Rife Brittany D, Mavian Carla, Chen Xinguang, Ciccozzi Massimo, Salemi Marco, Min Jae, Prosperi Mattia Cf
Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA.
Department of Epidemiology, University of Florida, Gainesville, FL USA.
Glob Health Res Policy. 2017 May 8;2:13. doi: 10.1186/s41256-017-0034-y. eCollection 2017.
Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21 century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics.
The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework. These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant .
Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.
系统动力学是研究种群内部和种群之间流行病学与病原体进化过程相互作用的学科，最初是在快速进化病毒的背景下定义的，并用于描述传播动态。自21世纪初以来，系统动力学的概念不断发展，其应用范围扩展到进化较慢的病原体，包括细菌和真菌，并用于识别疾病传播和病原体种群动态中的影响因素。
系统动力学方法现已成为开发比较系统发育工具的基本组成部分，这些工具能够将流行病学监测数据与分子序列纳入单一统计框架。这些创新工具极大地加强了对与人类免疫缺陷病毒（HIV）、寨卡病毒和登革热等病毒以及耐甲氧西林金黄色葡萄球菌等细菌的生长和传播相关的时间和地理起源、进化历史以及生态风险因素的科学研究。
通过对大量文献的广泛综述，我们讨论了传染病流行病学领域的发展历程和近期成果，强调了系统动力学的进展，以及全球研究新出现病原体流行的研究人员目前面临的挑战和局限性。
