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BACKGROUND Hepatitis B viruses (HBV) harboring mutations in the a-determinant of the Hepatitis B surface antigen (HBsAg) are associated with reduced reactivity of HBsAg assays. OBJECTIVES To evaluate the sensitivity and specificity of three HBsAg point-of-care tests for the detection of HBsAg of viruses harboring HBsAg mutations. STUDY DESIGN A selection of 50 clinical plasma samples containing HBV with HBsAg mutations was used to evaluate the performance of three HBsAg point-of-care tests (Vikia(®), bioMerieux, Marcy-L'Etoile, France. Alere Determine HBsAg™, Iverness Biomedical Innovations, Koln, Germany. Quick Profile™, LumiQuick Diagnostics, California, USA) and compared to the ARCHITECT HBsAg Qualitative(®) assay (Abbott Laboratories, Sligo, Ireland). RESULTS The sensitivity of the point-of-care tests ranged from 98% to 100%. The only false-negative result occurred using the Quick Profile™ assay with a virus harboring a D144A mutation. CONCLUSIONS The evaluated point-of-care tests revealed an excellent sensitivity in detecting HBV samples harboring HBsAg mutations.

Background Molecular methods based on phylogenetic differences in the 16S rRNA gene are able to characterise the microbiota of the respiratory tract in health and disease. Objectives Our goals were (1) to characterise bacterial communities in lower and upper airways of patients with interstitial lung disease (ILD) and (2) to compare the results with the microbiota of patients with Pneumocystis pneumonia (PCP) and normal controls. Methods We examined the upper and lower respiratory tract of 18 patients with ILD of whom 5, 6, and 7 had idiopathic interstitial pneumonia (IIP), non-IIP and sarcoidosis, respectively. In addition, six immune-compromised patients with PCP and nine healthy subjects were included as controls. Exclusion criteria were recent bacterial/viral respiratory tract infection, HIV-positivity and subjects receiving antibiotic therapy. Bronchoalveolar lavage fluid and oropharyngeal swabs were simultaneously collected, and microbiota was characterised by ultra-deep 16S rRNA gene sequencing. Results The microbiota in lower airways of the majority of patients (30; 90%) primarily consisted of Prevotellaceae, Streptococcaceae and Acidaminococcaceae. α and β diversity measurements revealed no significant differences in airway microbiota composition between the five different groups of patients. Comparison of bacterial populations in upper and lower respiratory tract showed significant topographical discontinuities for 7 (23%) individuals. Conclusions IIP, non-IIP and sarcoidosis are not associated with disordered airway microbiota and a pathogenic role of commensals in the disease process is therefore unlikely. Nevertheless, molecular analysis of the topographical microbiota continuity along the respiratory tract may provide additional information to assist management of individual patients.

OBJECTIVES A significant percentage of patients infected with HIV-1 experience only suboptimal CD4 cell recovery while treated with combination therapy (cART). It is still unclear whether viral properties such as cell tropism play a major role in this incomplete immune response. This study therefore intended to follow the tropism evolution of the HIV-1 envelope during periods of suppressive cART. METHODS Viruses from two distinct patient groups, one with good and another one with poor CD4 recovery after 5 years of suppressive cART, were genotypically analysed for viral tropism at baseline and at the end of the study period. RESULTS Patients with CCR5-tropic CC-motif chemokine receptor 5 viruses at baseline tended to maintain this tropism to the study end. Patients who had a CXCR4-tropic CXC-motif chemokine receptor 4 virus at baseline were overrepresented in the poor CD4 recovery group. Overall, however, the majority of patients presented with CCR5-tropic viruses at follow-up. CONCLUSIONS Our data lend support to the hypothesis that tropism determination can be used as a parameter for disease progression even if analysed long before the establishment of a poorer immune response. Moreover, the lasting predominating CCR5-tropism during periods of full viral control suggests the involvement of cellular mechanisms that preferentially reduce CXCR4-tropic viruses during cART.

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/bioMerieux) 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 (bioMerieux). 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.

Background Respiratory picornaviruses (enteroviruses and rhinoviruses) are commonly cited as causes of self-limited upper respiratory tract infection. However, it has recently been suggested that they may cause more severe respiratory disease. Immunofluorescence (IF) assays are rapid and inexpensive and are often used for the detection of respiratory viruses. Objectives We sought to develop an IF procedure, using commercially available reagents, for the detection of respiratory picornaviruses directly from nasopharyngeal aspirates (NPA). Study design From 1st November 2006 until 31st October 2007 all NPA from patients with respiratory infection were stained with the Light Diagnostic Pan-Enterovirus Reagent – “Blend” by IF (IF-ENVPAN). Those specimens which tested positive with this stain were further tested (subject to the availability of frozen specimen) with the xTAG respiratory viral panel, a multiplex PCR directed against respiratory picornaviruses, adenovirus (ADV), respiratory sincytial virus (RSV), influenza viruses A and B (IFA and IFB), parainfluenza virus (PIV) 1–4, human metapneumovirus (HMPV) and coronaviruses. Results 241/1122 NPA tested positive by IF-ENVPAN. 143 NPA were available for testing by xTAG respiratory viral panel. The multiplex PCR detected respiratory picornaviruses in 139 NPA, in 126 as the sole viral pathogen. Conclusions Our results indicate the potential of IF-ENVPAN for the laboratory detection of respiratory picornaviruses in clinical specimens. As far as we are aware, this is the first publication of such a method.

Background Chronic hepatitis B virus (HBV) infection affects up to 7 % of the European population. Specific HBV genotypes are associated with rapid progression to end-stage liver disease and sub-optimal interferon treatment responses. Although the geographic distribution of HBV genotypes differs between regions, it has not been studied in Switzerland, which lies at the crossroads of Europe. Methods In a retrospective analysis of 465 HBV samples collected between 2002 and 2013, we evaluated the HBV genotype distribution and phylogenetic determinants, as well as the prevalence of serological evidence of hepatitis delta, hepatitis C and HIV infections in Switzerland. Baseline characteristics of patients were compared across their region of origin using Fisher’s exact test and ANOVA, and risk factors for HBeAg positivity were assessed using logistic regression. Results The Swiss native population represented 15.7 % of HBV-infected patients living in Switzerland. In the overall population, genotype D was most prevalent (58.3 %), whereas genotype A (58.9 %) was the predominant genotype among the Swiss native population. The prevalence of patients with anti-HDV antibodies was 4.4 %. Patients of Swiss origin were most likely to be HBeAg-positive (38.1 %). HBV genotypes of patients living in Switzerland but sharing the same original region of origin were consistent with their place of birth. Conclusions The molecular epidemiology of HBV infection in Switzerland is driven by migration patterns and not by the genotype distribution of the native population. The prevalence of positive anti-HDV antibodies in our cohort was very low. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1234-z) contains supplementary material, which is available to authorized users.

Background: Haemodynamically significant congenital heart disease (CHD) is a risk factor for severe respiratory syncytial virus (RSV) disease in young children. Population based data on the incidence of RSV hospitalisations in CHD patients are needed to estimate the potential usefulness of RSV immunoprophylaxis using palivizumab. Aims: (1) To obtain population based RSV hospitalisation rates in children

During the past decade mumps outbreaks have occurred in several European countries with universal vaccination programs probably due to poor efficacy of the Rubini vaccine strain. However, the evolution of vaccine escape mutants has also been considered. A phylogenetic analysis was undertaken on 69 clinical mumps isolates obtained from 39 vaccinated and 22 non-vaccinated mumps cases (and six cases with unknown vaccination status) during an outbreak in 1998–2000. Two major strain clusters (SWI-H, SWI-C) with two subgroups each (SWI-H1/2, SWI-C1/2) were identified, which belonged to genotypes C and H. No association between viral clusters and vaccination status or a specific vaccine strain (Jeryl-Lynn or Rubini) was found. Cluster SWI-C1 occurred more frequently in the Western part of Switzerland (P

Background: The annual respiratory syncytial virus (RSV) epidemics vary in time and severity. The aims of this study were (1) to describe the time-related pattern of RSV epidemics in Switzerland and (2) to deduce the most effective time period for administration of prophylactic measures to high-risk patients. Patients and Methods: Descriptive study of (1) RSV hospitalizations between 1997 and 2001 at a pediatric hospital serving a population of 1 million and (2) of national RSV detection rates reported by diagnostic laboratories between 1988 and 1999. Results: 497 RSV hospitalizations and 8,574 reported RSV detections occurring during four and 12 epidemics, respectively, were analyzed. There was fixed alternation of minor and major epidemics differing in the number of RSV infections (two to fourfold), evolution (median interval from onset to peak 13 weeks, range 4–13 weeks vs 8 weeks, range 7–10 weeks; p = 0.065) and median duration (26 weeks, range 24-29 weeks vs 19.5 weeks, range 18–21 weeks; p = 0.005). For minor epidemics it was estimated that a maximum of 85.6% (range, 79.4–86.6%) of annual RSV infections could be covered by a standard five-dose regimen of the monoclonal anti-RSV antibody palivizumab, if initiated in week 50. During major epidemics the most effective time of initiation would be week 43 (88.7%; range 81.9–94.6%). Conclusion: RSV epidemiology in Switzerland is characterized by fixed biannual variation. In the absence of active RSV surveillance, such periodicity is useful for scheduling RSV prophylaxis and for hospital resources management.

Advanced neutron detectors for experiments at new spallation sources will require greater counting rate capabilities than previously attainable. This necessitates careful design of both detector and readout electronics. As part of a new instrument for protein crystallography at LANSCE, we are constructing a detector whose concept was described previously (IEEE Trans. Nucl. Sci. NS-46 (1999) 1916). Here, we describe the signal processing circuit, which is well suited for 3He detectors with a continuous interpolating readout. The circuit is based on standard charge preamplification, transmission of this signal over 20 meters or so, followed by sample and hold using a second order gated baseline restorer. This latter unit provides high rate capability without requiring pole-zero and tail cancellation circuits. There is also provision for gain-adjustment. The circuits are produced in surface mounted technology.

Recent results from the Front-End electronics of the Detector of Internally Reflected Cerenkov light (DIRC) for the BaBar experiment at SLAC (Stanford, USA) are presented. It measures to better than 1 ns the arrival time of Cerenkov photoelectrons detected in a 11000 phototubes array and their amplitude spectra. It mainly comprises 64-channel DIRC Front-End Boards (DFB) equipped with eight full-custom analog chips performing zero-cross discrimination with 2 mV threshold and pulse shaping, four full-custom digital time to digital chips (TDC) for timing measurements with 500 ps binning and a readout logic selecting hits in the trigger window, and DIRC Crate Controller cards (DCC) serializing the data collected front up to 16 DFBs onto a 1.2 Gb/s optical link. Extensive test results of the pre-production chips are presented, as well as system tests.

Enteroviruses (EV) are among the most common causes of aseptic meningitis. Standard diagnostic techniques are often too slow and lack sensitivity to be of clinical relevance. EV RNA can be detected within 5 h by a commercially available reverse transcription-PCR (RT-PCR) test kit. Cerebrospinal fluid (CSF) samples from 68 patients presenting with aseptic meningitis during a summer outbreak in Switzerland were examined in parallel with cell culture and commercial RT-PCR. RT-PCR was positive in all 16 CSF specimens positive by cell culture (100%). In addition, 42 of 52 (80%) CSF samples negative by cell culture were PCR positive. In 26 of these 42 (62%) patients, viral culture from other sites (throat swab or stool) was also positive. The CSF virus culture took 3 to 7 days to become positive. Echovirus 30 was the type most often isolated in this outbreak. The sensitivity of CSF RT-PCR based on clinical diagnosis during this aseptic meningitis outbreak in patients with negative bacterial culture results was 85%, i.e., considerably higher than the sensitivity of CSF virus culture (24%). We conclude that this commercial RT-PCR assay allows a positive diagnosis with minimal delay and may thus influence clinical decisions.

An analog chip is designed to receive from a PM, through a 50 Ω coaxial cable, signals rising in 3 ns, falling in 8 ns, and to provide: • digital signals for timing purposes, • multiplixed analog output, proportional to the input, for spectral measurements; there are 8 channels per chip with a common gain adjustment for the preamplifier, and individual control for the offset and threshold setting. The discriminator sensitivity is 2 mV. The dynamic range is from 2 to 100 mV. The noise equivalent at the input is ≈100 μV. The RMS time dispersion is less than 550 ps for 3 mV threshold. The shaping amplifier is of bipolar shape with 80 ns peaking time and 2.5 V mean output voltage. The cross talk between channels is less than 2%.

An 8-channel preamplifier-shaper circuit for use with detectors having a capacitance in the range 20–50 pF has been designed in 1.2 μ CMOS AMS technology. The shaper is designed so that the peaking time can be adjusted, by steps, in the range 200 ns–2 μs by simple digital control. The pole-zero cancellation circuit uses an original method of sensing the preamplifier feedback capacitor discharging current and producing an identical current to discharge the capacitance of the pole-zero cancellation circuit. The series noise resistance r s = 415 Ω has been measured (270 Ω of which is the protection resistor). The input capacitance of the preamplifier is 10 pF + the strays of the test box 10 pF for a total of 20 pF. The input PMOS transistor has a gm of 5 mA/V (from simulation) at 210 μA drain current. The cross-talk between channels is less than 1%.

Novel configurations of current and voltage-sensitive preamplifiers in DMILL technology intended for calorimetry applications are discussed. A broad set of noise characterisation tests, including room temperature, cryogenic operation and radiation effects, is given. It is shown that in cryogenic conditions the noise behaviour is considerably less current dependent than at room temperature.

Background Cytomegalovirus (CMV) infection is associated with significant morbidity and mortality in transplant recipients. Resistance against ganciclovir is increasingly observed. According to current guidelines, direct drug resistance testing is not always performed due to high costs and work effort, even when resistance is suspected. Objectives To develop a more sensitive, easy applicable and cost-effective assay as proof of concept for direct drug resistance testing in CMV surveillance of post-transplant patients. Study design Five consecutive plasma samples from a heart transplant patient with a primary CMV infection were analyzed by quantitative real-time polymerase chain reaction (rtPCR) as a surrogate marker for therapy failure, and by direct drug resistance detection assays such as Sanger sequencing and the novel primer extension (PEX) reaction matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based method. Results This report demonstrates that PEX reaction followed by MALDI-TOF analysis detects the A594V mutation, encoding ganciclovir resistance, ten days earlier compared to Sanger sequencing and more than 30 days prior to an increase in viral load. Conclusion The greatly increased sensitivity and rapid turnaround-time combined with easy handling and moderate costs indicate that this procedure could make a major contribution to improve transplantation outcomes.

We evaluated four tests for the detection of rubella virus-specific immunoglobulin M antibodies. Primarily, consecutive serum samples were tested by two different assays. Selected panels of sera from patients with proven or likely recent rubella and false-positive and true-negative results in the two primary assays were further tested with two recently developed, fully automated techniques. The four tests were comparable in overall accuracy, but their dynamic ranges may differ considerably. Ways to optimize the predictive values are discussed. We conclude that automated assays may be used without causing significant changes in diagnostic accuracy or distortions in notifications of the incidence of rubella compared with the use of established tools.

A prototype liquid argon preshower detector with a strip granularity of 2.5 mm has been tested at the CERN SPS in front of a liquid argon Accordion calorimeter. For charged tracks a signal-to-noise ratio of 9.4 and a space resolution of 340 μm were measured; the rejection power against overlapping photons produced in the decay of 50 GeV π 0 's is larger than 3; the precision on

The design and first results from double-sided silicon microstrip detectors designed for use in the DELPHI experiment at LEP are presented. The detectors are AC-coupled on both the n- and p-side. A novel readout scheme using a second metal layer has been implemented, allowing the readout of both coordinates on the same edge of the detector. The detectors have been tested in a high energy beam at the CERN SPS. Results on spatial resolution, pulse-height correlation and charge division are presented. The spatial resolution of the n-side has been measured as a function of the beam particle incident angle from 0 to 60°.

Some modification concerning the microplex MX3 128 channels chip (made by Rutherford Group) have been done. The noise is reduced by a factor of 3. The evaluation method and the new geometry are presented. This chip will be used for the DELPHI μ-vertex detector.

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 (46 mg/l vs. 11 mg/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.

Measurements are presented of the cross section ratios Rℓ = σℓ(e+e-→ℓ+ℓ -)/σhh(e+e-→hadrons) for ℓ = e, μ and τ using data taken from a scan around the Z0. The results are Re = (5.09±0.32±0.18)%, Rμ = (4.96±0.35±0.17)% and Rτ,=(4.72±0.38± 0.29)% where, for the ratio Re, the t-channel contribution has been subtracted. These results are consistent with the hypothesis of lepton universality and test this hypothesis at the energy scale s ∼ 8300 GeV2. The absolute cross sections σℓ(e+e-→ℓ +ℓ-) have also been measured. From the cross sections the leptonic partial widths Γe = (83.2±3.0±2.4) MeV, (ΓeΓμ) 1/2=(84.6±3.0±2.4) MeV and (ΓeΓτ) 1/2=(82.6±3.3±3.2) MeV have been extracted. Assuming lepton universality the ratio Γℓ/Γh=(4.89±0.20± 0.12) × 10-2 was obtained, together with Γℓ=(83.6±1.8±2.2) MeV. The number of light neutrino species is determined to be Nv=3.12±0.24±0.25. Al the data are consistent with the predictions of the standard model., 0, SCOPUS: ar.j, info:eu-repo/semantics/published