IPD

IPD performs automated analysis and genomic surveillance of pathogens, focusing on SARS-CoV-2, by processing heterogeneous Next Generation Sequencing (NGS) data.

Key Features:

• Automated Computational Pipeline: An automated pipeline processes single and paired-end sequencing data from diverse NGS platforms.
• Updated SARS-CoV-2 Analysis Module: An updated analysis module supports high-throughput genomic data processing for SARS-CoV-2.
• Clade Prediction Accuracy: Clade prediction uses the latest clade nomenclature and reports a prediction accuracy of 92.8%.
• Dynamic Database Updating: An updater module refreshes the variant database automatically using genome sequences from GISAID.
• Extensive Variant Database: Analysis of over 208,911 SARS-CoV-2 genome sequences produced approximately 2.58 million sample-wise variants.
• Comparative Analysis Capabilities: Facilitates comparative analyses of lineage-specific mutations across regions (UK, South Africa, Brazil, India), identifying overlapping and unique mutations indicative of convergent evolutionary trends.

Scientific Applications:

• Genomic Surveillance: Monitoring emergence and spread of SARS-CoV-2 variants within populations using NGS-derived variant data.
• Variant Identification: Identification of variants associated with breakthrough infections to investigate potential vaccine escape and infection dynamics.
• Adaptive Evolution Studies: Detection and comparison of convergent mutations to study adaptive evolution and lineage-specific mutation patterns.

Methodology:

IPD employs an automated computational pipeline and an updated SARS-CoV-2 analysis module to process single and paired-end NGS data, uses clade prediction with the latest clade nomenclature (reported 92.8% accuracy), integrates with GISAID for automatic variant-database updates, and analyzed >208,911 genomes to generate ~2.58 million sample-wise variants.