From trees to landscapes: molecular and spatial insights on the dynamic of swine viruses at different scales

In the pig industry viruses are dynamic and unpredictable players, whose evolution and spread require constant monitoring and surveillance. The fields of viral evolution and epidemiology are intrinsically linked, blending assumptions and insights derived from evolutionary studies and theoretical models with empirical observations from everyday veterinary practice and epidemiological surveys. This thesis examines the genetic and transmission patterns of swine viruses across various scales and swine categories, employing a multidisciplinary approach that combines statistical, molecular, and spatial methods. The different swine viruses examined are functional to study different aspects of viral dynamics, from origin and initial spread, to transmission and evolution across countries, environments and hosts. The manuscripts are organized from multi-country to local Italian regions, guiding the reader through a decreasing geographical scale. The study "Phylodynamic and phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) in Europe: Patterns and determinants" leverages the wide genetic diversity of PRRSV to reconstruct spatial and temporal processes of viral spread between different European countries, assessing factors driving cross-border transmissions. Recognizing the importance of pre-emptive analysis in mitigating potential viral threats, the study "Phylodynamic analysis of current Porcine circovirus 4 sequences: Does the porcine circoviruses evolutionary history repeat itself?" investigates the origins and evolutionary trajectories of PCV-4. Northern Italy's unique landscape, with its mix of intensive and family farms located in a geographically limited but heterogeneous setting, was used to study viral genetic features and link them with epidemiological patterns in different pig populations. The study "Molecular Survey on Porcine Parvoviruses (PPV1-7) and Their Association with Major Pathogens in Reproductive Failure Outbreaks in Northern Italy" examines PPV1-7 prevalence and clinical role in the intensive sector. Porcine circovirus 2 (PCV-2), with its widespread presence and intricate transmission dynamics, served as a model for studying viral spreading and evolution across diverse environments. Two studies, "Into the backyard: Multiple detections of PCV-2e in rural pig farms of Northern Italy. An unexpected ecological niche?" and "D for dominant: porcine circovirus 2d (PCV-2d) prevalence over other genotypes in wild boars and higher viral flows from domestic pigs in Italy," explore PCV-2 genetic diversity in both intensive farms, rural and wild populations, quantifying the contributions of various animal categories to transmission networks. A similar study was conducted for PCV-3, “Wilder than intense: higher frequency, variability, and viral flows of porcine circovirus 3 in wild boars and rural farms compared to intensive ones in northern Italy", which investigates PCV-3 strains circulating in different pig populations and their contact networks. Given the viral exchanges between commercial pigs and wild boars and the spread of African swine fever virus (ASFV) in Northern Italy, detailed data on wild boar distribution and movement became crucial. The study " Habitat suitability mapping and landscape connectivity analysis to predict African swine fever spread in wild boar population: a focus on Northern Italy" applies species distribution models and connectivity analysis to map local suitable habitats and main corridors for wild boar dispersal. The findings provided in this Ph.D. dissertation contribute to inform disease control strategies and biosecurity measures in diverse pig production and wildlife management contexts, to improve animal health and livestock management in response to evolving viral threats.