Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets

Since its first description, PCV2 has emerged as one of the most economically relevant diseases for the swine industry. Despite the introduction of vaccines effective in controlling clinical syndromes, PCV2 spread was not prevented and some potential evidences of vaccine immuno escape have recently been reported (“Complete genome sequence of a novel porcine circovirus type 2b variant present in cases of vaccine failures in the United States” (Xiao and Halbur, 2012) [1], “Genetic and antigenic characterization of a newly emerging porcine circovirus type 2b mutant first isolated in cases of vaccine failure in Korea” (Seo et al., 2014) [2]). In this article, we used a collection of PCV2 full genomes, provided in the present manuscript, and several phylogentic, phylodynamic and bioinformatic methods to investigate different aspects of PCV2 epidemiology, history and evolution (more thoroughly described in “PHYLODYNAMIC ANALYSIS of PORCINE CIRCOVIRUS TYPE 2 REVEALS GLOBAL WAVES of EMERGING GENOTYPES and the CIRCULATION of RECOMBINANT FORMS”[3]). The methodological approaches used to consistently detect recombiantion events and estimate population dymanics and spreading patterns of rapidly evolving ssDNA viruses are herein reported. Programs used are described and original scripts have been provided. Ensembled databases used are also made available. These consist of a broad collection of complete genome sequences (i.e. 843 sequences; 63 complete genomes of PCV2a, 310 of PCV2b, 4 of PCV2c, 217 of PCV2d, 64 of CRF01, 140 of CRF02 and 45 of CRF03.), divided in differnt ORF (i.e. ORF1, ORF2 and intergenic regions), of PCV2 genotypes and major Circulating Recombinat Forms (CRF) properly annotated with respective collection data and country. Globally, all of these data can be used as a starting point for further studies and for classification purpose

Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms

Since the first description of Porcine circovirus type 2 (PCV2), four genotypes (PCV2a, PCV2b, PCV2c and PCV2d) have been recognized and three of them have been shown to exhibit worldwide distribution. Here, the population dynamics of PCV2 has been reconstructed over time and the factors that have shaped its evolution determined. The results obtained confirm that PCV2 originated approximately at the beginning of the 20th century. The most recent common ancestor of genotypes PCV2a, PCV2b, PCV2c and PCV2d circulated in the 1950s, 1980s, 1960s and 1950s, respectively, and the population sizes of the individual genotypes remained low until the mid 90s, coinciding with the identification of PCV2 as a major pathogen of the pig industry. The population dynamics of PCV2 have been characterized by the appearance of periodic waves of distinct genotypes that, after an initial rise, spread following major swine commercial routes and were then superseded by subsequent emerging genotypes. Various recombinant forms displayed comparable population dynamics and spreading routes to those of major genotypes, suggesting that recombinant strains are able to compete with parental ones. The capsid gene is subjected to immune selection and evasion of the host immune response seems to be a major force for the emergence and spread of new genotypes. In contrast, the evolution of other genes appears to be constrained by the particular genomic organization of PCV2. In summary, obtained results suggest that changes in farming strategies, international trade, host population immunity, recombination and the constraints imposed by genome organization have all played a major role in the evolutionary dynamics of PCV2

Porcine circovirus type 2 (PCV2) evolution before and after the vaccination introduction: A large scale epidemiological study

open4noSince their commercialization, vaccines against Porcine circovirus type 2 (PCV2) have been the cornerstone control strategy. Nevertheless, the periodic emergence of new genotype waves and the recent reports of vaccine failure outbreaks have raised the question if widespread vaccination strategies could have driven viral evolution and affected different genotype fitness. To investigate this issue an in-deep analysis, based on a bioinformatics and biostatistics approach, has been implemented. ORF2 sequences from vaccinated and non-vaccinated populations (i.e. domestic pigs before and after vaccine introduction and wild boars) were considered. The action of selective forces on PCV2 strains has been analyzed and compared among groups. Remarkable differences were found in the selective forces acting on viral populations circulating in different “immune environments”. Particularly for PCV2a, a directional selection promoting a change in the viral capsid away from the vaccine specific antigenic determinants has been detected after vaccine introduction. Involved amino acids were previously reported to be part of viral epitopes whose variability is responsible of immune escape. Our findings support a change in PCV2 evolutionary pattern after widespread vaccination introduction and stress once more the compulsoriness of a continuous monitoring of PCV2 epidemiology to promptly act in response to the emergence of possible vaccine-escaping mutants.openFranzo, Giovanni; Tucciarone, Claudia Maria; Cecchinato, Mattia; Drigo, MicheleFranzo, Giovanni; Tucciarone, CLAUDIA MARIA; Cecchinato, Mattia; Drigo, Michel

Lack of Porcine circovirus 4 Genome Detection in Pig Samples from Italy and Spain

The genus Circovirus includes several species and mostly causes asymptomatic infections. Porcine circovirus 2 (PCV-2) and, with increasing evidence, Porcine circovirus 3 (PCV-3), have been associated with different clinical conditions all over the world. In 2019, a new porcine circovirus (PCV-4) was identified from diseased animals in China. Because of the lessons learned from PCV-2 and PCV-3, it appears mandatory to investigate the actual distribution of this new virus and its potential association with clinical outcomes. To this purpose, an exploratory study to detect PCV-4 by molecular methods was performed in Italy and Spain by testing more than 300 samples of different types (serum and tissues), collected from both healthy and diseased pigs and wild boar as well. All samples, independently from the country, type, health status and host, tested PCV-4 negative. Therefore, no evidence of PCV-4 presence was found in Italy and Spain through this exploratory study. Considering the dense pig trade among European countries, its presence in the continent can similarly be considered unlikely. The reasons behind the restricted PCV-4 distribution compared to other porcine circoviruses will require further investigations. Careful surveillance might nevertheless be important since prompt recognition of PCV-4 would allow the implementation of effective countermeasures to prevent its spreading and potential economic losses.info:eu-repo/semantics/publishedVersio

Evaluation of White Striping prevalence and predisposing factors in broilers at slaughter

White striping ( WS: ) is an alteration of breast and thigh muscles of broiler chickens characterized by the presence of white striations parallel to the direction of muscle fibers. This study was performed to evaluate the prevalence and the predisposing factors to WS in commercial broilers of different weight reared in northern Italy. Fifty seven broiler flocks, including animals of medium- and heavy-weight, were grossly evaluated at slaughter for the presence of WS. For each flock, breeding data (mean BW at slaughter, ADG, sex, color of skin and fat, genetic line, age, antibiotic treatment, and prevalence of deep pectoral myopathy) were collected and statistically analyzed to assess their correlation with WS. Histology of breast fillets affected by different grades of WS was performed to evaluate potential differences between medium- and heavy-weight broilers. The overall prevalence of WS in medium- and heavy-weight broilers (mean BW 2.59 \ub1 0.13 kg and 3.64 \ub1 0.34 kg, respectively) was 70.2 \ub1 7.9% and 82.51 \ub1 8.5%, respectively, while the percentage of severe WS was 13.3 \ub1 7.1% and 25.7 \ub1 12.8%, respectively. A strong correlation was found between presence of WS, BW at slaughter, and ADG (Pearson correlation = 0.69, P < 0.01; Pearson correlation = 0.67, P < 0.01). WS also closely correlated with the prevalence of deep pectoral myopathy (Spearman's Rho slaughterhouse 1 = 0.74, Spearman's Rho slaughterhouse 2 = 0.51, P < 0.01). No correlation was found between genetics or sanitary status of the flock and WS. Histology confirmed that breasts with WS lesions were affected by a polyphasic degenerative and necrotizing myopathy, and that the lesions, as expected, were more severe in heavy-weight broilers. In conclusion, WS is a major concern in commercial meat poultry reared in Italy, affecting more severely heavier broilers, and it is mainly related to the BW and ADG of animals

Evolution of infectious bronchitis virus in the field after homologous vaccination introduction

International audienceAbstractDespite the fact that vaccine resistance has been typically considered a rare phenomenon, some episodes of vaccine failure have been reported with increasing frequency in intensively-raised livestock. Infectious bronchitis virus (IBV) is a widespread avian coronavirus, whose control relies mainly on extensive vaccine administration. Unfortunately, the continuous emergence of new vaccine-immunity escaping variants prompts the development of new vaccines. In the present work, a molecular epidemiology study was performed to evaluate the potential role of homologous vaccination in driving IBV evolution. This was undertaken by assessing IBV viral RNA sequences from the ORF encoding the S1 portion of viral surface glycoprotein (S) before and after the introduction of a new live vaccine on broiler farms in northern-Italy. The results of several biostatistics analyses consistently demonstrate the presence of a higher pressure in the post-vaccination period. Natural selection was detected essentially on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. This evidence strongly supports the action of vaccine-induced immunity in conditioning viral evolution, potentially leading to the emergence of new vaccine-escape variants. The great plasticity of rapidly-evolving RNA-viruses in response to human intervention, which extends beyond the poultry industry, is demonstrated, claiming further attention due to their relevance for animal and especially human health

Epidemiologic-economic models and the One Health paradigm: echinococcosis and leishmaniasis, case studies in Veneto region, Northeastern Italy

Epidemiology and health economics have systemic interdependencies. The identification of the economic outcomes of any disease is operated by overlapping its epidemiology with the economic functions of the impacted entities. This communication presents two epidemiologic-economic models designed to evaluate the economic burden of cystic echinococcosis and leishmaniasis in Veneto (Northeastern Italy). Following a One Health approach, the research integrates expertise from different disciplines and institutions and fulfilled its first stage by defining the relevant cost categories and the data collection strategy for the two diseases in the study area. The two models identify the relevant epidemiological factors and the economic outcomes of infections in both animals and humans. The results, visualized in flow charts indicating the types of costs associated with these zoonoses, will guide data collection and the epidemiologic and economic assessment in the next research stages. This experience shows that One Health methods, although still innovative or unusual in many scientific and professional contexts, can be applied by using relatively limited resources and already available professional skills

Fibrinolysis in Dogs with Intracavitary Effusion: A Review

Physiologic fibrinolysis is a localized process in which stable fibrin strands are broken down by plasmin in response to thrombosis. Plasmin activation can also take place separately from the coagulation process, resulting in pathologic fibrinolysis. When plasmin activation exceeds the neutralizing capacity of plasmin inhibitors, severe bleeding can potentially take place. Although the processes which regulate coagulation and fibrinolysis in the blood are well known, it is less clear as to what extent the same processes take place in the body cavities and whether they influence systemic hemostasis. The results of the studies herein cited demonstrate that coagulation followed by fibrinogenolytic/fibrinolytic activity takes place in all kinds of canine ascitic and pleural fluids. Moreover, systemic clotting abnormalities suggesting primary fibrinolysis/primary hyperfibrinolysis (i.e., elevated plasma fibrin/fibrinogen degradation products [FDPs] and normal D-dimer concentrations with fibrinogen concentrations ≤ 100 mg/dL or above this cut-off, respectively) occur in dogs with intracavitary effusion. Enhanced fibrinolytic activity in dogs with intracavitary effusion can also be detected using rotational thromboelastometry (ROTEM), although the degree of agreement between ROTEM and FDPs, D-dimer and fibrinogen concentrations is poor. Finally, contrary to the thrombotic events commonly documented in some humans and cats with cardiac diseases, bleeding tendencies due to primary fibrinolysis/primary hyperfibrinolysis have been documented in dogs with cardiogenic ascites

Development and validation of direct PCR and quantitative PCR assays for the rapid, sensitive, and economical detection of porcine circovirus 3

Since the identification of species Porcine circovirus 2, the relevance of genus Circovirus has increased given its impact on the swine industry. A new species (Porcine circovirus 3, PCV-3) has been detected in association with various clinical conditions. Consequently, there is an urgent need for reliable and widely accessible tests for both routine diagnostic and research purposes. We developed a direct PCR (requiring no DNA extraction) and a quantitative (q)PCR targeting the conserved rep gene to detect the PCV-3 genome. Test performance was assessed by testing 120 field samples within different matrices. Both methods were sensitive (detection of 10 viral genome/µL), specific, and repeatable. The substantially perfect agreement between the 2 assays strongly supports their high sensitivity and specificity. The low cost and short processing time of the direct PCR protocol, together with the reliable quantitative results provided by qPCR, support the establishment of common testing guidelines.info:eu-repo/semantics/acceptedVersio

Towards improved, cost-effective surveillance of Ixodes ricinus ticks and associated pathogens using species distribution modelling

Various ticks exist in the temperate hilly and pre-alpine areas of Northern Italy, where Ixodes ricinus is the more important. In this area different tick-borne pathogen monitoring projects have recently been implemented; we present here the results of a twoyear field survey of ticks and associated pathogens, conducted 2009-2010 in North-eastern Italy. The cost-effectiveness of different sampling strategies, hypothesized a posteriori based on two sub-sets of data, were compared and analysed. The same two subsets were also used to develop models of habitat suitability, using a maximum entropy algorithm based on remotely sensed data. Comparison of the two strategies (in terms of number of ticks collected, rates of pathogen detection and model accuracy) indicated that monitoring at many temporary sites was more cost-effective than monthly samplings at a few permanent sites. The two model predictions were similar and provided a greater understanding of ecological requirements of I. ricinus in the study area. Dense vegetation cover, as measured by the normalized difference vegetation index, was identified as a good predictor of tick presence, whereas high summer temperatures appeared to be a limiting factor. The study suggests that it is possible to obtain realistic results (in terms of pathogens detection and development of habitat suitability maps) with a relatively limited sampling effort and a wellplanned monitoring strategy