Rates of evolutionary change in viruses: patterns and determinants

By Siobain Duffy, L. A. Shackelton, Edward C. Holmes. Nature reviews genetics, 2008

1,503 citations recorded by the source corpus.

Subfields: Ecology, Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/d28d16b8d4221c8d01f8d878494b98ba3b2ecc53

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Citations in the corpus

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. (2012, background): “The authors set out to examine the ability of current inference tools to estimate relatively low evolutionary rates such as those thought to commonly characterize dsDNA viruses (Duffy et al. 2008).”
The evolutionary dynamics of endemic human coronaviruses (2021, background): “Error-prone RNA-dependent RNA polymerases (RdRp) of RNA viruses such as SARS-CoV-2 contribute to short generation times and high mutation rates (Domingo 1997; Duffy et al. 2008).”
Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study (2020, background): “RNA-dependent RNA polymerases (RdRp) have high mutation rates, reaching from 1 in 1000 to 1 in 10000 nucleotides during replication [7, 14, 15].”
Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins (2011, background): “Such high evolutionary rates reflect both the poor fidelity of the viral polymerase [10], and the strong selection pressures to evade the human immunity [8,9,11–13] and, more recently, to develop drug resistance [14–”
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin (2014, background): “…of their surface proteins (Burton et al., 2012), other viruses with comparable mutation rates (such as measles) show little propensity for antigenic change (Duffy et al., 2008; Sheshberadaran et al., 1983), despite the fact that evasion of immunity would presumably confer a selective benefit.”
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants (2020, background): “However, replication fidelity is but one of several variables that affect viral population diversity (Duffy et al., 2008; Moya et al., 2000).”
Alignment-free sequence comparison: benefits, applications, and tools (2017, background): “A good example is viral genomes, which exhibit great variation in the number and order of genetic elements due to their high mutation rates, frequent genetic recombination events, horizontal gene transfers, gene duplications, and gene gains/losses [10].”
Life is Physics: Evolution as a Collective Phenomenon Far From Equilibrium (2010, background): “Examples of the ability of biological systems to defeat human attempts at mitigation include: (1) the world-wide spread of antibiotic resistance genes across distantly-related bacteria, crossing species and phylum boundaries and physical locations[30]; (2) the rapid evolution of cancer tumors in the”
Quasispecies Theory and the Behavior of RNA Viruses (2010, background): “The rapid evolution of RNA viruses complicates the management of chronic infections and the control of emerging infectious agents [1–3].”
The Evolution and Emergence of RNA Viruses (2009, background): “Although this theory has traditionally been applied to RNA viruses, that ssDNA viruses also exhibit very high rapid evolutionary rates, and similarly possess very small genome sizes, clearly supports this hypothesis (Duffy et al. 2008).”
Why do RNA viruses recombine? (2011, background): “Several studies have found that the rate of acquisition of deleterious mutations is indeed high in RNA viruses, such that U > 1 may be a realistic occurrenc”
Mechanisms of viral mutation (2016, background): “The neutral theory of molecular evolution posits a linear relationship between these two rates, but whereas mutation is a biochemical/genetic process, molecular evolution refers to the fixation of new alleles in populations [2, 3].”
Viral Mutation Rates (2010, background): “However, based on observations that some ssDNA viruses can evolve rapidly, it was recently suggested that they may have mutation rates close to those of RNA viruses (32).”
Evolutionary analysis of the dynamics of viral infectious disease (2009, background): “For example, the exceptionally high nucleotide mutation rate of a typical RNA viru”
Coronavirus Diversity, Phylogeny and Interspecies Jumping (2009, background): “First, the infidelity of RNA-dependent RNA polymerase of coronaviruses makes their mutation rates in the order of one per 1000 to 10000 nucleotides replicated, which makes them especially plastic (38, 39).”