Quantifying In-Host Quasispecies Evolution
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Ibañez-Lligoña, Marta (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Quer, Josep 1963- (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)

Date:	2023
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.
Grants:	Ministerio de Economía y Competitividad RD16/0016/0003 Ministerio de Economía y Competitividad IDI-20200297 Instituto de Salud Carlos III PI19/00301 Instituto de Salud Carlos III PI22/00258
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Quasispecies evolution ; Distributions similarity ; Quasispecies fitness partition ; Viral treatment ; Mutagenesis
Published in:	International journal of molecular sciences, Vol. 24 (january 2023) , ISSN 1422-0067

DOI: 10.3390/ijms24021301
PMID: 36674827

16 p, 586.7 KB

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