EpiViruSurf

EpiViruSurf analyzes amino acid changes within viral epitopes across populations to characterize epitope variability and potential immune escape.

Key Features:

• Viral Population Selection: Targeted analysis of amino acid changes within specified viral populations.
• Epitope Identification: Searches epitopes using the Immune Epitope Database or accepts custom epitopes defined by start and stop positions on a viral protein.
• Integration with ViruSurf: Uses ViruSurf as a repository of curated metadata and amino acid changes imported from GenBank, COVID-19 Genomics UK (COG-UK), and GISAID.
• Result Summarization: Generates per-epitope result tables with statistics on overlapping amino acid changes and the sequences carrying those alterations.
• Visualization with VirusViz: Provides visualization via the VirusViz application with epitope regions highlighted within viral proteins for comparative inspection.
• Distribution Analysis: Examines distributions of amino acid changes grouped by location, collection date, or lineage to reveal mutation patterns relevant to immune recognition.

Scientific Applications:

• Vaccine design: Identification of conserved and variable epitope regions to inform antigen selection.
• Antiviral drug development: Mapping epitope variability to assess potential impacts on therapeutic targets.
• Serological assay development: Evaluation of epitope conservancy to select stable targets for antibody detection.
• Immune escape assessment: Characterization of amino acid change distributions to evaluate risks of immune evasion.

Methodology:

Integration of sequence data and epitope information from GenBank, COVID-19 Genomics UK (COG-UK), and GISAID via two endpoints: http://gmql.eu/episurf/ (GenBank and COG-UK) and http://gmql.eu/episurf_gisaid/ (GISAID).