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Migration patterns and habitat use of adult barbel (Barbus barbus) and nase (Chondrostoma nasus) were monitored by radio telemetry over a period of 13 months along a 58-km-long section of the Austrian part of the Danube River. The study site is confined upstream and downstream by two hydropower plants, and contains a larger tributary, the Pielach River. Telemetry transmitters were implanted into fish caught in this tributary after spawning in June (25 individuals per species). The results show that both species use the entire available width and depth spectrum of the Danube along the full migratable river length. Nase had an average home range of 22.4 km, while that of barbel was 34.4 km. The habitat use of the two species differs significantly. While the nase was primarily encountered in the free-flowing section, barbel mainly used deep areas of the impoundment during the year. Nase showed a distinct site fidelity to certain areas in the free-flowing reach which were periodically revisited. During the spawning season, distinct homing behavior was observed in both species. All seven nase that could still be detected during the spawning season returned to the tributary (homing rate 100%). Six homing nase migrated up to the first migration barrier in the tributary but did not pass the existing fish passage facility. In contrast, only nine barbel returned to spawn in the tributary (homing rate 50%), while nine barbel were most likely using a spawning location in the head of impoundment section. Homing fish entered the tributary during darkness.

ZusammenfassungWeltweit ist die Aquakultur der am schnellsten wachsende Sektor in der tierischen Lebensmittelproduktion. Dieser Sektor wird voraussichtlich immer wichtiger werden, um den zukünftigen Nahrungsmittelbedarf zu decken. Im Binnenland Österreich ist der Selbstversorgungsgrad von Fisch mit 6 % insgesamt bzw. 48 % bei Süßwasserfischen eher gering. Um ein nachhaltiges Wachstum des Sektors zu ermöglichen und gleichzeitig negative Auswirkungen auf die verwendeten aquatischen Ökosysteme und andere Nutzungen der Ressource Wasser zu vermeiden, wurde ein räumlicher Analyse-Ansatz zur nachhaltigen Zonierung von Forellenzuchtbetrieben, mit einem Schwerpunkt auf Durchflussanlagen, entwickelt. Dabei wurden 17 land- und 17 gewässerbezogene räumliche Kriterien identifiziert und hinsichtlich ihrer Eignung für die Errichtung eines Forellenzuchtbetriebs klassifiziert. Anschließend wurden die Kriterien in einem integrativen GIS-basierten Modellierungsansatz kombiniert, um eine landesweite und räumlich explizite Zonierung von Eignungsgebieten innerhalb Österreichs vorzunehmen. Von insgesamt 8113 Teileinzugsgebieten (TEZG) mit einer mittleren Größe von 10 km2 wurden so 1295 TEZG als geeignet eingestuft. Für diese TEZG wurde eine potenzielle Produktionsmenge an Fisch abgeschätzt. Mit einer mittleren Produktion von 48,7 t pro Standort könnten in Summe 63.088 t Fisch in Durchflussanlagen österreichweit produziert werden. Die Ergebnisse sollen in weiterer Folge in einem Online-Tool zu Verfügung gestellt werden und so die Entscheidungsfindung von Investoren und Behörden unterstützen. Als Schnittstelle zwischen den unterschiedlichen Anwender:innen kann das Tool dazu beitragen, eine nachhaltige Entwicklung der Aquakultur in Österreich voranzutreiben und Konflikte und Fehlinvestitionen frühzeitig zu vermeiden.

ZusammenfassungIm Rahmen dieser Arbeit wurden Abflusskennwerte für Hochwasser (MJHQ), Mittelwasser (MQ) sowie Niederwasser (MJNQ, MJNQ7, Q95, Q98) für alle topografischen Einzugsgebiete der österreichischen Oberflächenwasserkörper inklusive der ausländischen hydrologischen Oberlieger-Regionen vorhergesagt. Die Regionalisierung der Abflusskennwerte wurde mit dem Machine-Learning-Modell XGBoost durchgeführt. Zentrale Grundlage für das Training von XGBoost war der LamaH-Datensatz, welcher für 859 beobachtete Einzugsgebiete in Zentraleuropa über 70 aggregierte Einzugsgebietseigenschaften und 15 meteorologische Zeitreihen umfasst. Anthropogene Beeinflussungen wie z. B. Jahresspeicher oder Überleitungen wurden durch zusätzlich erstellte Attribute bei der Vorhersage berücksichtigt. Die Testergebnisse haben gezeigt, dass bei der Vorhersage der Abflusskennwerte in unbeobachteten Einzugsgebieten mit einer Abweichung von rund 20 % zu rechnen ist, wobei diese Schätzung auch stark anthropogen beeinflusste Gebiete beinhaltet. Darüber hinaus wurden auch 90-%-Konfidenzintervalle der Vorhersagen mit einem Quantile-Random-Forest-Modell geschätzt und klassifiziert. Die Ergebnisse werden der Öffentlichkeit in Form von Shapefiles unter https://doi.org/10.5281/zenodo.6523372 kostenlos zur Verfügung gestellt.

ZusammenfassungAktuelle Konzepte für gewässerökologisch-hydromorphologische Sanierungen von Fließgewässern sehen meist eine (teilweise) Wiederherstellung der Gewässerdynamik vor. Folglich werden heute vermehrt Uferschutzbauten entfernt, Gerinneaufweitungen vorgenommen und verlandete Altarme wieder reaktiviert. Doch viele der daraus entstandenen neuen Gewässer(strukturen) erweisen sich mittel- bis langfristig nicht als selbsterhaltend. So neigen neu entstandene Nebenarme oft zur Verlandung und weitere Erhaltungsmaßnahmen sind erforderlich – selbst wenn bei der Planung auf historische Referenzen Bezug genommen wurde. Am Beispiel der Oberen Mur zwischen Fisching/Zeltweg und Leoben wird aufgezeigt, dass viele dieser zweifelsfrei ökologisch wertvollen Renaturierungsmaßnahmen keiner echten prozessorientierten „Fließgewässer-Redynamisierung“, sondern eher ökologisch motivierten Restrukturierungen mit Ablaufdatum entsprechen. Für eine langfristig erfolgreiche Sanierung würden die meisten Fließgewässer wesentlich mehr Raum und eine Integration morphodynamischer Prozesse benötigen, damit autochthone flussmorphologische und gewässerökologische Entwicklungszyklen möglich sind, die ein Mosaik an Habitaten unterschiedlicher Sukzessionsstadien hervorbringen.

Artificial sub-daily flow fluctuations caused by peak-operating hydropower plants are considered one of the most significant impacts on riverine ecosystems downstream of dams. These rivers have, therefore, been subject to numerous studies in recent decades. However, cyprinid fish, in contrast to salmonids, have hardly been addressed in hydropeaking studies yet, and extensive knowledge gaps remain. Therefore, our experimental study aims to assess the effects of rapid flow reductions on the early life stages of two European cyprinid indicator species, the common barbel (Barbus barbus L.) and the common nase (Chondrostoma nasus L.).We conducted mesocosm experiments (2.25×2 m) under semi-natural conditions at an outdoor experimental facility (http://hydropeaking.boku.ac.at), simulating different hydropeaking scenarios with varying down-ramping rates during day and night. At each trial, 100 fish from one species (body length

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020—the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland’s border closures decoupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 to 98% reduction in introductions during Switzerland’s strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred using a phylodynamic model. We found that transmission slowed 35 to 63% upon outbreak detection in summer 2020 but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.

Objective:Nosocomial transmission of influenza is a major concern for infection control. We aimed to dissect transmission dynamics of influenza, including asymptomatic transmission events, in acute care.Design:Prospective surveillance study during 2 influenza seasons.Setting:Tertiary-care hospital.Participants:Volunteer sample of inpatients on medical wards and healthcare workers (HCWs).Methods:Participants provided daily illness diaries and nasal swabs for influenza A and B detection and whole-genome sequencing for phylogenetic analyses. Contacts between study participants were tracked. Secondary influenza attack rates were calculated based on spatial and temporal proximity and phylogenetic evidence for transmission.Results:In total, 152 HCWs and 542 inpatients were included; 16 HCWs (10.5%) and 19 inpatients (3.5%) tested positive for influenza on 109 study days. Study participants had symptoms of disease on most of the days they tested positive for influenza (83.1% and 91.9% for HCWs and inpatients, respectively). Also, 11(15.5%) of 71 influenza-positive swabs among HCWs and 3 (7.9%) of 38 influenza-positive swabs among inpatients were collected on days without symptoms; 2 (12.5%) of 16 HCWs and 2 (10.5%) of 19 inpatients remained fully asymptomatic. The secondary attack rate was low: we recorded 1 transmission event over 159 contact days (0.6%) that originated from a symptomatic case. No transmission event occurred in 61 monitored days of contacts with asymptomatic influenza-positive individuals.Conclusions:Influenza in acute care is common, and individuals regularly shed influenza virus without harboring symptoms. Nevertheless, both symptomatic and asymptomatic transmission events proved rare. We suggest that healthcare-associated influenza prevention strategies that are based on preseason vaccination and barrier precautions for symptomatic individuals seem to be effective.

This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.

Neutralizing antibodies are considered a key correlate of protection by current SARS-CoV-2 vaccines. The ability of antibody-based therapies, including convalescent plasma, to affect established disease remains to be elucidated. Only few monoclonal therapies and only when used at a very early stage of infection have shown efficacy. Here, we conducted a proof-of-principle study of convalescent plasma therapy in a phase I trial in 30 COVID-19 patients including immunocompromised individuals hospitalized early after onset of symptoms. A comprehensive longitudinal monitoring of the virologic, serologic, and disease status of recipients in conjunction with detailed post-hoc seroprofiling of transfused convalescent plasma, allowed deciphering of parameters on which plasma therapy efficacy depends. Plasma therapy was safe and had a significant effect on viral clearance depending on neutralizing and spike SARS-CoV-2 antibody levels in the supplied convalescent plasma. Endogenous immunity had strong effects on virus control. Lack of endogenous neutralizing activity at baseline was associated with a higher risk of systemic viremia. The onset of endogenous neutralization had a noticeable effect on viral clearance but, importantly, even after adjusting for their endogenous neutralization status recipients benefitted from therapy with high neutralizing antibody containing plasma.In summary, our data demonstrate a clear impact of exogenous antibody therapy on the rapid clearance of viremia in the early stages of infection and provide directions for improved efficacy evaluation of current and future SARS-CoV-2 therapies beyond antibody-based interventions. Incorporating an assessment of the endogenous immune response and its dynamic interplay with viral production is critical for determining therapeutic effects.One Sentence SummaryThis study demonstrates the impact of exogenous antibody therapy by convalescent plasma containing high neutralizing titers on the rapid clearance of viremia in the early stages of SARS-CoV-2 infection.

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 SARS-CoV-2 genomes from Switzerland in 2020 - the 6th largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrast these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland’s border closures de-coupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 - 98% reduction in introductions during Switzerland’s strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Finally, we quantified local transmission dynamics once introductions into Switzerland occurred, using a novel phylodynamic model. We find that transmission slowed 35 – 63% upon outbreak detection in summer 2020, but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.One Sentence SummaryPhylogenetic and phylodynamic methods quantify the drop in case introductions and local transmission with implementation of public health measures.

Objectives To determine the most recent prevalence, transmission patterns and risk factors of transmitted drug-resistance mutations (TDRMs) in Cameroon, we initiated a multicentre study monitoring HIV-1 drug resistance in newly HIV-1-diagnosed individuals using a novel next-generation sequencing (NGS) assay applicable to fingerprick dried blood spot (DBS) samples. Methods Fingerprick DBS samples and questionnaires were collected from 360 newly HIV-1-diagnosed individuals in four hospitals in urban areas in Cameroon in the years 2015-16. We developed an HIV-1 protease and reverse transcriptase drug resistance genotyping assay applicable to DBS samples and HIV-1 genomes of groups M, N and O. The WHO 2009 list of mutations for surveillance of transmitted drug-resistant HIV strains was used to analyse TDRMs. Results Applying our 'DBS-NGS-genotypic resistance test', baseline HIV-1 drug resistance data were successfully obtained from 82.8% (298/360) of newly diagnosed individuals. At nucleotide frequencies >15%, TDRMs to NRTIs were observed in 3.0% (9/298), to NNRTIs in 4.0% (12/298) and to PIs in 1.3% (3/240). The NNRTI mutation K103N was most commonly detected (2.7%). Expanding the analysis to low-abundance TDRMs, i.e. 3%-15%, 12 additional individuals (4.0%) harbouring TDRMs were identified. Having unprotected sex with a known HIV-1-positive person was significantly associated with the transmission of DRMs (adjusted OR 9.6; 95% CI 1.79-51.3). Conclusions The prevalence of transmitted HIV-1 drug resistance is currently low in the study sites in Cameroon. Evidence of some risky sexual behaviours depicts a public health problem with possible implications for the prevention of new HIV-1 infections.

Climate change represents a major challenge for the management of native fish communities in Mediterranean rivers, as reductions in discharge may lead to a decrease in passability through small barriers such as weirs, both in temporary and perennial rivers. Through hydraulic modelling, we investigated how discharges from a large hydropower plant in the Tagus River are expected to affect the passability of native freshwater fish species through a rock weir (Pego, Portugal), equipped with a nature-like fish ramp. We considered not only mean daily discharge values retrieved from nearby gauging stations (1991–2005) for our flow datasets, but also predicted discharge values based on climatic projections (RCP) until the end of the century (2071–2100) for the Tagus River. Results showed that a minimum flow of 3 m3 s−1 may be required to ensure the passability of all species through the ramp and that passability was significantly lower in the RCP scenarios than in the historical scenario. This study suggests that climate change may reduce the passability of native fish species in weirs, meaning that the construction of small barriers in rivers should consider the decreases in discharge predicted from global change scenarios for the suitable management of fish populations.

Numerous riverine ecosystems in Iran are currently suffering due to various human activities, which are directly affecting the physico-chemical conditions of running waters and influencing the aquatic biota. In this study, we chose the cold-water streams of the Southern Caspian Sea Basin in Iran to analyse human pressures and develop a multi-metric fish index for the cold-water streams dominated by brown trout, Salmo trutta in this Basin. To do this, the fish and environmental data were sampled in 67 medium sized streams in the Caspian Mountains. In total, nine fish metrics were calculated. Moreover, 27 criteria describing major anthropogenic pressures for the entire sampling area were used to generate a regional pressure index that accounted for potential effects of multiple human pressures. For the index development, we first defined reference sites and then quantified differences of fish metrics between the reference and impacted sites. The multiple linear regressions were used for describing metric responses to natural environmental differences in the absence of any human pressures. Finally, by testing the ability of each metric for discrimination of impacted and reference sites as well as their sensitivity to a gradient of regional pressure index, the metrics density of brown trout and biomass of sub-adult brown trout explained human pressures best. Our multi-metric fish index performed well in discriminating between reference and impacted sites, giving a significant negative linear response to a gradient of regional pressure index. In general, the development of such an index offers an opportunity to enhance national bio-monitoring programmes in Iran.

Background Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus transmission in living-donor kidney transplantation. Methods Living kidney donors and their corresponding recipients were enrolled at the time of transplantation. Follow-up study visits for recipients were scheduled 4–6 weeks and 1 year thereafter. At each visit, plasma and urine samples were collected and transplant recipients were evaluated for signs of infection or other transplant-related complications. For metagenomic analysis, samples were enriched for viruses, amplified by anchored random polymerase chain reaction (PCR), and sequenced using high-throughput metagenomic sequencing. Viruses detected by sequencing were confirmed using real-time PCR. Results We analyzed a total of 30 living kidney donor and recipient pairs, with a follow-up of at least 1 year. In addition to viruses commonly detected during routine post-transplant virus monitoring, metagenomic sequencing detected JC polyomavirus (JCPyV) in the urine of 7 donors and their corresponding recipients. Phylogenetic analysis confirmed infection with the donor strain in 6 cases, suggesting transmission from the transplant donor to the recipient, despite recipient seropositivity for JCPyV at the time of transplantation. Conclusions Metagenomic sequencing identified frequent transmission of JCPyV from kidney transplant donors to recipients. Considering the high incidence rate, future studies within larger cohorts are needed to define the relevance of JCPyV infection and the donor’s virome for transplant outcomes., Kidney transplantation is inevitably associated with the transmission of viral and microbial pathogens. Using metagenomic virome sequencing, we revealed JC polyomavirus (JCPyV) transmission in 20% of cases, despite seropositivity. The relevance of JCPyV infection in kidney transplantation demands further attention.

Determination of SARS-CoV-2 antibody responses in the context of pre-existing immunity to circulating human coronavirus (HCoV) is critical for understanding protective immunity. Here we perform a multifactorial analysis of SARS-CoV-2 and HCoV antibody responses in pre-pandemic (N = 825) and SARS-CoV-2-infected donors (N = 389) using a custom-designed multiplex ABCORA assay. ABCORA seroprofiling, when combined with computational modeling, enables accurate definition of SARS-CoV-2 seroconversion and prediction of neutralization activity, and reveals intriguing interrelations with HCoV immunity. Specifically, higher HCoV antibody levels in SARS-CoV-2-negative donors suggest that pre-existing HCoV immunity may provide protection against SARS-CoV-2 acquisition. In those infected, higher HCoV activity is associated with elevated SARS-CoV-2 responses, indicating cross-stimulation. Most importantly, HCoV immunity may impact disease severity, as patients with high HCoV reactivity are less likely to require hospitalization. Collectively, our results suggest that HCoV immunity may promote rapid development of SARS-CoV-2-specific immunity, thereby underscoring the importance of exploring cross-protective responses for comprehensive coronavirus prevention., How the immune responses induced by SARS-CoV-2 and human coronavirus (hCoV) crosstalk is still unclear. Here the authors profile the humoral responses of prepandemic and SARS-CoV-2-infected donors to find that higher hCoV antibody titers are associated with SARS-CoV-2 negativity, and with reduced hospitalization in SARS-CoV-2 positive patients.

River systems have undergone a massive transformation since the Anthropocene. The natural properties of river systems have been drastically altered and reshaped, limiting the use of management frameworks, their scientific knowledge base and their ability to provide adequate solutions for current problems and those of the future, such as climate change, biodiversity crisis and increased demands for water resources. To address these challenges, a socioecologically driven research agenda for river systems that complements current approaches is needed and proposed. The implementation of the concepts of social metabolism and the colonisation of natural systems into existing concepts can provide a new basis to analyse the coevolutionary coupling of social systems with ecological and hydrological (i.e., ‘socio-ecohydrological’) systems within rivers. To operationalize this research agenda, we highlight four initial core topics defined as research clusters (RCs) to address specific system properties in an integrative manner. The colonisation of natural systems by social systems is seen as a significant driver of the transformation processes in river systems. These transformation processes are influenced by connectivity (RC 1), which primarily addresses biophysical aspects and governance (RC 2), which focuses on the changes in social systems. The metabolism (RC 3) and vulnerability (RC 4) of the social and natural systems are significant aspects of the coupling of social systems and ecohydrological systems with investments, energy, resources, services and associated risks and impacts. This socio-ecohydrological research agenda complements other recent approaches, such as ‘socio-ecological’, ‘socio-hydrological’ or ‘socio-geomorphological’ systems, by focusing on the coupling of social systems with natural systems in rivers and thus, by viewing the socioeconomic features of river systems as being just as important as their natural characteristics. The proposed research agenda builds on interdisciplinarity and transdisciplinarity and requires the implementation of such programmes into the education of a new generation of river system scientists, managers and engineers who are aware of the transformation processes and the coupling between systems.

Aquaculture is the fastest-growing animal food production sector and is expected to become increasingly important to meet future food demands. As a landlocked country, Austria’s self-sufficiency rate for fish is rather low with 6% in total and 48% for freshwater fish. Therefore, and in order to enable sustainable growth of the sector while avoiding negative impacts on the aquatic ecosystem and other uses, we developed aquaZone, a decision support tool for sustainable trout farm zoning. Thereby, 30 spatially explicit criteria related to environmental prerequisites, land use, legal constraints and water quality/quantity were defined, collected and classified according to their suitability for sustainable trout production. Criteria were combined in an integrative GIS-based modelling approach in order to perform the first countrywide and spatially-explicit zonation of suitable areas for aquaculture in Austria. Thereby, 7920 suitable areas with a mean size of 8.2 ha located in 1129 out of 5011 sub-basins (23%) were identified. The decision tree assigned the highest variable importance to water temperature, slope, agricultural unit, geology, nitrate retention capacity, fish region, minimum flow and pollution risk. These results should support decision making of investors and authorities in order to avoid conflicts and stranded investments at an early stage.

Rivers of the large Alpine valleys constitute iconic ecosystems that are highly threatened by multiple anthropogenic stressors. This stressor mix, however, makes it difficult to develop and refine conservation and restoration strategies. It is, therefore, urgent to acquire more detailed knowledge on the consequences and interactions of prevalent stressors on fish populations, in particular, on indicator species such as the European grayling Thymallus thymallus. Here, we conducted a multi-river, multi-stressor investigation to analyze the population status of grayling. Using explorative decision-tree approaches, we disentangled the main and interaction effects of four prevalent stressor groups: flow modification (i.e., hydropeaking), channelization, fragmentation, and water quality alteration. Moreover, using a modified variant of the bootstrapping method, pooled bootstrapping, we determined the optimal number of characteristics that adequately describe fish population status. In our dataset, hydropeaking had the strongest single effect on grayling populations. Grayling biomass at hydrological control sites was around eight times higher than at sites affected by hydropeaking. The primary parameters for predicting population status were downramping rate and peak amplitude, with critical ranges of 0.2–0.4 cm min-1 and 10–25 cm. In hydropeaking rivers, river morphology and connectivity were the preceding subordinated parameters. Repeating the procedure with pooled bootstrapping datasets strengthened the hypothesis that the identified parameters are most relevant in predicting grayling population status. Hence, hydropeaking mitigation based on ecological thresholds is key to protect and restore already threatened grayling populations. In hydropeaking rivers, high river network connectivity and heterogenous habitat features can dampen the adverse effects of pulsed-flow releases by offering shelter and habitats for all life cycle stages of fish. The presented approach of explorative tree analysis followed by post-hoc tests of identified effects, as well as the pooled bootstrapping method, offers a simple framework for researchers and managers to analyze multi-factorial datasets and draw solid management conclusions info:eu-repo/semantics/publishedVersion

Pathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early viral introductions from Germany, France, and Italy and many recent introductions from Germany and France. Over the summer, we quantify the number of non-traceable infections stemming from introductions, quantify the effective reproductive number, and estimate the degree of undersampling. Our framework can be applied to quantify evolution and epidemiology in other locations or for other pathogens based on genomic data.One Sentence SummaryWe quantify SARS-CoV-2 spread in Switzerland based on genome sequences from our nation-wide sequencing effort.

Austria has a share in three international river basins (Danube, Elbe, Rhine), but by far the most of its territory (> 96%) drains into the Danube. This Austrian territory accounts for 10% of the total area of the Danube River Basin and belongs entirely to the Upper Danube Basins, which extends from the source of the Danube in Germany to Bratislava at Austria’s eastern border to Slovakia. Austria contributes approx. 25% (ca. 50 km³/a ) to the total yearly discharge of the Danube into the Black Sea (ca. 200 km³/a).Human activities have severely altered the Upper Danube catchment, impacting both the main stem and the main pre-alpine tributaries. Due to the Upper Danube’s considerable natural gradient and mountainous character, this part of the Danube is extensively used for hydropower production. Ten large (> 10 MW) hydropower plants are situated along the Austrian Danube (out of a total of 41), and only two Danube stretches can still be characterized as free-flowing (Wachau, Nationalpark Donau-Auen). Besides energy generation, other human activities such as agriculture, shipping, industrialisation, urbanisation and tourism, have been and still are changing the process and system dynamics of the Upper Danube. Climate change is additionally affecting this already heavily impacted River System.The Upper Danube Austria and its pre-alpine network of tributaries is therefore an ideal case study region to investigate the multiple effects of human activities on riverine systems and was chosen as a “supersite” within Danubius-RI, the “International Centre for Advanced Studies on River-Sea Systems”. Danubius-RI is being developed as distributed Research Infrastructures with the goal to support interdisciplinary and integrated research on river-sea systems. DANUBIUS-RI aims to enable and support research addressing the conflicts between society’s demands, environmental change and environmental protection for river -sea systems worldwide and brings together research on freshwaters and the interface to marine waters, drawing on existing research excellence across Europe.The supersite “Upper Danube Austria and its pre-alpine network of tributaries” covers the freshwater spectrum within the river-sea continuum, ranging from alpine and pre-alpine headwater streams along major Danube tributaries to the Danube River, including adjacent floodplains in the Upper Danube catchment. The research focus lies on the interactive effects of climate change, land use pressures, and hydromorphological alterations on the biodiversity, ecological functions, and the ecosystem service provision of streams and rivers in the Upper Danube basin and their role within the catchment.The Supersite “Upper Danube Austria and its pre-alpine network of tributaries” joins forces of eight Austrian research institutions and is led by WasserCluster Lunz and the Institute for Hydrobiology and Aquatic Ecosystem Management (IHG) at the University of Natural Resources and Life Sciences, Vienna (BOKU). Research on sustainable management and restoration of riverine landscapes (WFD, FD, HD, Biodiversity Strategy) in the Upper Danube Catchment is an important contribution to a healthy River-Sea System of the Danube River Basin as a whole.

In ecosystems with high fish species endemicity, such as Mediterranean-type rivers, biogeographical differences among ecoregions present serious obstacles to developing broadly-applicable river bioassessment indices. This impediment has contributed to a serious time-lag in developing EU policy-relevant fish-based indices in the Eastern Mediterranean countries. Here we present the first model-based fish index for the Eastern Mediterranean (the Hellenic Fish Index, HeFI) in an effort to overcome biogeographic differences among the area's biotically heterogeneous rivers. The index is based on modelled reference conditions and employs site-specific electrofished fish samples from an extensive dataset from Greece that covers six freshwater ecoregions, including five transboundary river basins flowing through six countries. Environmental and anthropogenic pressure data were procured from 403 sampled river sites and ecologically-relevant traits were defined for 103 collected fish species. For the development of the index, we first diagnosed least degraded sites forming a calibrated reference site dataset and secondly quantified differences of fish metrics between the reference and impaired sites. Four trait-based fish metrics showed the best ability to discriminate between impaired and reference sites. The index performed well in discriminating anthropogenic pressure classes, giving a significant negative linear response to a gradient of anthropogenic degradation. HeFI successfully assessed both small and large rivers in different freshwater ecoregions. This geographically broad-scale index development shows that key trait-based reference conditions can be produced by a predictive model in remarkably heterogeneous rivers where range-restricted fishes dominate. This index promotes a screening-level bioassessment application that may be further developed and refined with relevant monitoring.

Zusammenfassung Der Unterlauf der Traisen wurde von 2012 bis 2016 im Rahmen eines LIFE+ Projektes auf rund 10 km Länge gänzlich neu gestaltet. Dabei wurde der alte kanalisierte Arm mit mehreren Sohlschwellen als Altwasser bzw. Überwasserkanal erhalten und ein völlig neuer, naturnaher Lauf durch den Auwald angelegt. Das begleitende Monitoring der Fischfauna wird jährlich mittels verschiedener Methoden durchgeführt und zeigt bereits im kurzen Zeitraum seit der Fertigstellung eine schnelle Besiedelung durch eine Vielzahl von Arten und sehr hohe Dichten. Während der alte Lauf keine Laich- und kaum Juvenilhabitate aufwies, sind im neuen Lauf sehr hohe Jungfischzahlen verschiedenster Arten zu beobachten. Vor allem die vollständige Öffnung des Kontinuums zur Donau am Ende der Bauarbeiten führte unmittelbar zu einem Anstieg und dem Nachweis der Reproduktion donautypischer Fischarten.

Cartridge-based multiplex panels covering numerous pathogens offer an advantage of minimal hands-on-time and short time to result to commercial RT-PCR assays. In this study, we evaluated the performance of the ePlex respiratory pathogen panel (RPP) compared to the Fast Track Diagnostics Respiratory pathogens 21 multiplex RT-PCR assay (FTD21) using 400 clinical respiratory samples. Discrepant results were further analysed by a reference nucleic acid amplification testing (NAT) and a composite reference approach was used for final interpretation. Discordant results were observed in 56 targets corresponding to 54 samples. Sensitivities and specificities were 85.5% and 99.9% for the ePlex RPP and 95.8% and 99.7% for the FTD21 system, respectively. Altogether, the ePlex RPP is a valuable tool for the rapid detection of a number of different respiratory viruses with the exception of the coronavirus family (low sensitivity ranging from 50-80%) and samples with a low pathogen load (Ct values >33).

High-head storage hydropower is deemed to be the ideal renewable energy source in Alpine regions to meet the increasing demand for daily peak electrical energy. However, this mode of operation - called hydropeaking - can imply severe hydrological and hydromorphological consequences for river ecosystems, affecting fish populations by e.g. drift and stranding of young life stages. Several fish-stranding experiments using physical models have been performed in the past, but until now very little is known about influences of time of day or gravel bank heterogeneity. We performed experiments during late summer 2013 with juvenile European grayling ( Thymallus thymallus ) (mean length: 53 mm) in a nature-like experimental channel enabling hydropeaking simulations. In the first experiments (n = 21) we observed relative drift and stranding rates for a single hydropeaking event focusing on the effect of time of day on a homogenous gravel bank. The second test series (n = 15) focused on two dewatering potholes installed as potential traps. Additional experiments (n = 6) were done with a reduced downramping rate to gain information about potential mitigation effects on stranding risk. During daytime and decreasing water level, we observed low drift rates of 15% and stranding rates below 5% in dewatering potholes and on homogenous gravel banks. However, in the presence of dewatering potholes, nighttime drift rates were about three times and stranding rates about ten times higher than on the homogenous gravel bank. A lowered downramping rate reduced drift to about a quarter and almost eliminated nocturnal stranding risk. These results might be used to effectively regulate water releases from high-head storage hydropower plants in a more suitable way for sensitive life stages of fish. Reducing the downramping rate or shifting peaks to daytime can reduce negative effects of hydropeaking in consideration of the morphological character of affected rivers.