Genotyping - NCBI

Genotyping - NCBI assigns genotypes and subtypes to viral nucleotide sequences by BLAST-based comparison against a reference sequence database to characterize HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) and to detect recombinant mosaic structure.

Key Features:

• Genotype and subtype assignment: Determines genotype(s) and subtype(s) of viral nucleotide sequences for HIV-1, HCV, and HBV.
• BLAST-based comparison: Uses BLAST (Basic Local Alignment Search Tool) to align query sequences against reference sequences.
• Reference sequence database: Compares queries to a comprehensive database of reference sequences representing known genotypes.
• User-defined references: Allows inclusion of user-defined reference sequences for comparison.
• Segmentation for mosaic detection: Segments query sequences to identify mosaic organization in recombinant viral genomes.
• Sliding-window analysis: Applies a sliding window approach during BLAST analysis to evaluate genotype assignments across sequence windows.
• Genotype visualization: Represents top-scoring genotypes with color-coded visualization to indicate genotype composition across sequence segments.

Scientific Applications:

• Viral subtype identification: Accurate identification and characterization of viral subtypes for HIV-1, HCV, and HBV.
• Recombinant detection: Detection and mapping of recombinant (mosaic) regions within viral sequences.
• Viral evolution studies: Supports analyses of viral evolution by comparing sequences to genotype reference sets.
• Transmission and epidemiology: Facilitates studies of transmission dynamics and epidemiology through genotype composition analyses.

Methodology:

Query sequences are segmented and analyzed with a sliding-window BLAST against a reference sequence database to compare top-scoring alignments and identify mosaic organization for genotype determination.