Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

Frontiers in Public Health

article

Kristof Theys¹  Philippe Lemey¹  Anne-Mieke Vandamme¹  Guy Baele¹ 

[1] Department of Microbiology, Rega Institute for Medical Research, Clinical and Epidemiological Virology

关键词: visualization;    phylogenetics;    phylogenomics;    phylodynamics;    infectious disease;    epidemiology;    evolution;   

DOI  :  10.3389/fpubh.2019.00208

学科分类：社会科学、人文和艺术（综合）

来源: Frontiers

【 摘 要 】

Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution assist in drawing conclusions from phylogenetic estimates and may even have potential to better inform public health and treatment decisions, but the design (and choice of what analyses are shown) is hindered by the complexity of information embedded within current phylogenetic models and the integration of available meta-data. In this review, we discuss visualization challenges for the interpretation and exploration of reconstructed histories of viral epidemics that arose from increasing volumes of sequence data and the wealth of additional data layers that can be integrated. We focus on solutions that address joint temporal and spatial visualization but also consider what the future may bring in terms of visualization and how this may become of value for the coming era of real-time digital pathogen surveillance, where actionable results and adequate intervention strategies need to be obtained within days.

【 授权许可】

CC BY