WAVES

WAVES visualizes and analyzes pathogen sequencing results from environmental samples, primarily wastewater, to support detection and monitoring of variants such as SARS-CoV-2 BA.1 and signature mutations like Spike S:E484A.

Key Features:

• Multi-layered Visualization: Displays geographic, temporal, and genomic views to reveal spatial patterns and temporal trends of pathogen spread.
• Variant and Mutation Frequency Analysis: Computes frequencies of detected pathogen variants and individual mutations from sequencing data.
• Configurability for Pathogens and Samples: Uses a configuration file to adapt analysis parameters and visualizations for different pathogens and environmental sample types.

Scientific Applications:

• Environmental Surveillance: Monitors pathogen prevalence and distribution in wastewater and other environmental samples.
• Public Health Surveillance and Early Detection: Detects and tracks emerging variants to inform public health responses, demonstrated for SARS-CoV-2 BA.1 and Spike mutation S:E484A.
• Epidemiological Assessment and Forecasting: Supports assessment of epidemiological situations and aids forecasting from integrated genomic and geographic data.

Methodology:

Processes sequencing data from environmental samples by integrating genomic data with geographic and temporal metadata to compute variant and mutation frequencies and enable epidemiological assessment and forecasting.