VirVarSeq

VirVarSeq detects low-frequency viral variants from Illumina massively parallel sequencing (MPS) data to characterize viral quasi-species and identify drug resistance–associated mutations in viruses such as HIV-1 and HCV.

Key Features:

• Adaptive base-calling accuracy filtering: Q-cpileup leverages nucleotide base call quality scores (Qs) to distinguish sequencing errors from genuine low-frequency mutations.
• FastQ input support: The pipeline performs variant calling directly from fastq files.
• Adaptive filtering strategy: Thresholds are optimized for individual samples within each sequencing run to reduce false positives on MPS platforms.
• Codon-level variant calling: Variants are called at the codon level to preserve linkage between SNPs and enable immediate biological interpretation related to antiviral drug responses.
• High sensitivity and specificity: Q-cpileup achieves high sensitivity with good specificity for detecting variants at frequencies as low as 0.5% compared with traditional SNP callers.

Scientific Applications:

• Viral quasi-species analysis: Characterization of intra-host diversity in viruses such as HIV-1 and HCV.
• Drug resistance detection: Identification of low-frequency drug resistance mutations relevant to antiviral treatment responses.
• Viral evolution and surveillance: Tracking emergence of resistant strains and evolutionary dynamics within sequencing runs.

Methodology:

Uses Q-cpileup to assess nucleotide base quality scores (Qs), applies a filtering step that differentiates true variants from sequencing errors with adaptive thresholds optimized per sample within each run, performs codon-level variant calling, and operates directly on fastq files.