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.
Funder
the Spanish Network for the Research in Infectious Diseases
Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business
Gilead’s biomedical research project
Subject
Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis
Reference15 articles.
1. Domingo, E., Parrish, C.R., and Holland, J.J. (2008). Origin and Evolution of Viruses, Academic Press, Elsevier. [2nd ed.].
2. Nei, M. (1987). Molecular Evolutionary Genetics, Columbia University Press. [1st ed.].
3. Viral Quasispecies Complexity Measures;Gregori;Virology,2016
4. Comprehensive Survey on Distance/Similarity Measures between Probability Density Functions;Cha;Int. J. Math. Model. Methods Appl. Sci.,2007
5. Gregori, J., Colomer-Castell, S., Campos, C., Ibañez-Lligoña, M., Garcia-Cehic, D., Rando-Segura, A., Adombie, C.M., Pintó, R., Guix, S., and Bosch, A. (2022). Quasispecies fitness partition to characterize the molecular status of a viral population. Negative effect of early ribavirin discontinuation in a chronically infected HEV patient. Int. J. Mol. Sci., 23.
Cited by
2 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献