This project aims to identify and characterize defective viral genomes (DVGs) present in laboratory-produced viral stocks using next-generation sequencing (NGS) technologies. DVGs are truncated, rearranged, or otherwise altered viral genomes that arise during viral replication and can significantly influence viral fitness, pathogenicity, and host immune responses.
Viral RNA will be extracted from viral stocks and prepared for high-throughput sequencing. Bioinformatic analyses will be performed to detect deletions, insertions, copy-back genomes, and other signatures characteristic of DVGs. The abundance, diversity, and genomic distribution of DVGs will be analyzed and compared across viral preparations.
The project will generate a comprehensive profile of DVG populations within viral stocks, providing insights into viral stock quality, replication dynamics, and the potential impact of DVGs on downstream experimental outcomes. The resulting datasets will contribute to a better understanding of defective viral genome generation and maintenance in viral populations.
