Viral quasispecies complexity measures

Josep Gregori, Celia Perales, Francisco Rodriguez-Frias, Juan I. Esteban, Josep Quer, Esteban Domingo

Research output: Contribution to journalReview articleResearchpeer-review

36 Citations (Scopus)

Abstract

© 2016 Elsevier Inc. 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.
Original languageEnglish
Pages (from-to)227-237
JournalVirology
Volume493
DOIs
Publication statusPublished - 1 Jun 2016

Keywords

  • Diversity indices
  • Gini-Simpson index
  • Hill numbers
  • Montserrat plots
  • Mutation frequency
  • Nucleotide diversity
  • Quasispecies profiles
  • Shannon entropy

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