Phylodynamic applications in 21st century global infectious disease research

Abstract

BackgroundPhylodynamics, 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.ResultsThe 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.ConclusionsCapitalizing 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s41256-017-0034-y) contains supplementary material, which is available to authorized users.

Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks

“…Nevertheless, the chain of collaboration between researchers, government, and producers in the animal sector is hard to maintain due to logistic, economic, and educational (i.e., lack of awareness and skill in phylodynamic methods) reasons. Nevertheless, recent scientific literature on the use of phylodynamic methods for animal disease surveillance is notably growing, which reflects the increased awareness between veterinarians about the capacities of such methods and the goodwill of the industry leaders to voluntarily share their data (37,132). Therefore, we anticipate a new era of animal disease prevention and control in the United States.…”

What is global health? Key concepts and clarification of misperceptions

“…Although few of the global health institutions, scholars and students have conducted or are going to conduct research studies with a global sample or delivered interventions to all people in all countries, all of them share a common goal: Preventing diseases and promoting health for all people in the world. For example, preventing HIV transmission within Wuhan would not necessarily be a global health project; but the same project can be considered as global if it is guided by a global perspective, analyzed with methods with global link such as phylogenetic analysis [52,53], and the goal is to contribute to global implications to end HIV/AIDS epidemic.…”

In silico analysis of RNA-dependent RNA polymerase of the SARS-CoV-2 and potentiality of the pre-existing drugs

“…These had increased the scope of a new branch of science, called "phylodynamics". Phylodynamics deals with those informations where the phylogenetic properties and the epidemic dynamics of viruses gets interconnected [43,44].…”