Abstract
Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light on how these dynamics impact viral genetic variation. Transmission dynamics can be considered at the level of cells within an infected host, individual hosts within a population, or entire populations of hosts. Many viruses, especially RNA viruses, rapidly accumulate genetic variation because of short generation times and high mutation rates. Patterns of viral genetic variation are therefore heavily influenced by how quickly transmission occurs and by which entities transmit to one another. Patterns of viral genetic variation will also be affected by selection acting on viral phenotypes. Although viruses can differ with respect to many phenotypes, phylodynamic studies have to date tended to focus on a limited number of viral phenotypes. These include virulence phenotypes, phenotypes associated with viral transmissibility, cell or tissue tropism phenotypes, and antigenic phenotypes that can facilitate escape from host immunity. Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread [2], spatio-temporal dynamics including metapopulation dynamics [3], zoonotic transmission, tissue tropism [4], and antigenic drift [5]. The quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics.
Highlights
The phylogeny of hepatitis B virus instead reflects a viral population that has remained roughly constant in size
Trees reconstructed from viral sequences isolated from chronically infected individuals can be used to gauge changes in viral population sizes within a host
In coining the term phylodynamics, Grenfell and coauthors [1] postulated that viral phylogenies ‘‘... are determined by a combination of immune selection, changes in viral population size, and spatial dynamics.’’ Their study showcased three features of viral phylogenies, which may serve as rules of thumb for identifying important epidemiological, immunological, and evolutionary processes influencing patterns of viral genetic variation
Summary
In coining the term phylodynamics, Grenfell and coauthors [1] postulated that viral phylogenies ‘‘... are determined by a combination of immune selection, changes in viral population size, and spatial dynamics.’’ Their study showcased three features of viral phylogenies, which may serve as rules of thumb for identifying important epidemiological, immunological, and evolutionary processes influencing patterns of viral genetic variation. A more balanced phylogeny may occur when a virus is not subject to strong immune selection or other source of directional selection An example of this is the phylogeny of HIV’s envelope protein inferred from sequences isolated from different individuals in a population (caricatured by Figure 3B). Ladder-like trees such as the one shown in Figure 3A could reflect the presence of directional selection, ladder-like trees could reflect sequential genetic bottlenecks that might occur with rapid spatial spread, as in the case of rabies virus [7] Because of this many-to-one mapping between process and phylogenetic pattern, research in the field of viral phylodynamics has sought to develop and apply quantitative methods to effectively infer process from reconstructed viral phylogenies (see Methods). Phylodynamic approaches have been used to examine the spread of Oseltamivir resistance in influenza A/H1N1 [20]
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