The Genome Sequencing Unit leverages next-generation sequencing (NGS) technologies to support outbreak investigations, pathogen identification, and antimicrobial resistance profiling. Our state-of-the-art workflows integrate both amplicon-based and hybrid-capture methods to perform whole viral pathogen sequencing on leading platforms such as the Illumina MiSeq and Oxford Nanopore Technology or ONT MinION.
Core Capabilities & Technologies
- Advanced NGS workflows including Illumina Microbial Amplicon Prep (IMAP) and hybrid-capture target enrichment and ONT rapid viral sequencing with targeted approaches.
- Robust bioinformatic analysis using platforms such as Illumina BaseSpace DRAGEN, CLC Genomics Workbench, and TerraBio.
- Quality control metrics routinely achieving high Q30 scores and optimal read depths for accurate variant calling.
- Integrated systems ensuring seamless data transfer and interoperability with bioinformatics.
Recent Projects and Initiatives
- Mpox Virus Sequencing: Validated an NGS workflow for detecting and classifying hMPXV clades (Clade I and II) using genome-specific primers on the Illumina MiSeq.
- HIV Genome Sequencing & DR Mutation Analysis: Developed streamlined protocols for HIV genotyping, enabling detection of drug resistance mutations from specimens with moderate viral loads.
- Respiratory Pathogens and SARS-CoV-2: Validated NGS protocol for sequencing SARS-CoV-2 and ongoing validation of sequencing assays for respiratory viruses including Influenza A/B and HPAI/H5N1 to enhance pathogen surveillance and outbreak response.
- Infrastructure Enhancements: Recent system upgrades and improved instrument connectivity have augmented our sequencing capacity and data interoperability.
Impact on Public Health
Our integrated sequencing efforts provide pivotal data for tracking pathogen evolution and informing public health interventions. By rapidly identifying variants and detecting resistance mutations, the Genome Sequencing Unit contributes to targeted outbreak response and the strategic allocation of resources.
