Viral quasispecies complexity measures

被引：86

作者：

Gregori, Josep ^{[1
,2
,3
]}

Perales, Celia ^{[2
,3
,4
]}

Rodriguez-Frias, Francisco ^{[3
,5
,6
]}

Esteban, Juan I. ^{[2
,3
,6
]}

Quer, Josep ^{[2
,3
,6
]}

Domingo, Esteban ^{[3
,4
]}

机构：

[1] Roche Diagnost, Sant Cugat Del Valles, Spain

[2] Univ Autonoma Barcelona, Liver Unit, Internal Med, Liver Dis Lab,Vall dHebron Inst Recerca,Hosp Univ, Barcelona 08035, Spain

[3] Inst Salud Carlos III, Ctr Invest Biomed Red Enfermedades Hepat & Digest, Madrid 28029, Spain

[4] Ctr Biol Mol Severo Ochoa CSIC UAM, Campus Cantoblanco, Madrid 28049, Spain

[5] HUVH, Dept Microbiol, Biochem Unit, Virol Unit, Barcelona 08035, Spain

[6] Univ Autonoma Barcelona, E-08193 Barcelona, Spain

来源：

VIROLOGY | 2016年 / 493卷

关键词：

Diversity indices; Shannon entropy; Gini-Simpson index; Hill numbers; Mutation frequency; Nucleotide diversity; Quasispecies profiles; Montserrat plots; PHYLOGENETIC DIVERSITY; LETHAL MUTAGENESIS; VIRUS; EVOLUTION; ESTIMATORS; FIDELITY;

D O I：

10.1016/j.virol.2016.03.017

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

Mutant spectrum dynamics (changes in the related mutants that compose viral populations) has a decisive impact on virus behavior. The several platforms of next generation sequencing (NGS) to study viral quasispecies offer a magnifying glass to study viral quasispecies complexity. Several parameters are available to quantify the complexity of mutant spectra, but they have limitations. Here we critically evaluate the information provided by several population diversity indices, and we propose the introduction of some new ones used in ecology. In particular we make a distinction between incidence, abundance and function measures of viral quasispecies composition. We suggest a multidimensional approach (complementary information contributed by adequately chosen indices), propose some guidelines, and illustrate the use of indices with a simple example. We apply the indices to three clinical samples of hepatitis C virus that display different population heterogeneity. Areas of virus biology in which population complexity plays a role are discussed. (C) 2016 Elsevier Inc. All rights reserved.

引用

页码：227 / 237

页数：11

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