VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants

Area of Science:

• Genomics
• Virology
• Epidemiology

Background:

• The COVID-19 pandemic necessitated continuous monitoring of SARS-CoV-2 evolution.
• Large-scale genome sequencing data is crucial for identifying and tracking novel viral variants and strains.
• Effective tools are needed for systematic genomic surveillance at various geographical scales.

Purpose of the Study:

• To develop and present VariantHunter, a flexible and user-friendly web application for monitoring SARS-CoV-2 evolution.
• To enable early detection and tracking of emerging viral variants and their spread.
• To support both lineage-independent and lineage-specific analyses for comprehensive genomic surveillance.

Main Methods:

• VariantHunter analyzes amino acid changes over 4-week intervals in specified geographical areas.
• It computes weekly prevalence and ranks changes based on prevalence shifts.
• The tool supports lineage-independent analysis for discovering new variants and lineage-specific analysis for evaluating known lineages.

Main Results:

• VariantHunter provides systematic monitoring of SARS-CoV-2 evolution at global and regional levels.
• It utilizes simple statistics and visual representations like diffusion charts and heatmaps.
• A dataset explorer allows users to visualize and refine their data selections.

Conclusions:

• VariantHunter empowers genomic surveillance by offering user-friendly tools for monitoring viral evolution.
• The application facilitates the identification and tracking of novel SARS-CoV-2 variants without requiring computational expertise.
• It is a freely accessible web application contributing to public health efforts during the pandemic.