A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing

Brief Bioinform. 2020 Sep 25;21(5):1766-1775. doi: 10.1093/bib/bbz086.

Abstract

Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.

Keywords: Illumina sequencing platform; analysis workflow; haplotype reconstruction; open-source software; sub-consensus SNV; viral quasispecies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Foot-and-Mouth Disease Virus / classification
  • Foot-and-Mouth Disease Virus / genetics*
  • Genes, Viral
  • Haplotypes*
  • High-Throughput Nucleotide Sequencing / methods*
  • Quasispecies*