title: Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets.
abstract: 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.
authors: Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy.
authors: Giovanni
authors: G
authors: Franzo
authors: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain.
authors: Martì
authors: M
authors: Cortey
authors: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain.
authors: Joaquim
authors: J
authors: Segalés
authors: MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK.
authors: Joseph
authors: J
authors: Hughes
authors: Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy.
authors: Michele
authors: M
authors: Drigo