Viral quasispecies complexity measures

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• 作者：Josep Gregori^a ; ^b ; ^c ; ^{josep.gregori@vhir.org" class="auth_mail" title="E-mail the corresponding author} ; Celia Perales^b ; ^c ; ^d ; Francisco Rodriguez-Frias^c ; ^e ; ^f ; Juan I. Esteban^b ; ^c ; ^f ; Josep Quer^b ; ^c ; ^f ; Esteban Domingo^c ; ^d
• 关键词：Diversity indices ; Shannon entropy ; Gini-Simpson index ; Hill numbers ; Mutation frequency ; Nucleotide diversity ; Quasispecies profiles ; Montserrat plots
• 刊名：Virology
• 出版年：2016
• 出版时间：June 2016
• 年：2016
• 卷：493
• 期：Complete
• 页码：227-237
• 全文大小：2311 K

文摘

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.