Phylodynamic applications in 21st century global infectious disease research

被引：28
作者：
Rife B.D. [1 ]
Mavian C. [1 ]
Chen X. [2 ]
Ciccozzi M. [3 ,4 ]
Salemi M. [1 ]
Min J. [2 ]
Prosperi M.C. [2 ]
机构：
[1] Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
[2] Department of Epidemiology, University of Florida, Gainesville, FL
[3] Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome
[4] Unit of Clinical Pathology and Microbiology, University Campus Biomedico of Rome, Rome
来源：
Global Health Research and Policy | / 2卷 / 1期
基金：
欧盟地平线“2020”;
关键词：
Comparative phylogenetics; Dengue; HIV; Molecular epidemiology; MRSA; Phylodynamics; Phylogeography; WGS; Zika;
D O I：
10.1186/s41256-017-0034-y
中图分类号：
学科分类号：
摘要：
Background: 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 21st 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. Results: 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 Staphylococcus aureus. Conclusions: 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. © 2017, The Author(s).
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共 97 条
[1]  
Lee K., Yach D., Kamradt-Scott A., Globalization and Health, (2011)
[2]  
Chen X., Understanding the development and perception of global health for more effective student education, Yale J Biol Med, 87, pp. 231-240, (2014)
[3]  
Gushulak B.D., MacPherson D.W., Globalization of infectious diseases: the impact of migration, Clin Infect Dis, 38, pp. 1742-1748, (2004)
[4]  
Lafferty K.D., The ecology of climate change and infectious diseases, Ecology, 90, pp. 888-900, (2009)
[5]  
Patz J., Epstein P.R., Burke T., Et al., Global climate change and emerging infectious diseases, J Am Med Assoc, 275, pp. 217-223, (1996)
[6]  
Tambo E., Chuisseu P.D., Ngogang J.Y., Et al., Deciphering emerging Zika and dengue viral epidemics: Implications for global maternal–child health burden, J Infect Public Health, 9, pp. 240-250, (2016)
[7]  
World Health Statistics: 2016, (2016)
[8]  
Abat C., Chaudet H., Rolain J.-M., Et al., Traditional and syndromic surveillance of infectious diseases and pathogens, Int J Infect Dis, 48, pp. 22-28, (2016)
[9]  
Hernan M.A., Hernandez-Diaz S., Robins J.M., A Structural Approach to Selection Bias, Epidemiology, 15, pp. 615-625, (2004)
[10]  
Coughlin S.S., Recall bias in epidemiologic studies, J Clin Epidemiol, 43, pp. 87-91, (1990)
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