Low levels of diversity among genomes of Porcine circovirus type 1 (PCV1) points to differential adaptive selection between Porcine circoviruses

AbstractSeveral features related with the evolutionary patterns among all the PCV1 genomes available at GenBank have been analyzed in the present work (diversity, number of genotypes, recombination, saturation, selection, evolutionary rate). The reported results point to low levels of nucleotide and amino acid diversity, low number of positively selected codons and a slow evolution rate. Compared with the other species of the Circoviridae family, the diversity is the lowest reported. This can be related with the fact that PCV1 is the single non-pathogenic member of the family. Overall, differential levels of adaptive evolution between PCV1 and PCV2 may explain the different diversity levels, and the different evolutionary and selection rates observed

Porcine Circovirus 2 Genotypes, Immunity and Vaccines: Multiple Genotypes but One Single Serotype

Identified for the first time in the 1990s, Porcine circovirus 2 (PCV-2) should not be considered an emerging virus anymore. Nevertheless, many aspects of its biology and epidemiology are still controversial. Particularly, its high evolutionary rate has caused the emergence of several variants and genotypes, alternating on the worldwide proscenium. The biological and practical implications of such heterogenicity are unfortunately largely unknown. The effectiveness of currently available vaccines against new genotypes that have emerged over time has been the topic of an intense debate and often inconclusive or contradictory results between experimental, field, and epidemiological studies have been gathered. The challenge in establishing an effective PCV-2 disease model, the peculiarities in experimental design and settings and the strains involved could justify the observed differences. The present work aims to summarize and critically review the available knowledge on PCV-2 genetic heterogeneity, immunity, and vaccine efficacy, organizing and harmonizing the available data from different sources, shedding light on this complex field and highlighting current knowledge gaps and future perspectives. So far, all vaccines in the market have shown great efficacy in reducing clinical signs associated to diseases caused by PCV-2, independently of the genotype present in the farm. Moreover, experimental data demonstrated the cross-protection of PCV-2a vaccines against the most widespread genotypes (PCV-2a, PCV-2b, and PCV-2d). Therefore, despite the significant number of genotypes described/proposed (PCV-2a to PCV-2i), it seems one single PCV-2 serotype would exist so far.info:eu-repo/semantics/publishedVersio

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

Revisiting Porcine Circovirus Disease Diagnostic Criteria in the Current Porcine Circovirus 2 Epidemiological Context

Current knowledge on porcine circovirus diseases (PCVD) caused by Porcine circovirus 2 (PCV-2) includes the subclinical infection (PCV-2-SI), systemic (PCV-2-SD) and reproductive (PCV-2-RD) diseases, and porcine dermatitis and nephropathy syndrome (PDNS). Criteria to establish the diagnosis of these conditions have not changed over the years; thus, the triad composed by clinical signs, lesions and viral detection in lesions are still the hallmark for PCV-2-SD and PCV-2-RD. In contrast, PCV-2-SI diagnosis is not usually performed since this condition is perceived to be controlled by default through vaccination. PDNS is diagnosed by gross and histopathological findings, and PCV-2 detection is not recognized as a diagnostic criterion. Molecular biology methods as a proxy for PCVD diagnoses have been extensively used in the last decade, although these techniques should be mainly considered as monitoring tools rather than diagnostic ones. What has changed over the years is the epidemiological picture of PCV-2 through the massive use of vaccination, which allowed the decrease in infectious pressure paralleled with a decrease in overall herd immunity. Consequently, the need for establishing the diagnosis of PCVD has increased lately, especially in cases with a PCV-2-SD-like condition despite vaccination. Therefore, the objective of the present review is to update the current knowledge on diagnostic criteria for PCVDs and to contextualize the interest of using molecular biology methods in the overall picture of these diseases within variable epidemiological scenarios of PCV-2 infection

Diagnosis by ruling out other diseases or conditions

Pig production is nowadays highly specialised, and is dominated by large, intensive, indoor-rearing production systems around the world. As farming systems have evolved, so also has our understanding of the factors influencing complex disease scenarios, in which well known and novel pathogens interact with the host, environment, and management and production systems. Such scenarios force farmers and veterinarians to be prepared to deal with the many factors contributing to the disease, and the correct and timely diagnosis of such diseases is the corner-stone of ensuring their control. The Greek word ‘diagnosis’ literally means ‘through thinking’.1 Although strategies to diagnose disease may vary according to different individuals or clinical presentations, adopting systematic approaches to ensure that decisions are focused and objective is imperative.2 Diagnosing a disease usually involves two steps. The first step (descriptive) is to try to answer the basic questions of ‘who has what, where, when, since when, how many and how’; in other words, historical, clinical and epidemiological data must be collected in an objective and reliable manner. The second step (deductive) is to establish a presumptive diagnosis, and formulate hypotheses on the causality of the condition considered, including a likely differential diagnostic list. The deductive step will also help inform the necessary control or prevention strategies. Achieving a correct diagnosis can be difficult even when well-established aetiological agents and risk factors contributing to the disease are known. In this context, periweaning failure-to-thrive syndrome (PFTS) in pigs is …info:eu-repo/semantics/acceptedVersio

Circovirus porcí 3 : un nou virus que infecta al porc

Els circovirus porcins (PCV) són agents vírics que infecten tan porcs domèstics com salvatges i fins el 2015 se'n coneixien 2 tipus: PCV-1 i PCV-2, sent l'últim el patogènic i per tant, el de major rellevància econòmica. Recentment, s'ha descobert el PCV-3, el qual també es considera un agent víric infecciós. En aquest article es destaquen les característiques del virus, la seva epidemiologia, òrgans en els quals s'ha trobat, mètodes de diagnòstic i la seva potencial associació amb malaltia al porc domèstic. En general, s'hi defensa la importància de conèixer l'estat de la qüestió de PCV-3 ja que podria resultar útil a nivell pràctic i també per la comunitat científica.Los circovirus porcinos (PCV) son agentes víricos que infectan cerdos domésticos y salvajes. Hasta 2015 solo se conocían dos tipos: PCV-1 y PCV-2, siendo el último el patogénico y por tanto, el de mayor relevancia económica. Recientemente, se ha descubierto el PCV-3, el cual también es considerado un agente vírico infeccioso. En este artículo se destacan las características del virus, su epidemiología, órganos en los cuales se ha hallado, métodos diagnósticos y su potencial asociación con enfermedad en el cerdo doméstico. En general, se defiende la importancia de conocer el estado de la cuestión de PCV-3 ya que podría resultar útil a nivel práctico y también para la comunidad científica.Porcine circoviruses (PCVs) are small viral agents which infect members of the family Suidade. Until 2015, two species of PCVs were known: PCV-1 and PCV-2, being the last the pathogenic one, hence the most economically relevant. Recently, PCV-3 has been discovered and it is also considered as a new infectious viral agent. In this article, characteristics of the virus, its epidemiology, tissues in which has been found, diagnostic methods and its potential association with disease in the domestic pig are reviewed. In general, it defends the importance of knowing PCV3's state of the art since it could be useful for both the industry and the scientific community

Cistomatosis Apocrina : primera descripción en la especie porcina

El estudio del Servicio de Diagnóstico de Patología Veterinaria (SDPV) de la UAB y el Servicio de Soporte a Mataderos (SESC) de IRTA-CReSA describe por primera vez la cistomatosi apocrina en la especie porcina, una enfermedad de las glándulas sudoríparas apocrinas ya estudiada en gatos y perros, entre otros, a partir de tres casos, en Cataluña. Aunque este estudio expone que la causa de la lesión es la misma, no se ha podido determinar sólo una en general (local o multifocal cutánea o sistémica) por falta de una muestra de análisis más amplia. Sin embargo, el origen congénito es una posibilidad abierta por todos los indicios encontrados.The study by the Veterinary Pathology Diagnostic Service (SDPV) of the UAB and the Slaughterhouse Support Network (SESC) of the IRTA-CReSA for the first time describes apocrine cystomatosis in the porcine species, a disease of the apocrine sweat glands already studied in other animal species such as cats and dogs. Based on three cases in Catalonia, this study states that although the cause of the condition is the same, it has not been possible to determine one single cause in general (local or multifocal cutaneous or systemic) due to the lack of a wider sample analysis. Nonetheless, all signs point to the possibility of a congenital origin

Porcine circovirus 3 (PCV-3) as a causal agent of disease in swine and a proposal of PCV-3 associated disease case definition

Porcine circovirus 3 (PCV-3) was discovered in 2015 using next-generation sequencing (NGS) methods. Since then, the virus has been detected worldwide in pigs displaying several clinical-pathological outcomes as well as in healthy animals. The objective of this review is to critically discuss the evidence existing so far regarding PCV-3 as a swine pathogen. In fact, a significant number of publications claim PCV-3 as a disease causal infectious agent, but very few of them have shown strong evidence of such potential causality. The most convincing proofs of disease association are those that demonstrate a clinical picture linked to multisystemic lymphoplasmacytic to lymphohistiocytic perivascular inflammation and presence of viral nucleic acid within these lesions. Based on these evidence, individual case definitions for PCV-3-reproductive disease and PCV-3-systemic disease are proposed to standardize diagnostic criteria for PCV-3-associated diseases. However, the real frequency of these clinical-pathological conditions linked to the novel virus is unknown, and the most frequent outcome of PCV-3 infection is likely subclinical based on its worlwide distribution.info:eu-repo/semantics/publishedVersio