Abstract
Classical phylogenetic methods such as neighbor-joining or maximum likelihood trees, provide limited inferences about the evolution of important pathogens and ignore important evolutionary parameters and uncertainties, which in turn limits decision making related to surveillance, control, and prevention resources. Bayesian phylodynamic models have recently been used to test research hypotheses related to evolution of infectious agents. However, few studies have attempted to model the evolutionary dynamics of porcine reproductive and respiratory syndrome virus (PRRSV) and, to the authors' knowledge, no attempt has been made to use large volumes of routinely collected data, sometimes referred to as big data, in the context of animal disease surveillance. The objective of this study was to explore and discuss the applications of Bayesian phylodynamic methods for modeling the evolution and spread of a notable 1-7-4 RFLP-type PRRSV between 2014 and 2015. A convenience sample of 288 ORF5 sequences was collected from 5 swine production systems in the United States between September 2003 and March 2015. Using coalescence and discrete trait phylodynamic models, we were able to infer population growth and demographic history of the virus, identified the most likely ancestral system (root state posterior probability = 0.95) and revealed significant dispersal routes (Bayes factor > 6) of viral exchange among systems. Results indicate that currently circulating viruses are evolving rapidly, and show a higher level of relative genetic diversity over time, when compared to earlier relatives. Biological soundness of model results is supported by the finding that sow farms were responsible for PRRSV spread within the systems. Such results cannot be obtained by traditional phylogenetic methods, and therefore, our results provide a methodological framework for molecular epidemiological modeling of new PRRSV outbreaks and demonstrate the prospects of phylodynamic models to inform decision-making processes for routine surveillance and, ultimately, to support prevention and control of food animal disease at local and regional scales.
Highlights
Porcine Reproductive and Respiratory Syndrome (PRRS) is, arguably, the most important swine disease in the United States due to the continuous emergence of new outbreaks that cause severe economic losses (Neumann et al, 2005; Holtkamp et al, 2013)
Our study provides quantitative estimates of mechanisms that lead to the emergence, spread and maintenance of the restriction fragment length polymorphism (RFLP) 1-7-4 porcine reproductive and respiratory syndrome virus (PRRSV) family throughout the U.S It further illustrates the prospects of the Bayesian approach in improving the decision making process related to reducing the impact of PRRS on the national swine industry with the long-term goal of successful control and prevention
Complete PRRS ORF5 nucleotide sequences (n = 6774) from field isolates obtained between January 1998 and April 2015 were provided by five independent swine production systems in the U.S with metadata on the date of isolation, system code (A, B, C, D, and E) and type of farm from which the sequences were isolated (Table S1)
Summary
Porcine Reproductive and Respiratory Syndrome (PRRS) is, arguably, the most important swine disease in the United States due to the continuous emergence of new outbreaks that cause severe economic losses (Neumann et al, 2005; Holtkamp et al, 2013). PRRSV is a singlestranded, enveloped RNA virus that belongs to the Arteriviridae family (Benfield et al, 1992). ORF5 encodes a major envelope surface glycoprotein (GP5) with high genetic diversity, has been widely used in molecular epidemiology studies of PRRSV (Kapur et al, 1996; Shi et al, 2010; Brar et al, 2015). Emerging PRRSV strains are capable of spreading over long distances, referred to as distance-independent dispersal, as a result of aerosol transmission, animal movements, and use or movement of contaminated semen, equipment, or trucks (Shi et al, 2010, 2013). Intensifying efforts toward designing effective and efficient surveillance programs, with the long-term goal of eliminating the disease, must be prioritized to minimize the current impact of the PRRSV on the US swine industry (Perez et al, 2015)
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