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Quantifying In-Host Quasispecies Evolution.


ABSTRACT: What takes decades, centuries or millennia to happen with a natural ecosystem, it takes only days, weeks or months with a replicating viral quasispecies in a host, especially when under treatment. Some methods to quantify the evolution of a quasispecies are introduced and discussed, along with simple simulated examples to help in the interpretation and understanding of the results. The proposed methods treat the molecules in a quasispecies as individuals of competing species in an ecosystem, where the haplotypes are the competing species, and the ecosystem is the quasispecies in a host, and the evolution of the system is quantified by monitoring changes in haplotype frequencies. The correlation between the proposed indices is also discussed, and the R code used to generate the simulations, the data and the plots is provided. The virtues of the proposed indices are finally shown on a clinical case.

SUBMITTER: Gregori J 

PROVIDER: S-EPMC9867078 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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Quantifying In-Host Quasispecies Evolution.

Gregori Josep J   Ibañez-Lligoña Marta M   Quer Josep J  

International journal of molecular sciences 20230109 2


What takes decades, centuries or millennia to happen with a natural ecosystem, it takes only days, weeks or months with a replicating viral quasispecies in a host, especially when under treatment. Some methods to quantify the evolution of a quasispecies are introduced and discussed, along with simple simulated examples to help in the interpretation and understanding of the results. The proposed methods treat the molecules in a quasispecies as individuals of competing species in an ecosystem, whe  ...[more]

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