A Past Discharges Assimilation System for Ensemble Streamflow Forecasts over France - Part 1: Description and Validation of the Assimilation System

Two Ensemble Streamflow Prediction Systems (ESPSs) have been set up at Météo-France. They are based on the French SIM distributed hydrometeorological model. A deterministic analysis run of SIM is used to initialize the two ESPSs. In order to obtain a better initial state, a past discharges assimilation system has been implemented into this analysis SIM run, using the Best Linear Unbiased Estimator (BLUE). Its role is to improve the model soil moisture by using streamflow observations in order to better simulate streamflow. The skills of the assimilation system were assessed for a 569-day period on six different configurations, including two different physics schemes of the model (the use of an exponential profile of hydraulic conductivity or not) and, for each one, three different ways of considering the model soil moisture in the BLUE state variables. Respect of the linearity hypothesis of the BLUE was verified by assessing of the impact of iterations of the BLUE. The configuration including the use of the exponential profile of hydraulic conductivity and the combination of the moisture of the two soil layers in the state variable showed a significant improvement of streamflow simulations. It led to a significantly better simulation than the reference one, and the lowest soil moisture corrections. These results were confirmed by the study of the impacts of the past discharge assimilation system on a set of 49 independent stations.JRC.H.7-Climate Risk Managemen

Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests.

High-throughput sequencing (HTS) technologies have the potential to become one of the most signi cant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, con rming and interpreting results. These guidelines cover any HTS test used for the detection and identi cation of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health

A Past Discharge Assimilation System for Ensemble Streamflow Forecasts over France - Part 2: Impact on the Ensemble Streamflow Forecasts

The use of ensemble streamflow forecasts is developing in the international flood forecasting services. Ensemble streamflow forecast systems can provide more accurate forecasts and useful information about the uncertainty of the forecasts, thus improving the assessment of risks. Nevertheless, these systems, like all hydrological forecasts, suffer from errors on initialization or on meteorological data, which lead to hydrological prediction errors. This article, which is the second part of a 2-part article, concerns the impacts of initial states, improved by a streamflow assimilation system, on an ensemble streamflow prediction system over France. An assimilation system was implemented to improve the streamflow analysis of the SAFRAN-ISBA-MODCOU (SIM) hydro-meteorological suite, which initializes the ensemble streamflow forecasts at Météo-France. This assimilation system, using the Best Linear Unbiased Estimator (BLUE) and modifying the initial soil moisture states, showed an improvement of the streamflow analysis with low soil moisture increments. The final states of this suite were used to initialize the ensemble streamflow forecasts of Météo-France, which are based on the SIM model and use the European Centre for Medium-range Weather Forecasts (ECMWF) 10-day Ensemble Prediction System (EPS). Two different configurations of the assimilation system were used in this study: the first with the classical SIM model and the second using improved soil physics in ISBA. The effects of the assimilation system on the ensemble streamflow forecasts were assessed for these two configurations, and a comparison was made with the original (i.e. without data assimilation and without the improved physics) ensemble streamflow forecasts. It is shown that the assimilation system improved most of the statistical scores usually computed for the validation of ensemble predictions (RMSE, Brier Skill Score and its decomposition, Ranked Probability Skill Score, False Alarm Rate, etc.), especially for the first few days of the time range. The assimilation was slightly more efficient for small basins than for large ones.JRC.H.7-Climate Risk Managemen

Detection of Banana Mild Mosaic Virus in musa in vitro plants: High-throughput sequencing presents higher diagnostic sensitivity than (IC)-RT-PCR and identifies a new betaflexiviridae species

The banana mild mosaic virus (BanMMV) (Betaflexiviridae, Quinvirinae, unassigned species) is a filamentous virus that infects Musa spp. and has a very wide geographical distribution. The current BanMMV indexing process for an accession requires the testing of no less than four plants culti-vated in a greenhouse for at least 6 months and causes a significant delay for the distribution of the germplasm. We evaluated the sensitivity of different protocols for BanMMV detection from in vitro plants to accelerate the testing process. We first used corm tissues from 137 in vitro plants and obtained a diagnostic sensitivity (DSE) of only 61% when testing four plants per accession. After thermotherapy was carried out to eliminate BanMMV infection, the meristem was recovered and further grown in vitro. The same protocol was evaluated in parallel on the corm tissue surrounding the meristem, as a rapid screening to evaluate virus therapy success, and was compared to the results obtained following the standard protocol. The obtained results showed 28% false negatives when conducting testing from corm tissues, making this protocol unsuitable in routine processes. Furthermore, RT-PCR and high-throughput sequencing (HTS) tests were applied on tissues from the base (n = 39) and the leaves (n = 36). For RT-PCR, the average DSE per sample reached 65% from either the base or leaves. HTS was applied on 36 samples and yielded 100% diagnostic specificity (DSP) and 100% DSE, whatever the sampled tissue, allowing the identification of a new Betaflex-iviridae species infecting Musa. These results suggest that a reliable diagnostic of BanMMV from in vitro plants using RT-PCR or HTS technologies might represent an efficient alternative for testing after greenhouse cultivation

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.Peer reviewe

Correction to: Safeguarding and using global banana diversity: a holistic approach

An amendment to this paper has been published and can be accessed via the original article

The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems

Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making. (C) 2018 The Authors. Published by Elsevier B.V.Peer reviewe

Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology (2021) 166:3567–3579. https://doi.org/10.1007/s00705-021-05266-wIn March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This work was also supported in part with federal funds from the National Cancer Institute (NCI), National Institutes of Health (NIH), under Contract No. 75N91019D00024, Task Order No. 75N91019F00130 to I.C., who was supported by the Clinical Monitoring Research Program Directorate, Frederick National Lab for Cancer Research. This work was also funded in part by Contract No. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of The National Biodefense Analysis and Countermeasures Center, a federally funded research and development center operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges partial support from the Special Research Initiative of Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University, and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Part of this work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001030), the UK Medical Research Council (FC001030), and the Wellcome Trust (FC001030).S