Viral Phylodynamics
By Erik M. Volz, Katia Koelle, Trevor Bedford. PLoS Comput. Biol., 2013
399 citations recorded by the source corpus.
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.
Subfields: Epidemiology, Genetics, Plant Science
View Paper: https://www.semanticscholar.org/paper/e052f0b66a6caafa16463c702d0990c0d320ed36
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Epidemiology
In Genetics
In Plant Science
Citations in the corpus
- Modeling infectious disease dynamics in the complex landscape of global health (2015, neutral): “Although samplingtheoryiswelldevelopedforstandardsurveillancedata,therela-tionshipbetweenasetofpathogen sequencesandthephylogenyinferredfromapopulationsampleismorecomplex( 11 ).”
- Nextstrain: real-time tracking of pathogen evolution (2017, methodology): “A suite of tools perform phylodynamic analysis (Volz et al., 2013), including subsampling, alignment, phylogenetic inference, temporal dating of ancestral nodes and discrete trait geographic reconstruction, including inference of the most likely transmission events.”
- Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations (2023, neutral): “Traditionally, phylodynamic approaches have been employed to retrospectively characterize lineage dynamics during outbreaks of viruses such as Zika [13–15], West Nile [16] and Ebola viruses [17,18].”