Journal of Clinical Virology

BackgroundIn the pandemic, testing for SARS-CoV-2 by RT-PCR in one of the pillars on which countermeasures are based. Factors limiting the output of laboratories interfere with the effectiveness of public health measures. Conserving reagents by pooling samples in low-probability settings is proposed, but may cause dilution and loss of sensitivity. MethodsWe tested an alternate approach (FACT) by simultaneously incubating multiple respiratory swabs in a single tube. This protocol was evaluated b...

Since the COVID-19 pandemic, many hospitals implemented a dual testing procedure for SARS-CoV-2 to assess the infection risk of an admitted patient. To allow for a short turn-around time, rapid antigen (Ag) testing via lateral flow tests (LFT) is combined with nucleic acid amplification testing (NAAT), requiring two nasopharyngeal swab collections. In this study, a novel, universal pathogen inactivation buffer (DNA/RNA Defend Pro (DRDP)) was evaluated for SARS-CoV-2 inactivation and simultaneous...

There is a requirement for easily accessible, high throughput serological testing as part of the SARS-CoV-2 pandemic response. Whilst of limited diagnostic use in an acute individual setting, its use on a population level is key to informing a coherent public health response. As experience of commercial assays increases, so too does knowledge of their precision and limitations. Here we present our experience of these systems thus far. We perform a spot sero-prevalence study amongst staff in a te...

In limelight of the ongoing pandemic SARS-CoV-2 testing is critical for the diagnosis of infected patients, contact-tracing and mitigating the transmission. Diagnostic laboratories are expected to provide appropriate testing with maximum accuracy. Real-time reverse transcriptase PCR (RT-PCR) is the diagnostic standard yet many commercial diagnostic kits have become available. However, only a handful of studies have reviewed their performance in clinical settings. The aim of this study was to com...

ObjectivesThis multicentre study investigated the utility of next-generation sequencing (NGS) to detect and generate hepatitis B virus (HBV) genomes in samples of low viral load (from 0.2 to 6207 IU/ml). Methods23 HBV DNA positive plasma samples of genotypes A-E and one HBV-negative control sample were assayed blindly via 9 established NGS methods from 6 European laboratories. Methods included untargeted metagenomics, pre-enrichment by probe-capture followed by Illumina sequencing, and HBV-spec...

The true prevalence and population seropositivity of SARS-CoV-2 infection remains unknown, due to the number of asymptomatic infections and limited access to high-performance antibody tests. To control the COVID-19 pandemic it is crucial to understand the true seroprevalence, but not every region has access to extensive centralized PCR and serology testing. Currently available rapid antibody tests lack the accuracy needed for recommendation by health authorities. To fill this gap, we analyzed an...

The sensitivity of SARS-CoV-2 RT-PCR tests developed by Charite (Germany), HKU (Hong-Kong), China CDC (China), US CDC (United-States), and Institut Pasteur, Paris (France) was assessed on SARS-CoV-2 cell culture supernatants and clinical samples. Although all RT-PCR assays performed well for SARS-CoV-2 detection, RdRp Institut Pasteur (IP2, IP4), N China CDC, and N1 US CDC were found to be the most sensitive.

In light of supply chain failures for reagents and consumables needed for purification of nucleic acid for detection of SARS-CoV-2 RNA by RT-PCR, we aim to verify the performance and utility of a non-extraction protocol for RT-PCR ("direct RT-PCR"). We report improved sensitivity compared to earlier reports of direct RT-PCR testing of swab samples, in particular at the lower limit of detection (sensitivity 93% overall; 100% for specimens with high to moderate viral titre, Ct <34; 81% for specim...

1BackgroundThe ongoing SARS-CoV-2 pandemic presents a unique challenge to diagnostic laboratories. There are preliminary studies correlating qRT-PCR results from different materials to clinical outcomes, yet, comparability is limited due to the plethora of different assays used for diagnostics. In this study we evaluate clinical performance and linear range for the SARS-CoV-2 IVD (cobas6800/8800 system, a fully automated sample-to-result platform) in different clinically relevant matrix material...

In this report, we describe the first national scale multi-laboratory evaluation of commercial quantitative PCR kits for detection of Monkeypox virus (MPXV) DNA. The objective of this study was to assess the performance of two kits by different diagnostic laboratories across Israel. A panel of 10 standardized samples was tested simultaneously using the Novaplex (15 laboratories) and Bio-Speedy (seven laboratories) kits. An in-house assay based on previously published tests was used as reference....

BackgroundViral culture is currently the most accurate method to demonstrate viability and infectivity of Severe acute respiratory syndrome Coronavirus (SARS-2 CoV). Routine clinical diagnosis, however, is mostly performed by PCR - based assays that do not discriminate between infectious and non-virus. Herein, we aimed to determine the correlation between positive viral cultures and either PCR positivity, the Cycle Threshold (Ct) or the number of viral copies. MethodsA systematic electronic lit...

Multiplex PCR panels have been used for the diagnosis of viral respiratory infections in the last years. While the types of manufacturer validated and thus officially approved materials are usually limited, the tested materials in the clinical routine or studies often vary, which presents a challenge in light of the new EU-IVDR guideline. Aim of our present study was to evaluate if testing of lower respiratory tract (LRT) or saline gargle specimens (SGS) provided an advantage compared to the tes...

We report a laboratory-based surveillance for SARS-CoV-2 using minipools of respiratory samples submitted for routine diagnostics. We tested a total of 70 minipools resembling 700 samples shortly before the upsurge of cases in Germany. We identified one SARS-CoV-2 positive patient. Our approach proved its concept, is easily adaptable and resource-saving.

The unprecedented scale of testing required to effectively control the coronavirus disease (COVID-19) pandemic has necessitated urgent implementation of rapid testing in clinical microbiology laboratories. To date, there are limited data available on the analytical performance of emerging commercially available assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and integration of these assays into laboratory workflows. Here, we performed a prospective validation study of a c...

Mitigation of the ongoing COVID-19 pandemic requires reliable and accessible laboratory diagnostic services. We evaluated the performance of one LDT and two commercial tests, cobas(R) SARS-CoV-2 (Roche) and Amplidiag(R) COVID-19 (Mobidiag), for the detection of SARS-CoV-2 RNA in respiratory specimens. 183 specimens collected from suspected COVID-19 patients were studied with all three methods to compare their performance. In relation to the reference standard, which was established as the result...

3.BackgroundAccess to rapid diagnosis is key to the control and management of SARS-CoV-2. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) testing usually requires a centralised laboratory and significant infrastructure. We describe the development and diagnostic accuracy assessment of a novel, rapid point-of-care RT-PCR test, the DnaNudge(R) platform CovidNudge test, which requires no laboratory handling or sample pre-processing. MethodsNasopharyngeal swabs are inserted directly into a...

RT-PCR is the gold standard to determine the etiology of respiratory viral infections caused by SARS-CoV-2, Influenza A, Influenza B, and Respiratory Syncytial Virus. Multiplex testing panels can test for infections or co-infections with these viruses at the point of care. Treatment using antiviral drugs and/or monoclonal antibodies and public health measures using vaccines and specific infection prevention practices depend upon accurate diagnoses. The AMDI Fast PCR Mini Respiratory Panel is a 1...

BackgroundThe recent COVID-19 pandemic has posed an unprecedented challenge to laboratory diagnosis, based on the amplification of SARS-CoV-2 RNA. With global contagion figures exceeding 4 million persons, the shortage of reagents for RNA extraction represents a bottleneck for testing globally. We present the validation results for a RT-qPCR protocol without prior RNA extraction. Because of its simplicity, this protocol is suitable for widespread application in resource-limited settings. Method...

BackgroundThe SARS-CoV-2 virus is responsible for the infectious respiratory disease called COVID-19 (COronaVIrus Disease). In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. We conducted a real-life study to evaluate the performance of two RDTs, COVID-PRESTO(R) and COVID-DUO(R), compared to the gold standard, RT-PCR. MethodsRT-PCR testing of SARS-Cov-2 was performe...

Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The ...