Nguyen Van Giap, Kim Hye Kwon, Moon Hyoung Joon, Park Seong Jun, Chung Hee Chun, Choi Min Kyung, Kim A Reum, Park Bong Kyun
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.
Research Evaluation Team, Institute for Basic Science, Daejeon, Republic of Korea.
Infect Genet Evol. 2014 Jan;21:320-8. doi: 10.1016/j.meegid.2013.11.023. Epub 2013 Dec 4.
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.
本研究应用了多种先进的基因分析工具，基于2005年至2013年长期期间开放阅读框5（ORF5）基因的变异，研究韩国1型猪繁殖与呼吸综合征病毒（PRRSV）的进化轨迹和流行病学动态。对大量全球范围的ORF5序列（n = 1127）进行的最大似然系统发育分析强烈表明，没有新的基因类型的1型PRRSV传入韩国猪场，迄今仅识别出两个正在流行的簇（I和II）。通过基于密码子的贝叶斯松弛时钟模型扩展，本研究能够区分同义替换和非同义替换，并证明虽然簇I和簇II之间同义替换的绝对速率（E[S]）相似，但簇间非同义替换的绝对速率（E[N]）存在显著差异。与外部分支相比，发现簇I在内部分支上的E[N]/E[S]比率相对于簇II有所升高。此外，预测在簇II中经历多样化选择的位点比簇I中少得多。利用贝叶斯天际线方法和新颖的贝叶斯出生-死亡天际线图方法，本研究通过揭示每个簇经历独特的流行增长以及揭示有效种群大小与有效繁殖数之间的相关性，深入了解了韩国1型PRRSV的流行病学动态。
