CoVEx: SARS-CoV-2 Mutation Explorer for genomic surveillance

Area of Science:

• * Genomics and Bioinformatics
• * Infectious Disease Epidemiology
• * Molecular Virology

Background:

• * Effective management of emerging diseases necessitates rapid pathogen identification and monitoring.
• * The COVID-19 pandemic highlighted challenges in promptly detecting and notifying about SARS-CoV-2 variants of interest and concern.
• * Existing platforms often lack integrated user sequence analysis and comparison with public databases like GISAID.

Purpose of the Study:

• * To introduce CoVEx, an accessible tool for analyzing and visualizing SARS-CoV-2 variant sequences.
• * To facilitate continuous monitoring of viral mutations and identification of novel variants.
• * To enable comparison of user-generated sequence data with global surveillance data.

Main Methods:

• * Development of CoVEx, a Python-based tool integrating quality control, alignment, genome annotation, lineage designation, and mutation analysis.
• * Implementation of an interactive mutation explorer and heatmap generation using Outbreak.info.
• * Validation using 108 raw SARS-CoV-2 sequence datasets.

Main Results:

• * CoVEx accurately assembled sequences and predicted Pangolin and Nextclade Pango lineages.
• * The tool identified a novel mutation, ORF1a:I2501T, within the Costa Rica GN.1 lineage.
• * Mutation profiles were compared against GISAID data, providing insights into global mutation prevalence.

Conclusions:

• * CoVEx is a valuable, user-friendly tool for SARS-CoV-2 variant analysis and visualization.
• * The tool aids in the discovery of novel mutations and tracking of viral evolution.
• * CoVEx provides critical information for researchers and public health officials in managing emerging infectious diseases.