| 王璐琦,熊海燕,王伟炳.系统发育研究在传染病分子流行病学中的应用[J].Chinese journal of Epidemiology,2022,43(2):282-285 |
| 系统发育研究在传染病分子流行病学中的应用 |
| Application of phylogenetic analysis in the molecular epidemiological study of infectious diseases |
| Received:July 01, 2021 |
| DOI：10.3760/cma.j.cn112338-20210701-00515 |
| KeyWord: 传染病 分子流行病学 系统发育 |
| English Key Word: Infectious disease Molecular epidemiology Phylogenetics |
| FundProject:国家自然科学基金（81673233）；上海市公共卫生体系建设三年行动计划（GWV-10.1-XK16） |
| Author Name | Affiliation | E-mail | | Wang Luqi | Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China | | | Xiong Haiyan | Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China | haiyanxiong@fudan.edu.cn | | Wang Weibing | Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China | |
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| Abstract: |
| 测序技术的快速发展导致病原体基因数据急剧增加，将这些数据与系统发育分析方法相结合，可用于阐述病原体的起源和进化、流行过程中的时空分布、参数变化以及抗原、毒力、耐药性等表型特征变化规律、病原体传播趋势预测等。本文简述了系统发育研究的目的和系统发育树的构建方法，阐述了距离法、最大简约法、最大似然法、贝叶斯法等常用系统发育重建方法的优缺点和适用范围，并重点回顾了系统动力学和系统地理学方法在国内外研究中的应用及主要流行病学参数的估计方法，通过综述也发现，病毒基因组数据建立的带有时间和地点注释的系统发育树越来越多地用于传染病疫情暴发调查和常规监测。 |
| English Abstract: |
| The rapid development of sequencing technology brings the explosive growth of pathogen genetic data. The combination of genomic data and phylogenetic method is being used to elaborate the origin and evolution of pathogens, the time and space distribution and parameter changes in the prevalence process, and how phenotypes like antigen, virulence, and resistance change over time. This method is also being used to predict pathogen transmission trends. In this study, we described the aim of phylogeny and the process of the phylogenetic construction method. We elaborated the advantages and disadvantages and scope of application of tree-building methods including distance-based, maximum parsimony, maximum likelihood and bayesian methods. We have reviewed the application and the estimation methods of major epidemiological parameters of phylodynamics and phylogeography in domestic and foreign studies. We concluded that the time- and location-scaled phylogenetic trees are increasingly used for outbreak investigation and routine surveillance of infectious diseases. |
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