Impact of Covid-19 on farming systems in Europe through the lens of resilience thinking.

Context: Resilience is the ability to deal with shocks and stresses, including the unknown and previously unimaginable, such as the Covid-19 crisis. Objective: This paper assesses (i) how different farming systems were exposed to the crisis, (ii) which resilience capacities were revealed and (iii) how resilience was enabled or constrained by the farming systems' social and institutional environment. Methods: The 11 farming systems included have been analysed since 2017. This allows a comparison of pre-Covid-19 findings and the Covid-19 crisis. Pre-Covid findings are from the SURE-Farm systematic sustainability and resilience assessment. For Covid-19 a special data collection was carried out during the early stage of lockdowns. Results and conclusions: Our case studies found limited impact of Covid-19 on the production and delivery of food and other agricultural products. This was due to either little exposure or the agile activation of robustness capacities of the farming systems in combination with an enabling institutional environment. Revealed capacities were mainly based on already existing connectedness among farmers and more broadly in value chains. Across cases, the experience of the crisis triggered reflexivity about the operation of the farming systems. Recurring topics were the need for shorter chains, more fairness towards farmers, and less dependence on migrant workers. However, actors in the farming systems and the enabling environment generally focused on the immediate issues and gave little real consideration to long-term implications and challenges. Hence, adaptive or transformative capacities were much less on display than coping capacities. The comparison with pre-Covid findings mostly showed similarities. If challenges, such as shortage of labour, already loomed before, they persisted during the crisis. Furthermore, the eminent role of resilience attributes was confirmed. In cases with high connectedness and diversity we found that these system characteristics contributed significantly to dealing with the crisis. Also the focus on coping capacities was already visible before the crisis. We are not sure yet whether the focus on short-term robustness just reflects the higher visibility and urgency of shocks compared to slow processes that undermine or threaten important system functions, or whether they betray an imbalance in resilience capacities at the expense of adaptability and transformability. Significance: Our analysis indicates that if transformations are required, e.g. to respond to concerns about transnational value chains and future pandemics from zoonosis, the transformative capacity of many farming systems needs to be actively enhanced through an enabling environment.

Using genomics for surveillance of veterinary infectious agents.

Factors such as globalisation, climate change and agricultural intensification can increase the risk of microbial emergence. As a result, there is a growing need for flexible laboratory-based surveillance tools to rapidly identify, characterise and monitor global (re-)emerging diseases. Although many tools are available, novel sequencing technologies have launched a new era in pathogen surveillance. Here, the authors review the potential applications of high-throughput genomic technologies for the surveillance of veterinary pathogens. They focus on the two types of surveillance that will benefit most from these new tools: hazard-specific surveillance (pathogen identification and typing) and early-warning surveillance (pathogen discovery). The paper reviews how the resulting sequencing data can be used to improve diagnosis and concludes by highlighting the major challenges that hinder the routine use of this technology in the veterinary field.

La mondialisation, le changement climatique et l'intensification de la production agricole sont des facteurs pouvant entraîner un risque accru d'émergence d'agents pathogènes infectieux. En conséquence, il est impératif de disposer d'outils de surveillance souples d'emploi au sein du laboratoire pour identifier, caractériser et contrôler rapidement les maladies émergentes et ré-émergentes au niveau mondial. Un grand nombre d'outils sont disponibles, mais ce sont les technologies de séquençage qui ont ouvert une nouvelle ère de la surveillance des agents pathogènes. Les auteurs passent en revue les différentes applications potentielles des technologies génomiques à haut débit dans le domaine de la surveillance des agents pathogènes vétérinaires. Ils examinent plus particulièrement les deux types de surveillance auxquels ces nouveaux outils vont le plus contribuer : la surveillance axée sur les dangers (identification et caractérisation des agents pathogènes) et la surveillance précoce en amont (découverte des agents pathogènes). Après avoir expliqué les perspectives d'amélioration des moyens diagnostiques en ayant recours à l'utilisation des données de séquençage, les auteurs soulignent les principales difficultés qui entravent l'utilisation systématique de cette technologie dans le domaine vétérinaire.

Factores como la mundialización, el cambio climático o la intensificación de la agricultura pueden acrecentar el riesgo de que surjan nuevos patógenos microbianos. De ahí la creciente necesidad de contar con herramientas flexibles de vigilancia en laboratorio, que permitan identificar, caracterizar y vigilar enfermedades (re)emergentes de importancia mundial. Aunque ya existen muchas herramientas, las novedosas técnicas de secuenciación han inaugurado una nueva era en la vigilancia de patógenos. Los autores examinan las posibles aplicaciones de las técnicas genómicas de alto rendimiento en el terreno de la vigilancia de patógenos veterinarios, centrándose en los dos tipos de vigilancia para los que más útiles serán estas nuevas herramientas: la vigilancia en función del riesgo específico (identificación y tipificación de patógenos) y la vigilancia de pronta alerta (descubrimiento de patógenos). Por último, tras explicar cómo se pueden utilizar los datos de secuenciación resultantes para mejorar el diagnóstico, los autores concluyen destacando los principales problemas que dificultan un uso sistemático de estas técnicas en el ámbito de la veterinaria.

Virulence comparison and quantification of horizontal bovine viral diarrhoea virus transmission following experimental infection in calves.

Bovine viral diarrhoea virus (BVDV) causes persistent infections by infecting the fetus of susceptible animals during gestation. These persistently infected (PI) animals are important sources of infection. On the contrary, transiently infected (TI) animals are believed to be less important, but transient infections with a severe BVDV-2 strain can spread explosively. To assess the importance of TI cattle in the epidemiology of BVDV, two experimental infections were performed to determine basic reproduction ratios (R0). In each experiment three calves were infected via intranasal inoculation and housed together with seven susceptible animals. Two strains isolated in Belgium were used, a virulent BVDV-1b and a virulent BVDV-2a field isolate, resulting in an R0 of 0.25 (95% CI 0.01; 1.95) and 0.24 (95% CI 0.01; 2.11), respectively. A PI animal was then introduced to the remaining uninfected animals and produced an R of +∞ (95% CI 1.88; +∞). These results support the suggestion that TI animals, compared to PI animals, contribute only a limited amount to BVDV spread. Additionally, the severe clinical symptoms observed in the field with these isolates could not be reproduced during these experiments, suggesting that other factors besides strain virulence influence the clinical manifestations evoked by BVDV.

Genetic and evolutionary perspectives on genogroup III, genotype 2 bovine noroviruses.

Bovine noroviruses are enteric pathogens that are detected in stool samples from cattle. Five genogroups are currently described in the genus Norovirus (family Caliciviridae), and within the genogroups, sequences are further divided into genotypes according to genetic homology and phylogenetic relationships. In this study, stool specimens from Belgian cattle were screened by RT-PCR. All of the sequences that were detected were phylogenetically related to genogroup III genotype 2 bovine noroviruses, confirming their higher prevalence in comparison with strains from genotype 1. When other sequences from around the world were introduced, phylogenetic inferences allowed neither the determination of phylogenetic lineages over time nor the deduction of topotypes for genotype 2 bovine noroviruses. Three complete genotype 2 bovine norovirus sequences were also compared genetically (Newbury2/1976 /UK, Dumfries/1994/UK and B309/2003/BE). Interestingly, the genetic divergence of the complete genomes of these three strains was relatively low, but a region of the N-terminal protein encoded by ORF1, the hypervariable region of the capsid gene encoded by ORF2, and a region of the minor structural protein encoded by ORF3 seem to be the most exposed to genetic evolution. Bayesian inference also showed that genetic evolution of genogroup III, genotype 2 bovine noroviruses over a 30-year period seemed to be lower than that already reported for noroviruses from the genotypes 3 and 4 in genogroup II.

Composition and diversity of the duodenal mucosa-associated microbiome in children with untreated coeliac disease.

BACKGROUND: Intestinal microbiome may play a role in the pathogenesis of coeliac disease (CD). Studies comparing intestinal microbiome in children with and without CD are contradictory. AIM: To compare the composition and diversity of the duodenal mucosa-associated microbiome in children with untreated CD and control children without CD and to identify specific gut bacteria associated with CD at diagnosis. METHODS: Total microbiome profile in small bowel biopsies of 42 children (21 with untreated CD and 21 age-matched controls) were analyzed by means of IS-pro, a 16S-23S interspacer (IS) region-based profiling method. RESULTS: Both groups showed a similar mucosa-associated microbiome pattern and diversity, with high concentrations of the genera Streptococcus, Lactobacillus, and Clostridium. CONCLUSION: Mucosa-associated duodenal microbiome composition and diversity did not differ between children with untreated CD and control children. Duodenal mucosa-associated bacteria do not seem to play an important role in the pathogenesis of CD.

Complete genome sequence of a novel bovine norovirus: evidence for slow genetic evolution in genogroup III genotype 2 noroviruses.

A new genogroup III genotype 2 bovine norovirus, B309/2003/BE, was entirely sequenced and genetically compared to the original Newbury2/1976/UK strain and to Dumfries/1994/UK, detected in 1976 and 1994, respectively. Interestingly, except in well-defined coding regions (N-terminal protein, 3A-like protease, hypervariable region of the capsid protein, and C-terminal part of the minor structural protein), very low genetic differences were noted between the entire genomes of these three strains along a 30-year-long period. It allowed some hypotheses of hotspots of genetic evolution through a low genetic evolution background in genotype 2 genogroup III bovine noroviruses.

Fatal outbreaks in dogs associated with pantropic canine coronavirus in France and Belgium.

Infection with pantropic canine coronavirus was detected during outbreaks in France and Belgium. This was concurrent in most cases with canine parvovirus 2c. One outbreak was a deadly acute systemic disease with a single pantropic canine coronavirus infection. This is the first report of a fatality associated with pantropic canine coronavirus alone outside Italy.

Linear alkylbenzene sulfonates (LAS) in sewage sludges, soils and sediments: analytical determination and environmental safety considerations.

Linear Alkylbenzenesulphonates (LAS), a major anionic surfactant used in laundry products, can be measured specifically in the environment by instrumental analysis. In addition to a desulphonation-gas chromatography approach, a method based on high performance liquid chromatography has been developed. The main features of the methods are outlined, and LAS concentrations measured in sewage sludge, sediments and sludge amended soils are reported. Knowledge of usage volumes, sewage treatment practices and environmental transport and transformation mechanisms has been used to predict concentrations of LAS. These calculated concentrations were found to agree well with those actually measured in the environment. Both measured and calculated ambient concentrations of LAS are below those which could produce potentially adverse effects in representative surface water, benthic and terrestrial organisms.