Evolutionary analysis of the dynamics of viral infectious disease

By Oliver George Pybus, Andrew Rambaut. Nature reviews genetics, 2009

619 citations recorded by the source corpus.

Many organisms that cause infectious diseases, particularly RNA viruses, mutate so rapidly that their evolutionary and ecological behaviours are inextricably linked. Consequently, aspects of the transmission and epidemiology of these pathogens are imprinted on the genetic diversity of their genomes. Large-scale empirical analyses of the evolutionary dynamics of important pathogens are now feasible owing to the increasing availability of pathogen sequence data and the development of new computational and statistical methods of analysis. In this Review, we outline the questions that can be answered using viral evolutionary analysis across a wide range of biological scales.

Subfields: Agronomy and Crop Science, Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/2ee5ce8d4350e37d0c69f359ed5764421ae1490d

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Citations in the corpus

Endogenous viruses: insights into viral evolution and impact on host biology (2012, background): “A number of studies have produced robust estimates of the ages, evolutionary rates and epidemiological dynamics of many viruses that currently infect humans, domestic animals and crop”
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) (2016, neutral): “Such data sets have become increasingly common in a range of biological disciplines, including infectious disease epidemiology, molecular ecology, molecular taxonomy, archaeology, and anthropology (e.g., Willerslev and Cooper 2005; Pybus and Rambaut 2009; Biek et al. 2015).”
Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. (2013, background): “HIV-1 recombination increases the complexity and frequency of recombinant forms (Zhang et al., 2010), while migration has driven the dissemination of subtypes to new regions and established new epidemics (Pybus and Rambaut, 2009).”
The early spread and epidemic ignition of HIV-1 in human populations (2014, methodology): “To investigate how the spatial expansion of HIV-1 in the DRC relates to its epidemic history, we estimated past growth rates for HIV-1 groups M and O in central Africa using methods based on coalescent theory (30), a population genetic model that links phylogenetic tree shape to the demographic hist”