Novel Approach for Identification of Defective Viral Genomes using NGS Data
Channel: HIVE Lab
Date: 2021-02-25

This is the first seminar on high throughput sequencing tools available in HIVE (High-performance Integrated Virtual Environment), hosted virtually. The seminar described defective viral genomes, and a tool for detecting them developed for HIVE. Dr. Konstantinos Karagiannis, lead scientist for the FDA HIVE instance, presented the DVG-profiler tool, as well as a viral quasispecies analysis using the HIVE platform.

Defective viral genomes (DVGs) are spontaneously generated by most viruses due to errors in the replication process and cannot replicate in the absence of a non-defective helper virus. Some DVGs are recognized to be important triggers of the antiviral innate immune response, and have therefore gained interest for their potential to alter the attenuation and immunogenicity of vaccines. High-throughput sequencing (HTS) (also known as next generation sequencing, or NGS) is a powerful way to look for DVGs and has an advantage over conventional methods like RT-PCR, which can detect only primer-specific species, but HTS requires careful data analysis to be applicable.

The DVG-profiler algorithm is a novel approach to accurately detect the DVGs in HTS data as a post sequence alignment process, and is useful for both basic virus research and for monitoring live attenuated vaccines for DVG content.

Relevant publications:
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216944; https://msphere.asm.org/content/5/5/e00551-20).

Contact: https://hive.biochemistry.gwu.edu/contactus