COJAC

COJAC analyzes co-occurrence of signature SARS-CoV-2 mutations within amplicon read pairs from wastewater sequencing to detect low-frequency variants and estimate their prevalence and transmission fitness.

Key Features:

• Co-occurrence analysis: Identifies simultaneous presence of signature mutations within read pairs in the same amplicon as indicators of low-frequency SARS-CoV-2 variants.
• Early detection and monitoring: Detects viral lineages in wastewater prior to clinical detection, demonstrated by identification of B.1.1.7 up to eight days before clinical samples.
• Statistical estimation of transmission fitness: Implements a statistical methodology to estimate the transmission fitness advantage of variants from wastewater data with fewer samples than clinical sampling.
• Population-level surveillance: Enables genomic sequencing-based monitoring of variant prevalence across communities, exemplified by tracking B.1.1.7 in an alpine ski resort.
• Comparative analysis: Compares wastewater-derived prevalence estimates with clinical-sample data, reporting equal or superior performance in local prevalence estimation.

Scientific Applications:

• Epidemiological surveillance: Provides early warning of emerging SARS-CoV-2 variants through wastewater-based genomic signals.
• Public health research: Supports analysis of variant dynamics and transmission fitness at the community level using environmental sequencing data.
• Outbreak management: Facilitates proactive detection of variants of concern prior to clinical confirmation to inform intervention strategies.

Methodology:

Performs genomic sequencing of wastewater samples, detects co-occurrence of signature mutations within amplicons/read pairs, uses those co-occurrences as markers to estimate variant prevalence and transmission fitness via statistical methods, and compares wastewater-derived estimates with clinical-sample data.