR (RT-ddPCR) for quantitative detection of infectious hematopoietic necrosis virus.

Infectious hematopoietic necrosis virus (IHNV) is an important pathogen of salmonid fishes. A validated universal reverse transcriptase quantitative PCR (RT-qPCR) assay that can quantify levels of IHNV in fish tissues has been previously reported. In the present study, we adapted the published set of IHNV primers and probe for use in a reverse-transcriptase droplet digital PCR (RT-ddPCR) assay for quantification of the virus in fish tissue samples. The RT-ddPCR and RT-qPCR assays detected 13 phylogenetically diverse IHNV strains, but neither assay produced detectable amplification when RNA from other fish viruses was used. The RT-ddPCR assay had a limit of detection (LOD) equating to 2.2 plaque forming units (PFU)/µl while the LOD for the RT-qPCR was 0.2 PFU/µl. Good agreement (69.4-100%) between assays was observed when used to detect IHNV RNA in cell culture supernatant and tissues from IHNV infected rainbow trout (Oncorhynchus mykiss) and arctic char (Salvelinus alpinus). Estimates of RNA copy number produced by the two assays were significantly correlated but the RT-qPCR consistently produced higher estimates than the RT-ddPCR. The analytical properties of the N gene RT-ddPCR test indicated that this method may be useful to assess IHNV RNA copy number for research and diagnostic purposes. Future work is needed to establish the within and between laboratory diagnostic performance of the RT-ddPCR assay.

Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species. Positivity rates were calculated and regression analysis was performed to determine any associations between technical specifications and performance. The accuracy of Aspergillus genus specific assays was 71.8%, significantly greater (P < .0001) than assays specific for individual Aspergillus species (47.2%). For genus specific assays the most often missed species were A. lentulus (25.0%), A. versicolor (24.1%), A. terreus (16.1%), A. flavus (15.2%), A. niger (13.4%), and A. fumigatus (6.2%). There was a significant positive association between accuracy and using an Aspergillus genus PCR assay targeting the rRNA genes (P = .0011). Conversely, there was a significant association between rRNA PCR targets and false positivity (P = .0032). To conclude current Aspergillus PCR assays are better suited for detecting A. fumigatus, with inferior detection of most other Aspergillus species. The use of an Aspergillus genus specific PCR assay targeting the rRNA genes is preferential.

Development and Diagnostic Evaluation of Loop-Mediated Isothermal Amplification Using a New Gene Target for Rapid Detection of Helicobacter pylori.

BACKGROUND: Helicobacter pylori cause chronic gastritis and subsequent diseases like gastric and duodenal ulcers and gastric adenocarcinoma. Current methods for detecting H. pylori have several disadvantages and it is of utmost importance to develop a simple, quick, accurate, and cost-effective diagnostic test. OBJECTIVES: The aim of this study was to set up and evaluate a diagnostic value of loop- mediated isothermal amplification (LAMP) for detecting H. pylori. PATIENTS AND METHODS: The analytical sensitivity values (limit of detection) of LAMP and polymerase chain reaction (PCR) were determined using serial dilutions of H. pylori DNA. Analytical specificity of the methods using new designed primers targeted ureC gene was also determined. RESULTS: The detection limits of the LAMP and PCR assay were similar and were 10 fg of pure DNA of H. pylori, which is equal to 6 copy numbers of H. pylori genome. Analytical specificity of the tests was 100% because the tests were positive only with H. pylori DNA. CONCLUSIONS: The analytical sensitivity of LAMP and PCR methods, using the designed primers, was 8 times more than any other reported methods. The designed methods are specific and sensitive for detection of H. pylori in different clinical and environmental samples.

A mathematical procedure to estimate the impact of a change in method on discordance or misclassification at a decision limit in laboratory method comparison studies.

BACKGROUND: Laboratories often adopt new methods. It would be useful to have a statistical procedure to estimate the incremental impact of a change in assay. METHODS: Mathematical modeling, statistical analysis, and case example. RESULTS: We derived equations to estimate the proportion of discordant results that can be attributed to the new laboratory method. The calculations were demonstrated by comparing eGFR values based on creatinine values determined using the enzymatic method (existing method) and Jaffe method (new method). The discordance rate at the 60 ml/min eGFR decision limit was 3.15%. In this example, we estimated that 60% of the discordant results could be attributed to the Jaffe method. CONCLUSION: The sources of discordance in a laboratory method comparison study can be divided into three categories: The baseline discordance due to imprecision in the established method, the incremental discordance due to imprecision in the new method, and lack of analytical specificity. Discordance due to imprecision can be attributed to each individual method. Discordance due to bias can be attributed to individual methods if information is available to estimate the rate of biased observations in either method. Such information can be used to estimate the incremental cost effectiveness associated with the adoption of a new method.