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Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases REVIEW published: 02 August 2019 doi: 10.3389/fpubh.2019.00208 Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases Kristof Theys, Philippe Lemey, Anne-Mieke Vandamme and Guy Baele* Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium 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 Edited by: public health and treatment decisions, but the design (and choice of what analyses Vitali Sintchenko, are shown) is hindered by the complexity of information embedded within current University of Sydney, Australia phylogenetic models and the integration of available meta-data. In this review, we discuss Reviewed by: Denis Baurain, visualization challenges for the interpretation and exploration of reconstructed histories University of Liège, Belgium of viral epidemics that arose from increasing volumes of sequence data and the wealth Sergey Eremin, of additional data layers that can be integrated. We focus on solutions that address joint World Health Organization, Switzerland temporal and spatial visualization but also consider what the future may bring in terms of John-Sebastian Eden, visualization and how this may become of value for the coming era of real-time digital University of Sydney, Australia pathogen surveillance, where actionable results and adequate intervention strategies *Correspondence: Guy Baele need to be obtained within days. [email protected] Keywords: visualization, phylogenetics, phylogenomics, phylodynamics, infectious disease, epidemiology, evolution Specialty section: This article was submitted to Infectious Diseases - Surveillance, 1. VIRUS EPIDEMIOLOGY AND EVOLUTION Prevention and Treatment, a section of the journal Despite major advances in drug and vaccine design in recent decades, viral infectious diseases Frontiers in Public Health continue to pose serious threats to public health, both as globally well-established epidemics Received: 07 April 2019 of e.g., Human Immunodeficiency Virus Type 1 (HIV-1), Dengue virus (DENV) or Hepatitis Accepted: 12 July 2019 C virus (HCV), and as emerging or re-emerging epidemics of e.g., Zika virus (ZIKV), Middle Published: 02 August 2019 East Respiratory Syndrome Coronavirus (MERS-CoV), Measles virus (MV), or Ebola virus Citation: (EBOV). Efforts to reconstruct the dynamics of viral epidemics have gained considerable attention Theys K, Lemey P, Vandamme A-M as they may support the design of optimal disease control and treatment strategies (1, 2). and Baele G (2019) Advances in Visualization Tools for Phylogenomic These analyses are able to provide answers to questions on the diverse processes underlying and Phylodynamic Studies of Viral disease epidemiology, including the (zoonotic) origin and timing of virus outbreaks, drivers of Diseases. Front. Public Health 7:208. spatial spread, characteristics of transmission clusters and factors contributing to enhanced viral doi: 10.3389/fpubh.2019.00208 pathogenicity and adaptation (3–5). Frontiers in Public Health | www.frontiersin.org 1 August 2019 | Volume 7 | Article 208 Theys et al. Visualization for Viral Phylodynamics Molecular epidemiological techniques have proven to be phylogenetic tree visualization efforts constituted an integral important and effective in informing public health and part of phylogenetic inference software packages and as such therapeutic decisions in the context of viral pathogens (6, 7), were restricted to simply showing the inferred phylogenies on given that most of the viruses with a severe global disease a command line or in a simple text file, often even without an burden are characterized by high rates of evolutionary change. accompanying graphical user interface. The longstanding use of These genetic changes are being accumulated in viral genomes phylogenies in molecular epidemiological analyses has however on a time scale similar to the one where the dynamics led to the emergence of increasingly feature-rich visualization of population genetic and epidemiological processes can be tools over time. The advent of the new research disciplines such as observed, which has lead to the definition of viral phylodynamics phylogenomics and phylodynamics necessitated more complex as the study of how epidemiological, immunological, and visualizations in order to accommodate projections of pathogen evolutionary processes act and potentially interact to shape dispersal onto a geographic map, ancestral reconstruction of viral phylogenies (8). As such, phylogenetic trees constitute a various types of trait data and appealing animations of the crucial instrument in studies of virus evolution and molecular reconstructed evolution and spread over time. Tree visualizations epidemiology, elucidating evolutionary relationships between resulting from these analyses are also complemented by visual sampled virus variants based on the temporal resolution in the reconstructions of other important aspects of the model genetic data of these fast-evolving viruses that allows resolving reconstructions, such as population size dynamics over time, their epidemiology in terms of months or years. Through transmission networks and estimates of ancestral states for traits the integration of population genetics theory, epidemiological of interest throughout the tree (15). data and mathematical modeling, insights into epidemiological, Across disciplines, adequate visualizations are pivotal to immunological, and evolutionary processes shaping genetic communicate, disseminate and translate research findings into variation can be inferred from these phylogenies. The field of meaningful information and actionable insights for clinical, phylodynamics has generated new opportunities to obtain a more research and public health officials. The aim to improve data- detailed understanding of evolutionary histories—through time driven decision making fits within a broader scope to establisha as well as geographic space—and transmission dynamics of both universal data visualization literacy (16). To this end, enhancing well-established viral epidemics and emerging outbreaks (9, 10). collaborations and dissemination of visualizations is increasingly The ability of molecular epidemiological analyses, and achieved through sharing of online resources for hosting phylodynamic analyses in particular, to fully exploit the annotated tree reconstructions (17), online workspaces (18) and information embedded in viral sequence data has significantly continuously updated pipelines that accommodate increasing improved through a combination of technological innovations data flow during infectious disease outbreaks (19) (see further and advances in inference frameworks during the past decades. sections for more information and examples of these packages). From a data perspective, genomic epidemiology is becoming Given the plethora of options for presenting and visualizing a standard framework driven by high-throughput sequencing results, and its importance for effectively communicating with technologies that are associated with reduced costs and a wide audience, choosing the appropriate representation and increasing turnover. Moreover, the portability and potential of visualization strategy can be challenging. Recent work on this rapid deployment on-site of these new technologies enable the topic focuses on navigating through all the available visualization generation of complete genome data from samples within hours options by offering clear guidelines on how to turn large datasets of taking the samples (11). This rising availability of whole- into compelling and aesthetically appealing figures (20). genome sequences increases the resolution by which historical events and epidemic dynamics can be reconstructed. From a methodological perspective, new developments in statistical 2. A FRAMEWORK FOR VISUALIZATION and computational methods along with advances in hardware infrastructure have allowed the analysis of ever-growing data A large array of software packages for performing phylogenetic sets, the incorporation of more complex models and the and phylodynamic analyses have emerged in the last decade, inclusion of information related to sample collection, infected in particularly for fast-evolving RNA viruses [see (10) for a host characteristics and clinical or experimental status (generally recent overview]. A more recent but similar trend can be known as metadata) (9, 10, 12, 13). seen for methodologies and applications aimed at visualization In contrast to a marked increase in the number of software of the output of these frameworks. In addition to the packages targetting increasingly efficient but complex approaches need to communicate these outputs in a visual manner, to infer annotated phylogenies by exploiting
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