The phylogeography of human viruses

@article{Holmes2004ThePO,
  title={The phylogeography of human viruses},
  author={E. Holmes},
  journal={Molecular Ecology},
  year={2004},
  volume={13}
}
  • E. Holmes
  • Published 2004
  • Biology, Medicine
  • Molecular Ecology
Viruses, especially those with RNA genomes, represent ideal organisms to study the dynamics of microevolutionary change. In particular, their rapid rate of nucleotide substitution means that the epidemiological processes that shape their diversity act on the same time‐scale as mutations are fixed in viral populations. Consequently, the branching structure of virus phylogenies provides a unique insight into spatial and temporal dynamics. Herein, I describe the key processes in virus… Expand
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References

SHOWING 1-10 OF 82 REFERENCES
Do human and JC virus genes show evidence of host-parasite codemography?
  • S. Wooding
  • Biology, Medicine
  • Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
  • 2001
TLDR
Nucleotide sequence diversity in human and JC virus DNA is consistent with a long-term demographic connection between the two species: both show evidence of large-scale population expansion, but genetic data also suggest that the twospecies have different patterns of population substructuring. Expand
Population dynamics of flaviviruses revealed by molecular phylogenies.
TLDR
An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. Expand
Phylogeographic patterns exhibited by Ontario rabies virus variants.
TLDR
This study confirms the geographical localization of these variants and extends the analysis to the less conserved G gene of these viruses and reveals a greater number of regionally localized variants. Expand
Ecology and evolution of rabies virus in Europe.
TLDR
The evolution of rabies viruses of predominantly European origin was studied by comparing nucleotide sequences of the nucleoprotein and glycoprotein genes, and by typing isolates using RFLP, revealing a number of distinct groups, each associated with a particular geographical area. Expand
Origins and evolution of AIDS viruses: estimating the time-scale.
TLDR
The primate lentiviruses comprise SIV strains from various host species, as well as two viruses, HIV-1 and HIV-2, that cause AIDS in humans, and date estimates still seem to be far too recent to be consistent with host-dependent evolution. Expand
Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus.
TLDR
It is determined that genotypes have experienced different selection pressures, with some evidence of positive selection in the Cosmopolitan genotype and one of the two Asian genotypes, but that the transition from sylvatic to human transmission was not accompanied by adaptive evolution of the E gene. Expand
The origin, emergence and evolutionary genetics of dengue virus.
  • E. Holmes, S. Twiddy
  • Biology, Medicine
  • Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
  • 2003
TLDR
Comparison of gene sequence data reveals that dengue virus has a relatively recent evolutionary history, with the four serotypes originating approximately 1000 years ago and only establishing endemic transmission in humans in the last few hundred years. Expand
Acute and persistent viral life strategies and their relationship to emerging diseases.
TLDR
It is suggested that persistent host-specific viral agents are the origin of emerging acute epidemic disease following adaptation of that virus to new host species and the consequences on viral fitness and the ecological and evolutionary relationships are considered. Expand
Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis
TLDR
A comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Expand
The evolution of RNA viruses: A population genetics view.
TLDR
This thesis has introduced some properties of RNA viruses that are relevant for studying evolution and tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus, a nonsegmented virus of negative strand. Expand
...
1
2
3
4
5
...