Tonight I continued watching the ONT webinar on advances in genomic profiling of respiratory viral pathogens. The second speaker was Nick Gauthier from BugSeq. The title of their session was “Translating metagenomics to the clinic.” The BugSeq team is working to develop clinical metagenomic pathogen agnostic approaches. BugSeq started working on an ONT mNGS platform to detect SARS-CoV-2 from nasopharyngeal swabs. Gauthier and team were impressed by the ability to detect and assemble viral genomes. With a collaboration with the University of British Columbia, BugSeq was able to automate and multiplex a workflow. The BugSeq web-based interface allows drag and drop analysis of sequences. The analytical trial generated promising results for detection of viral pathogens from 350 clinical samples. Real-time sequencing allows for shorter sequencing times. The team continues validating and improving the workflow. BugSeq has published their approach and unique databases. Gauthier noted that the NCBI reference human genome is contaminated with sequences! Databaes are also lacking some organisms. BugSeq’s genus-specific average nucleotide identity thresholds in analysis identified a unique Providencia species. BugSeq has been working with open-source bioinformatics tool developers to promote reproducibility. Gauthier and team are interested in using machine learning techniques to enhance analysis of multidimensional data. Simpler reports with key metrics and indicators about controls and pathogen detection help make BugSeq reports more accessible to clinicians. BARDA DRIVe and the Vancouver Coastal Health and UBC groups helped fund and work on these tools. I have used BugSeq and found it to be very user friendly!
