Covvfit

Covvfit estimates relative growth advantages of multiple competing SARS-CoV-2 variants from wastewater sequencing data using a statistical model.

Key Features:

• Variant fitness estimation: Estimates fitness advantages of multiple competing SARS-CoV-2 variants from wastewater sequencing data collected from different locations.
• Dynamic reconstruction: Reconstructs the dynamics of variant competition across successive pandemic waves using longitudinal wastewater sequencing datasets.
• Long-horizon prediction: Accurately predicts future variant dynamics over long prediction horizons once variants surpass a low detection threshold.
• Clinical validation: Generates wastewater-based estimates of fitness advantages that are efficient and accurate when compared with clinical data.

Scientific Applications:

• SARS-CoV-2 variant surveillance: Monitors the emergence and spread of SARS-CoV-2 variants with selective advantages over previously circulating strains using wastewater sequencing.
• Pandemic wave analysis: Reconstructs variant competition dynamics across successive waves of the COVID-19 pandemic from 2021-2025 wastewater data.
• Forecasting selection dynamics: Predicts future variant dynamics to support public health decision-making without relying solely on clinical genomic sequencing.

Methodology:

Covvfit implements a statistical model for estimating fitness advantages from wastewater sequencing data; computational steps are not explicitly detailed in the sources.