cov2clusters

cov2clusters produces stable genomic clusters from SARS-CoV-2 whole genome sequence (WGS) data to support analysis of transmission dynamics.

Key Features:

• Stable Clustering: Generates stable clusters from phylogenetic trees that remain consistent as new SARS-CoV-2 sequences are incorporated over time.
• High Accuracy: Predicts epidemiologically informed clusters from genomic data with reported high accuracy for inferring transmission links.
• Comparison with Existing Methods: Demonstrates improved cluster stability relative to previous phylogenetic clustering methods when sequence datasets expand.

Scientific Applications:

• Regional Surveillance: Identifies stable clusters of SARS-CoV-2 cases to support regional public health monitoring of viral spread.
• Epidemiological Insights: Links genomic cluster information with epidemiological data to inform analyses of transmission patterns and targeted interventions.

Methodology:

Leverages SARS-CoV-2 whole genome sequence (WGS) data to form clusters on phylogenetic trees and evaluates cluster consistency as additional sequences are added, with acknowledgement of integrating epidemiological data.