European multicenter evaluation of Xpert® Xpress SARS-CoV-2/Flu/RSV test

Rapid diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are paramount for reducing the spread of the current pandemic. During additional seasonal epidemics with influenza A/B and respiratory syncytial virus (RSV), the clinical signs and symptoms cannot be distinguished easily from SARS-CoV-2. Therefore, a new assay combining four targets in the form of the new Xpert Xpress SARS-CoV-2/Flu/RSV assay was evaluated. The assay was compared to the Xpert Xpress SARS-CoV-2, Xpert Xpress Flu/RSV, Seegene Flu/RSV, influenza A/B r-gene® and RSV/hMPV r-gene®. A total of 295 nasopharyngeal and throat swabs were tested at four institutes throughout Europe including 72 samples positive for SARS-CoV-2, 65 for influenza A, 47 for influenza B, and 77 for RSV. The sensitivity of the new assay was above 95% for all targets, with the highest for SARS-CoV-2 (97.2%). The overall correlation of SARS-CoV-2 Ct values between Xpert Xpress SARS-CoV-2 assay and Xpert Xpress SARS-CoV-2/Flu/RSV assay was high. The agreement between Ct values above 30 showed the multiplex giving higher Ct values for SARS-CoV-2 on average than the singleplex assay. In conclusion, the new assay is a rapid and reliable alternative with less hands-on time for the detection of not one, but four upper respiratory tract pathogens that may circulate at the same time

Development of endotoxin tolerance does not influence the response to a challenge with the mucosal live-attenuated influenza vaccine in humans in vivo

Introduction: The effects of bacterial infections on the response to subsequent viral infections are largely unknown. This is important to elucidate to increase insight into the pathophysiology of bacterial and viral co-infections, and to assess whether bacterial infections may influence the course of viral infections. Methods: Healthy male subjects received either bacterial endotoxin [Escherichia coli-derived lipopolysaccharide (LPS), 2 ng/kg, n = 15] or placebo (n = 15) intravenously, followed by intranasal Fluenz (live-attenuated influenza vaccine) 1 week later. Results: LPS administration resulted in increased plasma cytokine levels and development of endotoxin tolerance in vivo and ex vivo, illustrated by attenuated cytokine production upon rechallenge with LPS. Following Fluenz administration, infectivity for the Fluenz A/B strains was similar between the LPS-Fluenz and placebo-Fluenz groups (13/15 subjects in both groups). Also, the Fluenz-induced increase in temperature and IL-6, G-CSF and IP-10 concentrations in nasal wash were similar between both groups. Conclusion: While endotoxemia profoundly attenuates the immune response upon a second LPS challenge, it does not influence the Fluenz-induced immune response. These results suggest immune suppression after bacterial infection does not alter the response to a subsequent viral infection

Laboratory-based surveillance in the molecular era: The typened model, a joint data-sharing platform for clinical and public health laboratories

Laboratory-based surveillance, one of the pillars of monitoring infectious disease trends, relies on data produced in clinical and/or public health laboratories. Currently, diagnostic laboratories worldwide submit strains or samples to a relatively small number of reference laboratories for characterisation and typing. However, with the introduction of molecular diagnostic methods and sequencing in most of the larger diagnostic and university hospital centres in high-income countries, the distinction between diagnostic and reference/public health laboratory functions has become less clear-cut. Given these developments, new ways of networking and data sharing are needed. Assuming that clinical and public health laboratories may be able to use the same data for their own purposes when sequence-based testing and typing are used, we explored ways to develop a collaborative approach and a jointly owned database (TYPENED) in the Netherlands. The rationale was that sequence data - whether produced to support clinical care or for surveillance -can be aggregated to meet both needs. Here we describe the development of the TYPENED approach and supporting infrastructure, and the implementation of a pilot laboratory network sharing enterovirus sequences and metadata

An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment

The world is entering a new era of the COVID-19 pandemic in which there is an increasing call for reliable antibody testing. To support decision making on the deployment of serology for either population screening or diagnostics, we present a detailed comparison of serological COVID-19 assays. We show that among the selected assays there is a wide diversity in assay performance in different scenarios and when correlated to virus neutralizing antibodies. The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. The large variety of available serological assays requires proper assay validation before deciding on deployment of assays for specific applications

Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus

Background: Norovirus is a major cause of gastroenteritis, causing yearly epidemics and hospital outbreaks resulting in a high burden on health care. Detection and characterization of norovirus directly from clinical samples could provide a powerful tool in infection control and norovirus epidemiology. Objectives: To determine whether next-generation sequencing directly on fecal samples can accurately detect and characterize norovirus. Study design: Whole genome sequencing was performed on fecal samples from 10 patients with gastroenteritis. Norovirus infection had previously been confirmed by RT-PCR. Genotyping was performed using phylogenetic analysis. Results: From all clinical samples sufficient amounts of RNA were retrieved to perform wholetranscriptome sequencing for the detection of RNA-viruses. Complete genomic norovirus sequences were obtained from all clinical samples, permitting accurate genotyping by phylogenetic analysis. In addition, a complete coxsackie B1 virus genome was isolated. Conclusion: Detailed information on viral content can be obtained from fecal samples in a single-step approach, supporting clinical and epidemiological purposes. Next-generation sequencing performed directly on clinical samples can become a powerful tool in patient care and infection control. (C) 2015 Elsevier B.V. All rights reserved

Seroconversion after a third COVID-19 vaccine is affected by rituximab dose but persistence is not in patients with rheumatoid arthritis

Objectives : In patients with RA treated with (ultra-)low-dose rituximab (RTX), we investigated the association of dosing and timing of RTX on seroconversion after a third coronavirus disease 2019 (COVID-19) vaccination and the persistence of humoral response after a two-dose vaccination. Material and methods : In this monocentre observational study, patients from the COVAC cohort were included in the third vaccine analysis if humoral response was obtained 2-6 weeks after a third vaccination in previous non-responders and in the persistence analysis if a follow-up humoral response was obtained before a third vaccination in previous responders. Dichotomization between positive and negative response was based on the assay cut-off. The association between the latest RTX dose before first vaccination, timing between the latest RTX dose and vaccination and response was analysed with univariable logistic regression. Results : Of the 196 patients in the cohort, 98 were included in the third vaccine analysis and 23 in the persistence analysis. Third vaccination response was 19/98 (19%) and was higher for 200 mg RTX users [5/13 (38%)] than for 500 and 1000 mg users [7/37 (19%) and 7/48 (15%), respectively]. Non-significant trends were seen for higher response with lower dosing [200 vs 1000 mg: odds ratio (OR) 3.66 (95% CI 0.93, 14.0)] and later timing [per month since infusion: OR 1.16 (95% CI 0.97, 1.35)]. Humoral response persisted in 96% (22/23) and 89% (8/9) of patients who received RTX between the two measurements. Conclusions : Repeated vaccination as late as possible after the lowest RTX dose possible seems the best vaccination strategy. A once positive humoral response after COVID-19 vaccination persists irrespective of intercurrent RTX infusion

Risk Factors and Clinical Outcomes of Head and Neck Cancer in Inflammatory Bowel Disease: A Nationwide Cohort Study

Background Immunosuppressed inflammatory bowel disease (IBD) patients are at increased risk to develop extra-intestinal malignancies. Immunosuppressed transplant patients show increased incidence of head and neck cancer with impaired survival. This study aims to identify risk factors for oral cavity (OCC) and pharyngeal carcinoma (PC) development in IBD, to compare clinical characteristics in IBD with the general population, and to assess the influence of immunosuppressive medication on survival. Methods We retrospectively searched the Dutch Pathology Database to identify all IBD patients with OCC and PC between 1993 and 2011. Two case-control studies were performed: We compared cases with the general IBD population to identify risk factors, and we compared cases with non-IBD cancer patients for outcome analyses. Results We included 66 IBD patients and 2141 controls with OCC, 31 IBD patients and 1552 controls with PC, and 1800 IBD controls. Age at IBD diagnosis was a risk factor for OCC development, Crohn's disease (CD; odds ratio [OR], 1.04; 95% confidence interval [CI], 1.02-1.07), and ulcerative colitis (UC; OR, 1.03; 95% CI, 1.01-1.06). For PC, this applied to UC (OR, 1.05; 95% CI, 1.01-1.06). IBD OCC cases showed impaired survival (P = 0.018); in PC, survival was similar. There was no effect of immunosuppression on survival. Human papillomavirus (HPV) testing of IBD cases revealed 52.2% (12/23) HPV-positive oropharyngeal carcinomas (OPCs). Conclusion This study shows that IBD is associated with impaired OCC survival. Higher age at IBD diagnosis is a risk factor for OCC development. We found no influence of immunosuppression on survival; 52.2% of OPC in IBD contained HPV