Evaluation of the DiaSorin LIAISON SARS-CoV-2 antigen assay on nasopharyngeal swabs in two different SARS-CoV-2 pandemic waves in Switzerland: The impact of the Omicron variant on its performance.

Background SARS-CoV-2 antigen tests reliably detect individuals with high viral loads and provide an efficient diagnostic tool to manage the current SARS-CoV-2 pandemic. However, mutations in SARS-CoV-2 variants of concerns that appeared after validation of most antigen tests might impact their diagnostic performance. Objectives To assess the impact of the Omicron variant on the performance of the DiaSorin LIAISON SARS-CoV-2 antigen test, we evaluated its sensitivity and specificity on nasopharyngeal swabs (NPS) compared to rRT-PCR in the second and the Omicron pandemic wave in Switzerland. Study design A random selection of NPS from patients undergoing SARS-CoV-2 diagnostics by rRT-PCR were collected during the second and the Omicron pandemic wave and further analyzed by the LIAISON antigen test. Sensitivity and specificity compared to rRT-PCR were calculated. Results Test performance did not change in the two investigated periods. The overall sensitivity of 75.8% in the second and 76.5% in the Omicron wave increased to 87.1% and 88.4%, excluding samples with rRT-PCR Ct-value >30. By lowering the cut-off from 200 TCID50/ml to 62 TCID50/ml to discriminate between negative and positive samples using a ROC-curve, the sensitivity resulted in 88.8% for the second and 93.3% for the Omicron pandemic wave. The specificity of the LIAISON antigen test was 100% in both collectives. Conclusion Omicron variant does not seem to affect the performance of the LIAISON antigen test. The WHO recommended sensitivity of ≥80% for antigen testing was fulfilled during both pandemic periods in samples with Ct-value <30 or by optimizing the assay cut-off

Acute flaccid myelitis in Switzerland - association with enterovirus D68.

Poliomyelitis-like acute flaccid myelitis associated with enterovirus D68 (EV-D68) has emerged globally during the past decade. Here we describe the first documented case reported from Switzerland, and a second, suspected case occurring in temporal association. AFM occurs primarily in children, is usually heralded by a febrile, respiratory prodrome followed by acute-onset, usually asymmetrical, limb weakness with some predilection for the upper extremities, and respiratory muscle compromise in one third of reported cases. There is no specific therapy and the majority of cases result in permanent neurological sequelae. A comprehensive diagnostic workup and timely reporting to the health authorities are essential. Surveillance of respiratory and stool samples for EV-D68 and other neurotropic enteroviruses is in place in several European countries and warrants consideration in Switzerland. This could entail the extension of the poliomyelitis surveillance program of the Federal Office of Public Health by monitoring and enteroviral typing of respiratory samples from patients with acute flaccid paralysis

Striking Decrease of Enteroviral Meningitis in Children During the COVID-19 Pandemic.

We report the unprecedented complete absence of pediatric enteroviral meningitis in 2020 in the area of Bern, Switzerland. Presumably an unintended effect of coronavirus disease 2019 public health measures, this finding highlights the potential of community-wide nonpharmaceutical interventions for controlling the circulation of a major pediatric pathogen, which is mainly transmitted by the fecal-oral route

Twelve years' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay

<p>Abstract</p> <p>Background</p> <p>Direct immunofluorescence assays (DFA) are a rapid and inexpensive method for the detection of respiratory viruses and may therefore be used for surveillance. Few epidemiological studies have been published based solely on DFA and none included respiratory picornaviruses and human metapneumovirus (hMPV). We wished to evaluate the use of DFA for epidemiological studies with a long-term observation of respiratory viruses that includes both respiratory picornaviruses and hMPV.</p> <p>Methods</p> <p>Since 1998 all children hospitalized with respiratory illness at the University Hospital Bern have been screened with DFA for common respiratory viruses including adenovirus, respiratory syncytial virus (RSV), influenza A and B, and parainfluenza virus 1-3. In 2006 assays for respiratory picornaviruses and hMPV were added. Here we describe the epidemiological pattern for these respiratory viruses detected by DFA in 10'629 nasopharyngeal aspirates collected from 8'285 patients during a 12-year period (1998-2010).</p> <p>Results</p> <p>Addition of assays for respiratory picornaviruses and hMPV raised the proportion of positive DFA results from 35% to 58% (p < 0.0001). Respiratory picornaviruses were the most common viruses detected among patients ≥1 year old. The seasonal patterns and age distribution for the studied viruses agreed well with those reported in the literature. In 2010, an hMPV epidemic of unexpected size was observed.</p> <p>Conclusions</p> <p>DFA is a valid, rapid, flexible and inexpensive method. The addition of assays for respiratory picornaviruses and hMPV broadens its range of viral detection. DFA is, even in the "PCR era", a particularly adapted method for the long term surveillance of respiratory viruses in a pediatric population.</p

Evaluation of the Roche antigen rapid test and a cell culture-based assay compared to rRT- PCR for the detection of SARS-CoV-2: A contribution to the discussion about SARS-CoV-2 diagnostic tests and contagiousnes

Background The most sensitive method to detect SARS-CoV-2 relies on rRT-PCR; however, viral RNA can be detected weeks/months after clinical resolution. Since rRT-PCR cannot discern between non- and infectious virus, it is unclear whether the presence of viral RNA after recovery reflects infectious SARS-CoV-2. However, recent studies suggest a positive correlation between antigen rapid tests (Ag-RDT) and virus isolation that is more suited to assess contagiousness. Objectives To assess the utility of SARS-CoV-2 diagnostic tests in different settings we evaluated the performance of Ag-RDT-based and a cell culture-based SARS-CoV-2 assay in comparison to rRT-PCR. Study design A total of 61 Nasopharyngeal-Swabs tested positive by cobasⓇ SARS-CoV-2 rRT-PCR were in parallel evaluated with the Roche Ag-RDT and a cell culture-based assay to detect SARS-CoV-2. Results SARS-CoV-2 was successfully isolated in 51/61 samples corresponding to 83.6%, which was 97.3% or 96.2% when considering samples with E-gene Ct-value <25 and <28, respectively. In comparison, the Ag-RDT showed an overall sensitivity of 85.2%, that increased to 100% and 96.2% using an E-gene Ct-value cut-off of <25 and <28, respectively. There was an overall good agreement between the commercial Ag-RDT and our in-house cell culture-based SARS-CoV-2 detection assay. However, SARS-CoV-2 could be isolated from two samples that tested negative by Ag-RDT. Conclusions Our results support the use of the Roche Ag-RDT to detect SARS-CoV-2 exposure in large scale populations. However, it is recommended to use rRT-PCR, potentially in conjunction with cell culture-based SARS-CoV-2 assay, to support clinicians in making decisions regarding fragile patient groups

Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing.

Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains

Severe acute respiratory distress syndrome (ARDS) induced by human adenovirus B21: Report on 2 cases and literature review.

Severe pneumonia and ARDS caused by human adenovirus B21 infections (HAdV-B21) is a rare, but a devastating disease with rapid progression to multiorgan failure and death. However, only a few cases were reported so far. Infections appear associated with increased disease severity and higher mortality in infected critically ill patients. Possible factors contributing to infection are underlying psychiatric disease resulting in institutionalization of respective patients, and polytoxicomania. Controlled data on the therapy of severe adenovirus infections are lacking and remains experimental. In conclusion, data on HAdV-B21 infections causing severe pneumonia or ARDS are scarce. Controlled clinical trials on the therapy of adenovirus pneumonia are non existent and thus there is no established therapy so far. ICU physicians should be aware of this potentially devastating disease and further studies are needed

Immunofluorescence versus xTAG multiplex PCR for the detection of respiratory picornavirus infections in children

BACKGROUND: Polymerase chain reaction (PCR) is a sensitive tool for detection of respiratory picornaviruses. However, the clinical relevance of picornavirus detection by PCR is unclear. Immunofluorescence (IF), widely used to detect other respiratory viruses, has recently been introduced as a promising detection method for respiratory picornaviruses. OBJECTIVES: To compare the clinical manifestations of respiratory picornavirus infections detected by IF with those of respiratory picornavirus infections detected by xTAG multiplex PCR in hospitalized children. STUDY DESIGN: During a 1-year period, nasopharyngeal aspirates (NPA) from all children hospitalized due to an acute respiratory infection were prospectively analyzed by IF. All respiratory picornavirus positive IF samples and 100 IF negative samples were further tested with xTAG multiplex PCR. After exclusion of children with co-morbidities and viral co-infections, monoinfections with respiratory picornaviruses were detected in 108 NPA of 108 otherwise healthy children by IF and/or PCR. We compared group 1 children (IF and PCR positive, n=84) with group 2 children (IF negative and PCR positive, n=24) with regard to clinical manifestations of the infection. RESULTS: Wheezy bronchitis was diagnosed more often in group 1 than in group 2 (71% vs. 46%, p=0.028). In contrast, group 2 patients were diagnosed more frequently with pneumonia (17% vs. 6%, p=0.014) accompanied by higher levels of C-reactive protein (46mg/l vs. 11mg/l, p=0.009). CONCLUSIONS: Picornavirus detection by IF in children with acute respiratory infection is associated with the clinical presentation of wheezy bronchitis. The finding of a more frequent diagnosis of pneumonia in picornavirus PCR positive but IF negative children warrants further investigation

Comparison of respiratory and Meningitis/Encephalitis viruses detected by FilmArray® multiplex PCR versus real-time PCR

Introduction: Fast and reliable pathogen detection is important for adequate management of infections. Although real-time PCR (rtPCR) is usually the most sensitive method for direct pathogen detection, it requires experienced technicians, includes several working steps and has a turnaround time of multiple hours. Therefore this method is not ideal for emergency diagnostics. The FDA cleared, fully automated sample to answer, FilmArray® (FA) multiplex PCR system (BioFire/bioMérieux) detects a broad spectrum of pathogens in ∼70 min. To optimize our diagnostic services during weekends and off-peak times, we compared the FA Respiratory Panel (RP) and FA Meningitis/Encephalitis (ME) Panel to our routinely used rtPCR assay. The FA panels detect 20 respiratory pathogens (17 viruses, 3 bacteria) in nasopharyngeal swabs (NPS) and 14 M/E pathogens (7 viruses, 6 bacteria, Cryptococcus neoformans/gattii) in cerebrospinal fluids (CSF). Materials and methods: With FA we tested 84 retrospective samples (23 NPS, 29 broncheoalveolar lavages [BALs], 32 CSF) and 60 prospectively collected NPS that required urgent testing during the 2015/2016 flu season by FA and rtPCR. FA sample input volume was 300 ml for RP and 200 ml for ME. Commercial RP and ME quality control panels (MMQC Inc., Scarborough, USA), containing samples positive and negative for each analyte detected by the FA panels, were tested multiple times. For rtPCR, nucleic acids were extracted from 220 ml of sample and eluted in 55 ml using NucliSENS easyMAG (bioMérieux). Respiratory viruses were analyzed by real-time PCR using a combination of 7 duplex Respiratory Multi Well System r-gene™ (RG) assays (influenza A/B, RSV/hMPV, HRV&EV/cell control, ADV/HBoV, HCoV/HPIV1-4) (Argene/bioMerieux), according to manufacturer's instructions. Additionally, we expanded FA RP testing to include (BALs), by implementing one additional sample preparation step. CSF was analyzed for virus using laboratory developed tests (LDTs) certified by the Swiss authorities. Results: RP and ME quality control panel results were 100% concordant with expected results. For all NPS, both tests, FA RP and RG, identified one or more viruses in 45/83 (54.2%) samples. FA RP and RG results correlated for 42/48 viruses detected (87.5%). FA RP detected an additional 3 HRV/EV and RG detected additionally 1 FluA, 1 ADV and 1 HRV/EV. Positive percent agreement (PPA) between RG (laboratory standard) and FA RP for NPS was 93.3% and negative percent agreement (NPA) was 92.7%. Overall correlation was 93.2%. Results from BALs yielded 92% PPA, 93.1% NPA and overall correlation of 92.4%. For FA ME testing, 31/33 CSF samples had identical FA ME and LDT results with an overall correlation of 94.4%. FA ME did not detect 2 parechovirus low level LDT positive samples (Ct 36.3 and 37.0). Using LDTs as the laboratory standard, FA ME PPA and NPA were 93.9% and 100%, respectively. Conclusion: Results obtained with the FilmArray® RP and ME panels were highly concordant with our currently used diagnostic methods, demonstrating excellent performance. The simplicity of the FilmArray® system, requiring less than 5 min of hands-on time, easy to read reports, and low sample volume allows for testing during off shifts and when urgent results are required. The comprehensiveness of the FilmArray® panels is ideal for diagnosing clinical syndromes where there are many potential causes