WNV Typer

WNV Typer classifies and genotypes West Nile virus (genus Flavivirus, family Flaviviridae) sequences to support epidemiological surveillance and evolutionary analyses.

Key Features:

• Alignment-Free Methodology: Uses return time distribution (RTD) analysis of k-mers as an alignment-free alternative to molecular phylogeny of complete coding sequences.
• Optimal K-mer Length: Validated using a k-mer length of 7 for optimal classification and genotyping of known WNV lineages.
• High Sensitivity and Specificity: Reports 100% sensitivity and 100% specificity for genotyping in validation.
• Computational Efficiency: Eliminates sequence alignment to provide a time-efficient approach suitable for large-scale genomic datasets.
• Objective Typing Criteria: Provides objective criteria for consistent and reproducible WNV genotype assignments.

Scientific Applications:

• Epidemiological Surveillance: Assigns genotypes from genomic data to monitor WNV spread and distribution.
• Research into Viral Evolution: Enables study of evolutionary changes and lineage emergence in WNV.
• Public Health Interventions: Informs public health strategies by identifying prevalent WNV strains in different regions.

Methodology:

Analysis of return time distributions (RTDs) of k-mers from complete genome sequences, using an alignment-free statistical assessment of nucleotide pattern properties (k=7 validated) for classification and genotyping.