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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, spatio-temporal dynamics including metapopulation dynamics, zoonotic transmission, tissue tropism, and antigenic drift. The quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics. == Sources of phylodynamic variation == In coining the term ''phylodynamics'', Grenfell and coauthors〔 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. ; The relative lengths of internal versus external branches will be affected by changes in viral population size over time (see figure 1)〔 : Rapid expansion of a virus in a population will be reflected by a "star-like" tree, in which external branches are long relative to internal branches. Star-like trees arise because viruses are more likely to share a recent common ancestor when the population is small, and a growing population has an increasingly smaller population size towards the past. Compared to a phylogeny of an expanding virus, a phylogeny of a viral population that stays constant in size will have external branches that are shorter relative to branches on the interior of the tree. The phylogeny of HIV provides a good example of a star-like tree, as the prevalence of HIV infection rose rapidly throughout the 1980s (caricatured by figure 1A). The phylogeny of hepatitis B virus (caricatured by figure 1B) instead reflects a viral population that has remained roughly constant in size. Similarly, trees reconstructed from viral sequences isolated from chronically infected individuals can be used to gauge changes in viral population sizes within a host. ; The clustering of taxa on a viral phylogeny will be affected by host population structure (see figure 2)〔 : Viruses within similar hosts, such as hosts that reside in the same geographic region, are expected to be more closely related genetically if transmission occurs more commonly between them. The phylogenies of measles and rabies virus (caricatured by figure 2A) illustrate viruses with strong spatial structure. These phylogenies stand in contrast to the phylogeny of human influenza, which does not appear to exhibit strong spatial structure over extended periods of time. Clustering of taxa, when it occurs, is not necessarily observed at all scales, and a population that appears structured at some scale may appear panmictic at another scale, for example at a smaller spatial scale. While spatial structure is the most commonly observed population structure in phylodynamic analyses, viruses may also have nonrandom admixture by attributes such as the age, race, and risk behavior. This is because viral transmission can preferentially occur between hosts sharing any of these attributes. ; Tree balance will be affected by selection, most notably immune escape (see figure 3)〔 : The effect of directional selection on the shape of a viral phylogeny is exemplified by contrasting the trees of influenza virus and HIV's surface proteins. The ladder-like phylogeny of influenza virus A/H3N2's hemagglutinin protein bears the hallmarks of strong directional selection, driven by immune escape (caricatured by figure 3A). In contrast, 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). Interestingly, phylogenies of HIV's envelope protein from chronically infected hosts resemble influenza's ladder-like tree (caricatured by figure 3A). This highlights that the processes affecting viral genetic variation can differ across scales. Indeed, contrasting patterns of viral genetic variation within and between hosts has been an active topic in phylodynamic research since the field's inception.〔 Although these three phylogenetic features are useful rules of thumb to identify epidemiological, immunological, and evolutionary processes that might be impacting viral genetic variation, there is growing recognition that the mapping between process and phylogenetic pattern can be many-to-one. For instance, although ladder-like trees such as the one shown in figure 3A could reflect the presence of directional selection, ladder-like trees could also reflect sequential genetic bottlenecks that might occur with rapid spatial spread, as in the case of rabies virus. 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). The consideration of other data sources (e.g., incidence patterns) may aid in distinguishing between competing phylodynamic hypotheses. Combining disparate sources of data for phylodynamic analysis remains a major challenge in the field and is an active area of research. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Viral phylodynamics」の詳細全文を読む スポンサード リンク
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