Virus genome dynamics under different propagation pressures: reconstruction of whole genome haplotypes of west nile viruses from NGS data

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• 作者：Cornell Kortenhoeven (1) (2) (3)
  Fourie Joubert (4)
  Armanda DS Bastos (2)
  Celia Abolnik (1) (3)
  
  1. Poultry Section ; Department of Production Animal Studies ; Faculty of Veterinary Science ; University of Pretoria ; Old Soutpan Road ; Onderstepoort ; 0110 ; South Africa
  2. Department of Zoology and Entomology ; Faculty of Natural and Agricultural Sciences ; Mammal Research Institute ; University of Pretoria ; Lynwood Road ; Pretoria ; South Africa
  3. ARC-Ondestepoort Veterinary Institute ; 100 Old Soutpan Road ; Onderstepoort ; 0110 ; South Africa
  4. Department of Biochemistry ; Faculty of Natural and Agricultural Sciences ; University of Pretoria ; Lynwood Road ; Pretoria ; South Africa
  
• 关键词：West Nile virus ; Quasispecies Reconstruction ; Mutation ; Selection Equilibrium ; Cell Tropism
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：2,424 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies population variants. These variants are not discernable in the consensus genome at the time of emergence, and the maintenance of mutation-selection equilibria of population variants is greatly underestimated. The emergence of lineage 1 WNV strains has been studied extensively, but recent epidemics caused by lineage 2 WNV strains in Hungary, Austria, Greece and Italy emphasizes the increasing importance of this lineage to public health. In this study we explored the quasispecies dynamics of minority variants that contribute to cell-tropism and host determination, i.e. the ability to infect different cell types or cells from different species from Next Generation Sequencing (NGS) data of a historic lineage 2 WNV strain. Results Minority variants contributing to host cell membrane association persist in the viral population without contributing to the genetic change in the consensus genome. Minority variants are shown to maintain a stable mutation-selection equilibrium under positive selection, particularly in the capsid gene region. Conclusions This study is the first to infer positive selection and the persistence of WNV haplotype variants that contribute to viral fitness without accompanying genetic change in the consensus genotype, documented solely from NGS sequence data. The approach used in this study streamlines the experimental design seeking viral minority variants accurately from NGS data whilst minimizing the influence of associated sequence error.