Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

Introduction: Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.Methods: Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix,One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed.Results: Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection.Conclusion: A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

CRISPR/Cas9-mediated glycolate oxidase disruption is an efficacious and safe treatment for primary hyperoxaluria type I

CRISPR/Cas9 technology offers novel approaches for the development of new therapies for many unmet clinical needs, including a significant number of inherited monogenic diseases. However, in vivo correction of disease-causing genes is still inefficient, especially for those diseases without selective advantage for corrected cells. We reasoned that substrate reduction therapies (SRT) targeting non-essential enzymes could provide an attractive alternative. Here we evaluate the therapeutic efficacy of an in vivo CRISPR/Cas9-mediated SRT to treat primary hyperoxaluria type I (PH1), a rare inborn dysfunction in glyoxylate metabolism that results in excessive hepatic oxalate production causing end-stage renal disease. A single systemic administration of an AAV8-CRISPR/Cas9 vector targeting glycolate oxidase, prevents oxalate overproduction and kidney damage, with no signs of toxicity in Agxt1(-/-) mice. Our results reveal that CRISPR/Cas9-mediated SRT represents a promising therapeutic option for PH1 that can be potentially applied to other metabolic diseases caused by the accumulation of toxic metabolites

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: wet lab procedure

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Latest physics results of TJ-II flexible heliac

This paper is devoted to the presentation of the most relevant recent Physics results obtained in the TJ-II flexible heliac. Firstly ECRH modulation and plasma breakdown studies are summarised; then the particle control techniques used to obtain reproducible discharges with density under control are presented. Transport studies show internal heat transport barriers that reduce heat conductivity to neoclassical values, and ELM-like transport events, similar to those observed in tokamaks and in other stellarators before and during H mode transition. Evidence of ExB sheared has been observed both in the proximity of rational surfaces. Finally, a high resolution Thomsom Scattering system has shown Te and ne profile structures

Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for i

Modelling the potential impacts of climate change on the hydrology of the Aipe river basin in Huila, Colombia

[EN] The dynamics of a global world, and humans performing as a new geological force, require that an effort is undertaken to make robust decisions in order to devise strategies for the management and adaptation to climate change. This study aims to investigate the potential impact of climate change on the hydrology of the Aipe river basin in Huila, Colombia. The abcd Thomas model (four parameters) was calibrated and validated for the stream flows of the Aipe catchment (1992¿2012). The sensitivity and identifiability of the parameters were evaluated using the Monte Carlo Analysis Toolbox (MCAT). The results show the ability of the model to simulate the monthly stream flow (Nash¿Sutcliffe efficiency coefficient of 0,89). The most influential parameters are: a (water storage in the soil) and c (contribution to the aquifer). From the simulated scenarios, the baseline (1992¿2012) was estimated to be an average flow of 15,44 m3s¿1; the trend extrapolation scenario estimated a rate 13,79 m3s¿1 (¿10,64%); while for the multi-model assembly scenario it was 9,34 m3s¿1 (¿39,47%) and for the A2 scenario it was 5,74 m3s¿1 (¿62,60%). Lastly, we propose a set of strategies for adaptation to climate change that are committed to the integral management of water resources.[ES] La dinámica de un mundo global y el hombre como nueva fuerza geológica plantean la necesidad de tomar decisiones robustas, diseñar estrategias de manejo y de adaptarse al cambio climático. Este estudio investiga la respuesta hidrológica de la cuenca hidrográfica del río Aipe (688.9 km2 ), en Huila, Colombia, en acorde con los escenarios de cambio climático desde 2011 a 2040. El modelo hidrológico abcd de Thomas (4 parámetros) fue calibrado y validado comparando el caudal simulado y lo observado en el punto de cierre de la cuenca (en la estación Puente Carretera), usando series históricas mensuales (1992¿2012). Realizamos la evaluación de la sensibilidad e identificabilidad de los parámetros con la herramienta `Monte Carlo Analysis Toolbox¿ (MCAT). Los resultados muestran que el modelo es capaz de representar adecuadamente los caudales mensuales observados en el punto de desagüe de la cuenca, al encontrarse un índice de eficiencia de Nash¿Sutcliffe (NSE) de 0,89. Los parámetros más influyentes son a (almacenamiento del agua en el suelo) y c (aporte al acuífero). Con respecto a la simulación de los escenarios, la línea base (1992¿2012) estimó un caudal medio de 15,44 m3 s ¿1 ; el escenario de extrapolación de tendencias estimó un caudal de 13,79 m3 s ¿1 (¿10,64%); el escenario de ensamble multi-modelo de 9,34 m3 s ¿1 (¿39,47%) y el escenario A2 de 5,74 m3 s ¿1 (¿62,60%). Proponemos una batería de medidas de adaptación al cambio climático que buscan la gestión integral del recurso hídrico.Romero-Cuellar, J.; Buitrago-Vargas, A.; Quintero-Ruiz, T.; Francés, F. (2018). Simulación hidrológica de los impactos potenciales del cambio climático en la cuenca hidrográfica del río Aipe, en Huila, Colombia. RIBAGUA - Revista Iberoamericana del Agua. 5(1):63-78. https://doi.org/10.1080/23863781.2018.1454574S63785

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries