title: ORF5-based evolutionary and epidemiological dynamics of the type 1 porcine reproductive and respiratory syndrome virus circulating in Korea.
abstract: This study applied a number of advanced genetic analysis tools to investigate the evolutionary trajectories and epidemiological dynamics of Korean type 1 PRRSV based on variations in the ORF5 gene over a long-term period from 2005 to 2013. Maximum likelihood phylogenetic analysis performed on large, worldwide ORF5 sequences (n=1127) strongly suggested no further introduction of genetically novel type 1 PRRSV into Korean pig farms, with the identification of only two clusters (I and II) in circulation to date. Using a codon-based extension of the Bayesian relaxed clock model, this study was able to distinguish between synonymous and non-synonymous substitutions and demonstrated that, while the absolute rates of synonymous substitution (E[S]) were similar between clusters I and II, the absolute rate of non-synonymous substitution (E[N]) was significantly different between the clusters. Cluster I was found to have an elevated E[N]/E[S] ratio relative to cluster II on the internal branches, compared to the external branches. Additionally, many fewer sites were predicted under diversifying selection in cluster II than in cluster I. Utilizing the Bayesian skyride method and the novel Bayesian birth-death skyline plot method, this study provided insights into the epidemiological dynamics of type 1 PRRSV in Korea by revealing that each cluster experienced a unique epidemic growth and by uncovering correlations between the effective population size and effective reproductive number.
authors: Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea; Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Hanoi University of Agriculture, Hanoi, Viet Nam.
authors: Van Giap
authors: VG
authors: Nguyen
authors: Research Evaluation Team, Institute for Basic Science, Daejeon, Republic of Korea.
authors: Hye Kwon
authors: HK
authors: Kim
authors: Research Unit, Green Cross Veterinary Products, Yongin, Republic of Korea.
authors: Hyoung Joon
authors: HJ
authors: Moon
authors: Viral Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors: Seong Jun
authors: SJ
authors: Park
authors: Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea.
authors: Hee Chun
authors: HC
authors: Chung
authors: Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea.
authors: Min Kyung
authors: MK
authors: Choi
authors: Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea.
authors: A Reum
authors: AR
authors: Kim
authors: Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea. Electronic address: parkx026@snu.ac.kr.
authors: Bong Kyun
authors: BK
authors: Park
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D001499:Bayes Theorem; D019143:Evolution, Molecular; D059645:Mutation Rate; D016366:Open Reading Frames; D010802:Phylogeny; D019318:Porcine Reproductive and Respiratory Syndrome / Q000453:epidemiology / Q000821:virology*; D019316:Porcine respiratory and reproductive syndrome virus / Q000145:classification* / Q000235:genetics*; D012367:RNA, Viral; D056910:Republic of Korea / Q000453:epidemiology; D013552:Swine
chemical_list: D012367:RNA, Viral
keywords: Epidemiological dynamics; Evolutionary dynamics; Korean type 1 PRRSV