A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

Enabling planetary science across light-years. Ariel Definition Study Report

Ariel, the Atmospheric Remote-sensing Infrared Exoplanet Large-survey, was adopted as the fourth medium-class mission in ESA's Cosmic Vision programme to be launched in 2029. During its 4-year mission, Ariel will study what exoplanets are made of, how they formed and how they evolve, by surveying a diverse sample of about 1000 extrasolar planets, simultaneously in visible and infrared wavelengths. It is the first mission dedicated to measuring the chemical composition and thermal structures of hundreds of transiting exoplanets, enabling planetary science far beyond the boundaries of the Solar System. The payload consists of an off-axis Cassegrain telescope (primary mirror 1100 mm x 730 mm ellipse) and two separate instruments (FGS and AIRS) covering simultaneously 0.5-7.8 micron spectral range. The satellite is best placed into an L2 orbit to maximise the thermal stability and the field of regard. The payload module is passively cooled via a series of V-Groove radiators; the detectors for the AIRS are the only items that require active cooling via an active Ne JT cooler. The Ariel payload is developed by a consortium of more than 50 institutes from 16 ESA countries, which include the UK, France, Italy, Belgium, Poland, Spain, Austria, Denmark, Ireland, Portugal, Czech Republic, Hungary, the Netherlands, Sweden, Norway, Estonia, and a NASA contribution

Microbiology and shellfish : issues and future developments

The shellfish safety has long been considered a public health problem. The implementation of a regulation based on a bacterial indicator of faecal contamination has significantly reduced outbreaks of bacterial origin. However, epidemics of viral gastroenteritis due to the presence of noroviruses from human sewage persist. We demonstrated few years ago that oysters are not just a passive filter but are able to select some viral strains, via the presence of specific ligands, very similar to ligands observed in humans for these same virus. Ongoing developments, in conjunction with the application of metagenomic tools, will allow us to better understand the fate of some human pathogens after their release into the coastal environment.La salubrité des coquillages est considérée depuis fort longtemps comme un problème de santé publique. La mise en place d’une réglementation basée sur un indicateur bactérien de contamination d’origine fécale a permis de diminuer significativement les épidémies d’origine bactérienne. Cependant, les épidémies de gastroentérites virale dues à la présence de norovirus issus de rejet humains persistent. Des travaux de recherche nous ont permis de mettre en évidence que l’huître n’est pas simplement un filtre passif mais est capable de sélectionner certaines souches virales, via la présence de ligands spécifiques, très proches des ligands observés chez l’homme pour ces mêmes virus. Les développements en cours en lien avec l’utilisation des outils de metagénomique, vont nous permettre de mieux appréhender le devenir de certains micro-organismes pathogènes humains après leurs rejets dans l’environnement côtier

A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks

Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability between replicates especially with lower viral concentrations. Using shellfish samples, targeted metagenomics was compared to Sanger-sequencing of cloned amplicons and was able to identify a higher diversity of NoV GII and GIV strains. It allowed phylogenetic analyses of VP1 sequences and the identification, in most samples, of GII.17[P17] strains, also identified in related clinical samples. Despite several limitations, combining RdRp- and VP1-targeted metagenomics is a sensitive approach allowing the study NoV diversity in low-contaminated foods and the identification of NoV strains implicated in outbreaks

A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks

Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability between replicates especially with lower viral concentrations. Using shellfish samples, targeted metagenomics was compared to Sanger-sequencing of cloned amplicons and was able to identify a higher diversity of NoV GII and GIV strains. It allowed phylogenetic analyses of VP1 sequences and the identification, in most samples, of GII.17[P17] strains, also identified in related clinical samples. Despite several limitations, combining RdRp- and VP1-targeted metagenomics is a sensitive approach allowing the study NoV diversity in low-contaminated foods and the identification of NoV strains implicated in outbreaks

Intérêt des essais interlaboratoires dans la validation d’un indicateur national de suivi épidémiologique de l’épidémie de SARS-CoV-2 par les eaux usées (en France)

Introduction et objectifs  Le consortium Obépine (Observatoire épidémiologique dans les eaux usées) a développé un outil de surveillance épidémiologique de la circulation du SARS-CoV-2 dans les eaux usées. Cet outil est un indicateur basé sur la quantification du virus dans les eaux usées prélevées dans 168 stations couvrant le territoire national et l’outre-mer, par un réseau de laboratoires. L’utilisation opérationnelle, dans la surveillance épidémiologique de l’épidémie, de l’indicateur de tendances construit selon des modèles mathématiques nécessite de s’assurer que les laboratoires du réseau sont en capacité de rendre des résultats homogènes et justes. L’organisation de comparaisons inter-laboratoires (CIL) est un moyen permettant de s’en assurer. Dans le cadre du réseau OBEPINE trois CIL ont été réalisées, seul le dernier fait l’objet de cette présentation. Matériels et Méthodes Cinq échantillons d'eau usée identiques et naturellement contaminés par du SARS-CoV-2 ont été envoyés aux laboratoires participants, ainsi qu’un sixième non contaminé afin de vérifier la spécificité des méthodes appliquées. Chacun des laboratoires a été évalué selon deux paramètres : la fidélité et la justesse respectivement évaluées par la statistique k de Mendel et le score Z. En l'absence méthode normalisée, les participants ont appliqué l’approche quantitative utilisée au sein de leur laboratoire. Les séquences cibles de la RT-qPCR pour cet essai étaient le gène RdRp IP4, le gène CoV E. Résultats, discussion et conclusion Vingt-trois laboratoires ont participé à l’essai. Les valeurs assignées (calculées à partir des résultats de l’ensemble des participants) étaient de 4,79 et 4,67 unités Log cRNA/L respectivement pour le gène RdRp IP4 et le gène CoV E. Pour le gène RdRp IP4, huit laboratoires ont obtenu des résultats non satisfaisants et deux laboratoire des résultats discutables. Pour le gène CoV E, cinq laboratoires ont obtenu des résultats non satisfaisants et deux laboratoire des résultats discutables. Un laboratoire a détecté le virus dans l’échantillon négatif. La majorité des résultats non satisfaisants est liée à un problème de fidélité (dispersion importante des valeurs obtenues par le laboratoire pour un même échantillon). Un travail pour identifier et comprendre l’origine des différences entre laboratoires a été initié. L’amélioration de la performance des laboratoires passe également par la standardisation de la méthode (normalisation).

Noroviruses are highly infectious but there is strong variation in host susceptibility and virus pathogenicity

Noroviruses are a major public health concern: their high infectivity and environmental persistence have been documented in several studies. Genetic sequencing shows that noroviruses are highly variable, and exhibit rapid evolution. A few human challenge studies have been performed with norovirus, leading to estimates of their infectivity. However, such incidental estimates do not provide insight into the biological variation of the virus and the interaction with its human host. To study the variation in infectivity and pathogenicity of norovirus, multiple challenge studies must be analysed jointly, to compare their differences and describe how virus infectivity and host susceptibility vary. Since challenge studies can only provide a small sample of the diversity in the natural norovirus population, outbreaks should be exploited as an additional source of information. The present study shows how challenge studies and ‘natural experiments’ can be combined in a multilevel dose response framework. Infectivity and pathogenicity are analysed by secretor status as a host factor, and genogroup as a pathogen factor. Infectivity, characterized as the estimated mean infection risk when exposed to 1 genomic copy (qPCR unit)is 0.28 for GI norovirus, and 0.076 for GII virus, both in Se+ subjects. The corresponding risks of acute enteric illness are somewhat lower, about 0.2 (GI) and 0.035 (GII), in outbreaks. Se− subjects are protected, with substantially lower risks of infection (0.00007 and 0.015 at a dose of 1 GC of GI and GII virus, respectively). The present study shows there is considerable variability in risk of infection and especially risk of acute symptoms following infection with norovirus. These challenge and outbreak data consistently indicate high infectivity among secretor positives and protection in secretor negatives

Optimization of PMAxx pretreatment to distinguish between human norovirus with intact and altered capsids in shellfish and sewage samples

Shellfish contamination by human noroviruses (HuNoVs) is a serious health and economic problem. Recently an ISO procedure based on RT-qPCR for the quantitative detection of HuNoVs in shellfish has been issued, but these procedures cannot discriminate between inactivated and potentially infectious viruses. The aim of the present study was to optimize a pretreatment using PMAxx to better discriminate between intact and heat-treated HuNoVs in shellfish and sewage. To this end, the optimal conditions (30 min incubation with 100 μM of PMAxx and 0.5% of Triton, and double photoactivation) were applied to mussels, oysters and cockles artificially inoculated with thermally-inactivated (99 °C for 5 min) HuNoV GI and GII. This pretreatment reduced the signal of thermally-inactivated HuNoV GI in cockles and HuNoV GII in mussels by > 3 log. Additionally, this pretreatment reduced the signal of thermally-inactivated HuNoV GI and GII between 1 and 1.5 log in oysters. Thermal inactivation of HuNoV GI and GII in PBS, sewage and bioaccumulated oysters was also evaluated by the PMAxx-Triton pretreatment. Results showed significant differences between reductions observed in the control and PMAxx-treated samples in PBS following treatment at 72 and 95 °C for 15 min. In sewage, the RT-qPCR signal of HuNoV GI was completely removed by the PMAxx pretreatment after heating at 72 and 95 °C, while the RT-qPCR signal for HuNoV GII was completely eliminated only at 95 °C. Finally, the PMAxx-Triton pretreatment was applied to naturally contaminated sewage and oysters, resulting in most of the HuNoV genomes quantified in sewage and oyster samples (12 out of 17) corresponding to undamaged capsids. Although this procedure may still overestimate infectivity, the PMAxx-Triton pretreatment represents a step forward to better interpret the quantification of intact HuNoVs in complex matrices, such as sewage and shellfish, and it could certainly be included in the procedures based on RT-qPCR

Optimization of PMAxx pretreatment to distinguish between human norovirus with intact and altered capsids in shellfish and sewage samples

Shellfish contamination by human noroviruses (HuNoVs) is a serious health and economic problem. Recently an ISO procedure based on RT-qPCR for the quantitative detection of HuNoVs in shellfish has been issued, but these procedures cannot discriminate between inactivated and potentially infectious viruses. The aim of the present study was to optimize a pretreatment using PMAxx to better discriminate between intact and heat-treated HuNoVs in shellfish and sewage. To this end, the optimal conditions (30 min incubation with 100 μM of PMAxx and 0.5% of Triton, and double photoactivation) were applied to mussels, oysters and cockles artificially inoculated with thermally-inactivated (99 °C for 5 min) HuNoV GI and GII. This pretreatment reduced the signal of thermally-inactivated HuNoV GI in cockles and HuNoV GII in mussels by > 3 log. Additionally, this pretreatment reduced the signal of thermally-inactivated HuNoV GI and GII between 1 and 1.5 log in oysters. Thermal inactivation of HuNoV GI and GII in PBS, sewage and bioaccumulated oysters was also evaluated by the PMAxx-Triton pretreatment. Results showed significant differences between reductions observed in the control and PMAxx-treated samples in PBS following treatment at 72 and 95 °C for 15 min. In sewage, the RT-qPCR signal of HuNoV GI was completely removed by the PMAxx pretreatment after heating at 72 and 95 °C, while the RT-qPCR signal for HuNoV GII was completely eliminated only at 95 °C. Finally, the PMAxx-Triton pretreatment was applied to naturally contaminated sewage and oysters, resulting in most of the HuNoV genomes quantified in sewage and oyster samples (12 out of 17) corresponding to undamaged capsids. Although this procedure may still overestimate infectivity, the PMAxx-Triton pretreatment represents a step forward to better interpret the quantification of intact HuNoVs in complex matrices, such as sewage and shellfish, and it could certainly be included in the procedures based on RT-qPCR.This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) (RYC-2012-09950 and RYC-2013-12442) and the Spanish National Institute for Agriculture and Food Research and Technology (INIA) co-financed by the European Social Fund (Project RTA2014-00024-C03). Financial support has been co-sponsored by the European Regional Development Fund (FEDER). GS and JRD were supported by the “Ramón y Cajal” Young Investigator.Peer reviewe

Optimization of PMAxx pretreatment to distinguish between human norovirus with intact and altered capsids in shellfish and sewage samples

Shellfish contamination by human noroviruses (HuNoVs) is a serious health and economic problem. Recently an ISO procedure based on RT-qPCR for the quantitative detection of HuNoVs in shellfish has been issued, but these procedures cannot discriminate between inactivated and potentially infectious viruses. The aim of the present study was to optimize a pretreatment using PMAxx to better discriminate between intact and heat-treated HuNoVs in shellfish and sewage. To this end, the optimal conditions (30 min incubation with 100 μM of PMAxx and 0.5% of Triton, and double photoactivation) were applied to mussels, oysters and cockles artificially inoculated with thermally-inactivated (99 °C for 5 min) HuNoV GI and GII. This pretreatment reduced the signal of thermally-inactivated HuNoV GI in cockles and HuNoV GII in mussels by > 3 log. Additionally, this pretreatment reduced the signal of thermally-inactivated HuNoV GI and GII between 1 and 1.5 log in oysters. Thermal inactivation of HuNoV GI and GII in PBS, sewage and bioaccumulated oysters was also evaluated by the PMAxx-Triton pretreatment. Results showed significant differences between reductions observed in the control and PMAxx-treated samples in PBS following treatment at 72 and 95 °C for 15 min. In sewage, the RT-qPCR signal of HuNoV GI was completely removed by the PMAxx pretreatment after heating at 72 and 95 °C, while the RT-qPCR signal for HuNoV GII was completely eliminated only at 95 °C. Finally, the PMAxx-Triton pretreatment was applied to naturally contaminated sewage and oysters, resulting in most of the HuNoV genomes quantified in sewage and oyster samples (12 out of 17) corresponding to undamaged capsids. Although this procedure may still overestimate infectivity, the PMAxx-Triton pretreatment represents a step forward to better interpret the quantification of intact HuNoVs in complex matrices, such as sewage and shellfish, and it could certainly be included in the procedures based on RT-qPCR.This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) (RYC-2012-09950 and RYC-2013-12442) and the Spanish National Institute for Agriculture and Food Research and Technology (INIA) co-financed by the European Social Fund (Project RTA2014-00024-C03). Financial support has been co-sponsored by the European Regional Development Fund (FEDER). GS and JRD were supported by the “Ramón y Cajal” Young Investigator.Peer reviewe