The evolutionary history of hepaciviruses

In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.

Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.

[Repetitive inappropriate sexual behaviour as a symptom of agitated depression: catatonic stereotypy?]

Catatonia is a psychomotor syndrome characterised by multiple symptoms like stereotypies - repetitive, abnormally frequent, non-goal-directed movements. A problem is the lack of unanimity regarding the number of symptoms needed for diagnosis. We describe repetitive inappropriate sexual behaviour in a patient with bipolar depression and excited catatonia with Bush-Francis Catatonia Rating Scale score of 12. Electroconvulsive therapy resulted in disappearance of catatonia and inappropriate sexual behaviour and remission of depression. A recurrent episode with similar inappropriate sexual behaviour was successfully treated with electroconvulsive therapy. We interpreted the repetitive inappropriate sexual behaviour as a catatonic stereotypy. Similar stereotypies are reported in children with autism. Tics and self-injury in patients with autism are described as a stereotypy within catatonia. The agitated depression is another possible diagnosis with the repetitive inappropriate sexual behaviour as an example of psychomotor agitation. More research is needed towards repetitive inappropriate sexual behaviour as a possible stereotypy within catatonia.

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a large collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, eighty were found positive for the presence of hepaciviruses in twenty-nine different host species. We, here, report fifty-six novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages. Furthermore, we provide strong evidence for hepacivirus co-infections in rodents, which were exclusively found in four sampled species of brush-furred mice. We also detect evidence of recombination within specific host lineages. Our study expands the available hepacivirus genomic data and contributes insights into the relatively deep evolutionary history of these pathogens in rodents. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics.

Assessment of estrogenic compounds in paperboard for dry food packaging with the ERE-CALUX bioassay

Paperboard used as packaging, a non-inert material, can transfer chemicals into food. Over the years, endocrine disrupting compounds (EDCs), such as NonylPhenols (NPs), BisPhenol A (BPA) and phthalates have been shown to migrate from packaging materials into food. Due to chronic exposure and mixture effects of these EDCs, they could cause health effects even at very low doses. Many EDCs are still unknown and many more are still unregulated. The ERE-CALUX bioassay was used as a bioanalytical tool to investigate estrogenic activities of paperboard food packaging and its characteristics, including recycling rate and printing ink. A "worst case" scenario with full extraction is compared to a dry food migration experiment. By measuring an overall estrogenic activity, known and unknown estrogenic chemicals and mixture effects are taken into account and the data are compared to molecule specific analysis. Estrogenic activities ranged from 682 ± 66 pg E2 eq./dm2 to 3250 ± 400 pg E2 eq./dm2 for "worst case" extraction and from 347 ± 30 pg E2 eq./dm2 to 1350 ± 70 pg E2 eq./dm2 for migration experiments. A two-factor ANOVA revealed a relationship between estrogenic activity and the recycling rate of the paperboard, but no significant difference with printing ink was observed for these paperboard samples. Bis(2-ethylhexyl)phthalate (DEHP), dibutyl phthalate (DBP), butyl benzyl phthalate (BBP) and 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH) were determined in all extraction and migrations experiment samples. A Spearman rank correlation analysis showed a relationship between the estrogenic activity and the total phthalates as well as with each compound individually.

Endocrine activity in an urban river system and the biodegradation of estrogen-like endocrine disrupting chemicals through a bio-analytical approach using DRE- and ERE-CALUX bioassays

The Zenne River, crossing the Brussels region (Belgium) is an extremely urbanized river impacted by both domestic and industrial effluents. The objective of this study was to monitor the occurrence and activity of Endocrine Active Substances (EAS) in river water and sediments in the framework of the Environmental Quality Standards Directive (2008/105/EC and 2013/39/EU). Activities were determined using Estrogen and Dioxin Responsive Elements (ERE and DRE) Chemical Activated Luciferase Gene Expression (CALUX) bioassays. A potential contamination source of estrogen active compounds was identified in the river at an industrial area downstream from Brussels with a peak value of 938 pg E2 eq./L water (above the EQS of 0.4 ng/L) and 195 pg E2 eq./g sediment. Estrogens are more abundantly present in the sediments than in the dissolved phase. Principal Component Analysis (PCA) showed high correlations between Suspended Particulate Matter (SPM), Particulate (POC) and Dissolved Organic Carbon (DOC) and estrogenic EAS. The dioxin fractions comply with previous data and all were above the United States Environmental Protection Agency (US EPA) low-level risk, with one (42 pg TCDD eq./g sediment) exceeding the high-level risk value for mammals. The self-purifying ability of the Zenne River regarding estrogens was examined with an in vitro biodegradation experiment using the bacterial community naturally present in the river. Hill coefficient and EC₅₀ values (Effective Concentration at 50%) revealed a process of biodegradation in particulate and dissolved phase. The estrogenic activity was decreased by 80%, demonstrating the ability of self-purification of estrogenic compounds in the Zenne River.

Experience with phosphorus removal and sludge handling and disposal in Flanders

The way excess sludge must be disposed of is a key factor in the choice of the appropriate phosphorus removal technique at municipal wastewater treatment plants. In Europe the ongoing trend of tightening the sludge spreading rules called for a serious reduction of its agricultural utilisation and the expansion of the (co-)incineration disposal route, which led to a shift towards more sophisticated sludge handling techniques. This paper illustrates the impact of different sludge handling techniques on the performance of chemical and enhanced biological phosphorus removal at municipal WWTPs. The main conclusion is that although enhanced biological phosphorus removal is particularly sensitive to the problem of return liquors from sludge treatment processes indirect dewatering and anaerobic stabilisation cannot be discarded altogether when considering its implementation.

A new one-dimensional clarifier model--verification using full-scale experimental data

A new one-dimensional clarifier model was developed, including components of existing models, and extended with a height-dependent cross-sectional area and two flowrate-dependent dispersion coefficients. This model is evaluated using data from a detailed one-month measuring campaign on a full-scale wastewater treatment plant. The data included hourly sludge concentration profile, sludge heights at 10 minute intervals, sludge concentrations in inlet, effluent and recycle flows and regular settling properties characterised by batch setting tests. Due to the poor quality concentration measurements at the surface of the clarifier, the model was not calibrated to perform well in concentration predictions at this surface. However, excellent descriptive capabilities were obtained for sludge profiles and blanket level. The Cho et al. setting velocity function was found to be significantly better in terms of description capability than the more traditional Vesilind function.

Renovation of the WWTP hove

The provision of reliable treatment has always been a priority in sanitary engineering. However, there is an ever-increasing pressure to meet desirable standards at reduced costs. This paper sets out a methodology to enhance the likelihood of a satisfactory allocation of the resources while providing reliable treatment. The procedure was gradually developed to optimise the massive capital investment of the Flemish Government to comply with the effluent standards set in the EU Directive 271/91. The methodology makes an extended use of dynamic modelling. To facilitate the identification and estimation of the uncertainty, a probabilistic Monte Carlo engine is coupled to the dynamic models. In doing so this approach provides a way of explicitly incorporating uncertainty and variability in the process analysis. The procedure is examined in an upgrade of a conventional WWTP towards stricter effluent norms on nutrients. The results suggest that the procedure can support the decision-making process under uncertainty conditions and enhance the likelihood of meeting effluent standards not entailing above-normal capital investments. The analysis led to reducing the capital investment by 43%, producing savings of more than 1.2 million Euros.