Assessment of the clinical and analytical performance of three Seegene Allplex SARS-CoV-2 assays within the VALCOR framework.

The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing for the early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pandemic has ended, accurate assays are still needed to monitor viral spread at national levels and beyond through population and wastewater surveillance. To enhance early detection, SARS-CoV-2 assays should have high diagnostic accuracy and should be validated to assure accurate results. Three distinct SARS-CoV-2 assays were evaluated with clinical samples using the VALCOR (VALidation of SARS-CORona Virus-2 assays) framework, with the TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We evaluated clinical sensitivity, specificity, limit of detection (LOD), and overall concordance between comparator and three index Allplex SARS-CoV-2 assays (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), and Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance and LOD of index assays were assessed using a dilution series of three synthetic SARS-CoV-2 sequence reference materials (RMs). Ninety SARS-CoV-2 positives and 90 SARS-CoV-2 negatives were tested. All Allplex assays had 100.0% sensitivity (95%CI = 95.9%-100.0%). Allplex-SC2 and Allplex-SC2Fast assays had 97.8% specificity (95%CI = 92.3%-99.7%) and 98.9% overall concordance [κ = 0.978 (95%CI = 0.947-1.000)]. Allplex-SC2FabR assay showed 100.0% specificity (95%CI = 95.9%-100.0%) and 100.0% overall concordance [κ = 1.000 (95%CI = 1.000-1.000)]. LOD assessment of index assays revealed detection down to 2.61 × 102 copies/mL in clinical samples, while the analytical LOD was 9.00 × 102 copies/mL. In conclusion, the evaluation of the three Seegene Allplex SARS-CoV-2 assays showed high sensitivity and specificity and an overall good assay concordance with the comparator. The assays showed low analytical LOD using RM and even a slightly lower LOD in clinical samples. Non-overlapping target gene sequences between SARS-CoV-2 assays and RMs emphasize the need for aligning targeted sequences of diagnostic assays and RMs.IMPORTANCEThe coronavirus disease 2019 pandemic has a significant impact on global public health, economies, and societies. As shown through the first phases of the pandemic, accurate and timely diagnosis is crucial for disease control, prevention, and monitoring. Though the pandemic phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has concluded, diagnostic assays remain in demand to monitor SARS-CoV-2 at the individual patient level, regionally, and nationally, as well as to remain an infectious disease preparedness instrument to monitor any new SARS-CoV-2 dissemination across borders using population and wastewater surveillance. The anticipation by WHO and central health care policy entities such as the Center for Disease Control, EMA, and multiple national health authorities is that SARS-CoV-2 will reside as an endemic respiratory disease for years to come. The key strategic consideration is hence shifting from combating a pandemic situation with a high number of patients to instead allowing precise diagnostics of suspected patients with the intention of correct management in a low-prevalence setting.

New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants.

Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets of genetic changes that confer to the virus higher transmissibility and ability to evade existing immunity. The continuous evolution of SARS-CoV-2 may pose challenges for current treatment options and diagnostic tools. In this study, we have first evaluated the performance of the 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use for the detection of SARS-CoV-2 and found that only one assay has reduced performance against Omicron. We then developed a new duplex real-time RT-PCR assay based on the amplification of two ultra-conserved elements present within the SARS-CoV-2 genome. The new duplex assay successfully detects all of the tested SARS-CoV-2 variants of concern (including Omicron sub-lineages BA.4 and BA.5) from both clinical and wastewater samples with high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay. This new assay, in addition to clinical testing, could be adopted in surveillance programs for the routine monitoring of SARS-CoV-2's presence in a population in wastewater samples. Positive results with our assay in conjunction with negative results from an Omicron-specific assay may provide timely indication of the emergence of a novel SARS-CoV-2 variant in a certain community and thereby aid public health interventions.

Single and multi-laboratory validation of a droplet digital PCR method.

The authorisation of genetically modified food and feed in the EU is subject to the provision of evidence of safety and of the availability of reliable analytical methods. These methods represent an essential tool for official laboratories to enforce a harmonised market control. Here the validation of droplet digital PCR (dPCR) methods has been performed for studying if the performance and acceptance parameters set by EU and other international guidelines for the analysis of genetically modified organisms (GMO) in food and feed are suitable and achievable also with such methods. The single-laboratory validation study showed that performance requirements set for GMO analysis by real time PCR can also be used to assess dPCR-based methods. Moreover, trueness and precision were assessed for both simplex and duplex formats in a multi-laboratory validation study organised according to international standards. Overall, the data on trueness, repeatability and reproducibility precision resulting from the collaborative study are satisfying the acceptance criteria for the respective parameters as stipulated in the EU and other international guidance such as the Codex Committee on Methods of Analysis and Sampling (CCMAS). For instance, the duplex droplet dPCR method for MON810 showed relative repeatability standard deviations from 1.8% to 15.7%, while the relative reproducibility standard deviation was found to be between 2.1% and 16.5% over the dynamic range studied. Moreover, the relative bias of the dPCR methods was well below 25% across the entire dynamic range. In addition, other aspects supporting the application of digital PCR for the control of GMOs on the market were experimentally assessed such as the conversion of the measurement results from copy number ratio to mass fraction, the influence of the DNA extraction step and of the ingredient content. It was found that the DNA extraction step added only a limited contribution to the variability of the measurement results under the studied conditions. The decreasing amount of the target ingredient content may decrease the level of precision of the method, although within the acceptance range of GMO performance parameters.

A qualitative RT-PCR assay for the specific identification of the SARS-CoV-2 B.1.1.529 (Omicron) Variant of Concern.

OBJECTIVES: The aim of this study was to develop a RT-PCR assay for the specific detection of the SARS-CoV-2 Omicron Variant of Concern (VOC) as a rapid alternative to sequencing. METHODS: A RT-PCR was designed in silico and then validated using characterised clinical samples containing Omicron (both BA.1 and BA.2 lineages) and the Omicron synthetic RNA genome. As negative controls, SARS-CoV-2 positive clinical samples collected in May 2020, and synthetic RNA genomes of the isolate Wuhan Hu-1 and of the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Iota (B.1.526), Epsilon (B.1.429) and Delta (B.1.617.2) SARS-CoV-2 VOC were used. RESULTS: Experiments performed using as templates the synthetic RNA genomes demonstrate the high specificity of the PCR-method for the SARS-CoV-2 Omicron. Despite the synthetic RNAs were used at high copy numbers, specific signal was mainly detected with the Omicron synthetic genome. Only a non-specific late signal was detected using the Alpha variant genome, but these results were considered negligible as Alpha VOC has been replaced by the Delta and it is not circulating anymore in the world. Using our method, we confirmed the presence of Omicron on clinical samples containing this variant but not of other SARS-CoV-2 lineages. The method is highly sensitive and can detect up to 1 cp of the Omicron virus per µl. CONCLUSIONS: The method presented here, in combination with other methods in use for detection of SARS-CoV-2, can be used for an early identification of Omicron.

Expression of GM content in mass fraction from digital PCR data.

Nowadays the quantification of the content of genetically modified (GM) constituents in food or feed products is performed by using either quantitative real-time PCR (qPCR) or digital PCR (dPCR). The latter is increasingly used. Therefore, experimental protocols for the quantification of 52 GM events authorised in the EU have been converted into a digital format and minimum performance characteristics for dPCR methods are detailed. Because of the need to harmonise the transformation of PCR results between two different measurement scales, 50 conversion factors for Certified Reference Materials (CFCRM) have been experimentally determined by three and sometimes four independent expert laboratories. The uncertainty of each CFCRM has been estimated to express dPCR results in mass fraction with a consistent uncertainty contribution. In 38 out of 58 cases, the validated qPCR methods (for 52 event-specific and 6 taxon-specific measurements) could easily be transferred into dPCR methods by using the same oligo sequences, final oligo concentration or annealing temperatures for the dPCR procedure. Laboratories have nevertheless used different strategies to improve the resolution or to reduce the so-called rain in their dPCR outcome. Those modifications were needed for PCR procedures that could not be converted without changes into a digital format. Therefore, exclusion/quality criteria such as the maximum rate of partitions with intermediate fluorescence "rain", the minimum resolution and repeatability are suggested for dPCR methods. The CFCRM determined in this study were generally in agreement with the declared zygosity of the GM parental donor for hemizygous maize events. In a limited number of GM events the CFCRM values were significantly different when measured with different maize-specific (ZmAdh1 or hmgA) genes.

Validation by collaborative trial of a method for the determination by GC-MS and LC-MS/MS of boar taint marker compounds in pork tissue.

Meat from male pigs may develop an off-flavour, commonly known as boar taint. Castration of male piglets prevents the potential formation of off-flavour. In the suggested method, three marker compounds for boar taint (skatole, androstenone and indole) are quantified in pork fat by isotope dilution gas chromatography mass spectrometry (GC-MS) or by isotope dilution liquid chromatography tandem mass spectrometry (LC-MS/MS). This method was validated by collaborative trial according to ISO 5725-2:1994. The studied concentration ranges included sensorial thresholds. The repeatability relative standard deviation (RSDr) ranges from 3% to 10% and the reproducibility relative standard deviation (RSDR) from 10% to about 30%. The method has proven to be robust and free from matrix interferences. The method performance characteristics are compliant with requirements for official control methods in the area of food contaminants; therefore, the method is regarded as fit for its intended purpose.

Can official control laboratories quantify reliably fipronil in eggs? Evidence from a proficiency testing round.

A proficiency testing (PT) round dedicated to assess the competence of European Union (EU) National Reference Laboratories (NRLs), EU Official Control Laboratories (OCLs) and OCLs from associated countries for the determination of the insecticide fipronil in eggs is described. The content of the target analytes (sum of fipronil plus its metabolite fipronil sulfone, expressed as fipronil in the PT test material) was set around the regulated Maximum Residue Level (MRL) set by EU legislation. The PT was organised by the European Commission's (EC) Directorate General (DG) Joint Research Centre (JRC) - in agreement with the EC DG for Health and Food Safety (SANTE) - following a request by the Belgian Authorities. Eighty-six NRLs and OCLs from 22 EU Member States, Norway, Serbia and Albania participated. The test items used were two materials made of frozen liquid eggs, processed and characterised at the JRC facilities in Geel (Belgium). The majority of the participants (94%) were shown to have a satisfactory performance, expressed as z scores, thus demonstrating the analytical capability of most of the participating NRLs and OCLs to enforce the relevant EU Regulations ((EC) 396/2005 and 1127/2014). Furthermore, 93% of the participants who provided a compliance statement classified, correctly, one of the test items as non-compliant.

Analytical method for the trace determination of esterified 3- and 2-monochloropropanediol and glycidyl fatty acid esters in various food matrices.

Fatty acid esters of 3-monochloro-1,2-propanediol (3-MCPDEs), of 2-monochloro-1,3-propanediol (2-MCPDEs) and of 2,3-epoxy-1-propanol or glycidol (GEs), which are considered to be deleterious to human health, may occur in a broad variety of food samples. A proper risk assessment of those substances requires the availability of robust occurrence data; in this respect concerns have been raised regarding the reliability of results obtained with the currently available methods to determine those substances in processed food. This article presents an indirect analytical procedure for the simultaneous determination of 3-MCPDEs, 2-MCPDEs and GEs in a wide variety of food products after extraction by pressurised liquid extraction (PLE) and determination by gas chromatography mass-spectrometry (GC-MS). For the differentiation of MCPDEs and GEs, the latter were first converted to monobromopropanediol esters (MBPDEs) in acid aqueous solution of sodium bromide. MCPDEs and MBPDEs were then hydrolysed under acidic conditions followed by derivatisation of the released free (non-esterified) form in ethyl acetate with phenyl boronic acid (PBA). Quantification of the analytes was carried out using the isotopic labelled analogues of both MCPDEs and GEs. Limits of detection (LODs) and limits of quantitation (LOQs) were in the range of 7-17mgkg(-1) and 13-31mgkg(-1) respectively, while the working range of the method was between LOQ and 1850mgkg(-1) expressed on fat basis. The developed method was successfully applied for the analysis of the target compounds in more than 650 different food samples covering the following commodities: bread and rolls, fine bakery wares, smoked fish products, fried and roasted meat, potato based snacks and fried potato products, cereal-based snacks and margarines.

Single-laboratory validation of a saponification method for the determination of four polycyclic aromatic hydrocarbons in edible oils by HPLC-fluorescence detection.

An analytical method is reported for the determination of four polycyclic aromatic hydrocarbons (benzo[a]pyrene (BaP), benz[a]anthracene (BaA), benzo[b]fluoranthene (BbF) and chrysene (CHR)) in edible oils (sesame, maize, sunflower and olive oil) by high-performance liquid chromatography. Sample preparation is based on three steps including saponification, liquid-liquid partitioning and, finally, clean-up by solid phase extraction on 2 g of silica. Guidance on single-laboratory validation of the proposed analysis method was taken from the second edition of the Eurachem guide on method validation. The lower level of the working range of the method was determined by the limits of quantification of the individual analytes, and the upper level was equal to 5.0 µg kg(-1). The limits of detection and quantification of the four PAHs ranged from 0.06 to 0.12 µg kg(-1) and from 0.13 to 0.24 µg kg(-1). Recoveries of more than 84.8% were achieved for all four PAHs at two concentration levels (2.5 and 5.0 µg kg(-1)), and expanded relative measurement uncertainties were below 20%. The performance of the validated method was in all aspects compliant with provisions set in European Union legislation for the performance of analytical methods employed in the official control of food. The applicability of the method to routine samples was evaluated based on a limited number of commercial edible oil samples.

Aflatoxin measurements: how HPLC methods have evolved over the last 20 years?

The Institute for Reference Materials and Measurements (IRMM) has provided high quality certified reference materials for decades. Certified reference materials for mycotoxin analysis have been available from the IRMM since 1985. Since then, IRMM has generally characterised reference materials by interlaboratory studies with expert laboratories. Such measurement exercises are based on routinely used analytical procedures in the laboratory, but are driving their performance to the best achievable quality under the given circumstances. Reference materials for aflatoxin measurements have been certified by such studies in 1991, 1993, 2008 and 2009. After two decades, it is time to look back, reflect and ask some questions. How have HPLC methods for the analysis of aflatoxins evolved over the last 20 years? Is there a trend towards a preferred methodology? Does this evolution reflect improvements due to the introduction of standardised methods? Is there an improvement in performance parameters such as repeatability, reproducibility and measurement uncertainty? To answer these questions, data from six interlaboratory studies, performed in the last 20 years for the certification of aflatoxins in peanut meal, peanut butter and animal feed, have been re-evaluated. It is concluded that there is a trend towards a preferred methodology, which reflects developments in standardised methods. No significant improvement in repeatability, reproducibility or measurement uncertainty could, however, be detected in expert laboratories for mycotoxin analysis.

Determination of molar absorptivity coefficients for major type-B trichothecenes and certification of calibrators for deoxynivalenol and nivalenol.

This paper presents results from the European Commission-funded project Doncalibrant, the objective of which was to produce calibrators with certified mass fractions of the Fusarium toxins deoxynivalenol (DON), 3-acetyldeoxynivalenol (3-Ac-DON), 15-acetyldeoxynivalenol (15-Ac-DON), and nivalenol (NIV), in acetonitrile. The calibrators, available in ampoules, were sufficiently homogeneous, with between-bottle variations (s (bb)) of less than 2%. Long-term stability studies performed at four different temperatures between -18 and 40 degrees C revealed no significant negative trends (at a confidence level of 95%). Molar absorptivity coefficients (in L mol(-1) cm(-1)) were determined for all four toxins (DON: 6805 +/- 126, NIV: 6955 +/- 205, 3-Ac-DON: 6983 +/- 141, 15-Ac-DON: 6935 +/- 142) on the basis of a mini-interlaboratory exercise. The overall uncertainty of the calibrators' target values for DON and NIV were evaluated on the basis of gravimetric preparation data and include uncertainty contributions from possible heterogeneity, storage, and transport. The Doncalibrant project resulted in the production of calibrators for DON (IRMM-315) and NIV (IRMM-316) in acetonitrile with certified mass fractions of 25.1 +/- 1.2 microg g(-1) and 24.0 +/- 1.1 microg g(-1), respectively. Both CRMs became commercially available from the Institute for Reference Materials and Measurements (IRMM, Geel, Belgium) at the beginning of 2007.

Rapid simultaneous determination of major type A- and B-trichothecenes as well as zearalenone in maize by high performance liquid chromatography-tandem mass spectrometry.

A novel method for the simultaneous determination of the Fusarium mycotoxins nivalenol, deoxynivalenol, fusarenon-X, 3-acetyl-deoxynivalenol, the sum of 3-acetyl-deoxynivalenol and 15-acetyl-deoxynivalenol, diacetoxy-scirpenol, HT-2 toxin, T-2 toxin and zearalenone in maize has been developed using gradient RP-LC with atmospheric pressure chemical ionization triple quadrupole mass spectrometry (LC-APCI-MS/MS). Swift clean-up of maize samples was performed with MycoSep #226 columns. Quantification of zearalenone was performed with zearalanone as internal standard (IS), while no IS was used for the trichothecenes. Detection of the mycotoxins was carried out in the multiple reaction monitoring (MRM) mode. Method performance characteristics were estimated after analysis of spiked blank maize samples. Calibration curves were linear between 10 and 1000 microg/kg and the limits of detection ranged from 0.3 to 3.8 microg/kg depending on the mycotoxin. Moreover, the accuracy of the method was confirmed by comparing analytical data to certified values from reference materials for deoxynivalenol and zearalenone.

Molecularly imprinted polymer-assisted sample clean-up of ochratoxin A from red wine: merits and limitations.

A new analytical method for the determination of the carcinogenic mycotoxin ochratoxin A (OTA) in red wines has been developed involving a two-dimensional solid-phase extraction (SPE) clean-up protocol on C18-silica and a target-selective molecularly imprinted polymer (MIP). Prior removal of the interfering acidic matrix compounds by C18 solid-phase extraction was crucial for a successful clean-up as direct sample loading onto the MIP led to poor recoveries. The combined solid-phase extraction protocol afforded extracts suitable for sensitive ochratoxin A quantification by HPLC-fluorescence detection. Preliminary validation of the method performance with spiked (0.033-1.0 ng OTA/ml) and commercial red wines provided recoveries >90% and < 10%, with limit of detection (LOD) and limit of quantification (LOQ) of 0.01 and 0.033 ng/ml. However, a similarly favorable performance characteristics was observed in control experiments in which the MIP was replaced by the corresponding non-imprinted polymer (NIP). These findings provide evidence that under the employed experimental conditions specific analyte binding to imprinted binding sites plays a minor role in selective OTA retention. In the framework of this study, other problems inherent to MIP-based solid-phase extraction have been addressed. These include the reproducible preparation of MIP materials with consistent molecular recognition characteristics, the potential for repeated use of MIP, unfavorable polymer swelling in application-relevant solvents, potential sample contamination by template bleeding, and slow analyte binding kinetics.