Virus Genotyping Tools

Virus Genotyping Tools performs high-throughput genotyping of rapidly evolving viruses, including Human Immunodeficiency Virus type-1 (HIV-1), Hepatitis B and C, human T-lymphotropic virus type-1 (HTLV-1), human herpesvirus type-8 (HHV8), and human papillomavirus (HPV), to assign genotypes and detect recombinants for diagnostic and epidemiological purposes.

Key Features:

• High-Throughput Genotyping: Processes large volumes of viral sequences to determine genotypes at scale.
• Alignment with Curated Reference Strains: Aligns query sequences against a predefined, curated set of reference strains for comparative analysis.
• Sliding-Window Phylogenetic Analysis: Performs phylogenetic analysis on multiple overlapping alignment segments using a sliding-window technique.
• Statistical Genotype Assignment: Assigns genotypes and sub-genotypes per segment based on highest bootstrap (>70%) and bootscanning (>90%) scores.
• Recombinant Classification: Identifies and classifies recombinant versus non-recombinant virus sequences.

Scientific Applications:

• Diagnostic Genotyping: Identification of virus genotypes to inform clinical diagnosis and treatment decisions.
• Integration into Drug Resistance Algorithms: Use within HIV drug resistance algorithms, including those at Stanford University and European databases, to support resistance interpretation.
• Large-Scale Sequence Genotyping: Genotyping of large numbers of sequences across databases for research and surveillance purposes.

Methodology:

Query viral sequences are aligned to a curated set of reference strains and subjected to phylogenetic analysis on multiple overlapping alignment segments using a sliding-window approach, with per-segment genotype and sub-genotype assignment based on highest bootstrap (>70%) and bootscanning (>90%) scores and classification of recombinant versus non-recombinant sequences.