Abstract
The US swine industry has been impaired over the last 25 years by the far-reaching financial losses caused by the porcine reproductive and respiratory syndrome (PRRS). Here, we explored the relations between the spatial risk of PRRS outbreaks and its phylodynamic history in the U.S during 1998–2016 using ORF5 sequences collected from swine farms in the Midwest region. We used maximum entropy and Bayesian phylodynamic models to generate risk maps for PRRS outbreaks and reconstructed the evolutionary history of three selected phylogenetic clades (A, B and C). High-risk areas for PRRS were best-predicted by pig density and climate seasonality and included Minnesota, Iowa and South Dakota. Phylodynamic models demonstrated that the geographical spread of the three clades followed a heterogeneous spatial diffusion process. Furthermore, PRRS viruses were characterized by typical seasonality in their population size. However, endemic strains were characterized by a substantially slower population growth and evolutionary rates, as well as smaller spatial dispersal rates when compared to emerging strains. We demonstrated the prospects of combining inferences derived from two unique analytical methods to inform decisions related to risk-based interventions of an important pathogen affecting one of the largest food animal industries in the world.
Highlights
Are commonly characterized by annual seasonal increases in the number of observed outbreaks, with incidence of cases being low during spring and summer and high during fall and winter[15]
This study represents the first attempt to explore the potential of combining novel analytical methods including maximum entropy and Bayesian phylodynamic modeling to provide insights into the spatial and evolutionary epidemiology of viral diseases, using PRRSv in the U.S a working example
We demonstrated that pig density and climate seasonality were important factors for maintaining endemic PRRSv strains, and, they likely shaped genetic diversity over time as well as spatiotemporal diffusion patterns
Summary
Are commonly characterized by annual seasonal increases in the number of observed outbreaks, with incidence of cases being low during spring and summer and high during fall and winter[15]. Past PRRSv evolutionary epidemiology studies either focused on establishing associations between phylogenetics and outbreak characteristics in different geographical levels[7, 27,28,29], or discriminating between endemic and emerging strains to infer about their spread and maintenance within affected swine populations[7, 10, 30,31,32] Those studies relied on traditional phylogenetic methods to either genotype new viruses using the restriction fragment length polymorphism (RFLP) patterns, or assess correlations between the similarities of nucleotide sequences and spatio-temporal outbreak dynamics[33]. The application of more robust analytical pipelines that specializes in characterizing spatiotemporal dynamics of PRRSv strains can be of great value for the swine industry by improving surveillance, and subsequently control and prevention measures
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
