Success Case: Development of a Comprehensive HIV-1 Panel
HIV-1 is known for its high mutation rate and genetic diversity, including numerous subtypes and circulating recombinant forms (CRFs). These characteristics make it challenging to comprehensively detect all variants using conventional targeted sequencing methods. To address this issue, Celemics collaborated with the Korea Disease Control and Prevention Agency (KDCA) to develop a hybridization-based HIV-1 target enrichment panel. Leveraging this advanced capture-based approach, the panel and corresponding bioinformatics analysis pipeline incorporate genomic information from diverse HIV-1 variants. The effectiveness of this enrichment technology was validated through extensive testing with actual virus samples. This comprehensive panel demonstrates excellent accuracy and broad applicability for genetically diverse HIV-1 viruses, making it a powerful tool for public health surveillance and infectious disease monitoring
Key Features of Comprehensive HIV-1 Panel
- Flexible Design Reflecting Diverse Subtypes
The panel was designed using genome sequences collected from Los Alamos National Lab (LANL) HIV sequence database. It incorporates 17 single subtypes from the M group and three major CRFs that are frequently observed. To address regions not sufficiently covered by the initial probe set, a new design strategy was developed and applied. This approach added additional probes, enabling higher coverage across diverse HIV-1 variants
- In Silico Validation of Probe Design
The final probe set was validated using in silico analysis based on numerous HIV-1 sequences registered in the LANL HIV sequence database. Although the initial design showed less than 40% coverage for some strains, the final probe set achieved over 90% coverage across all HIV-1 genome sequences, demonstrating the design’s completeness and reliability.
- Analysis Algorithm for Accurate Subtype Classificationn
To enhance downstream data analysis, we developed an algorithm that combines alignment and de novo assembly approaches. This allowed the pipeline to accurately distinguish not only pure subtypes but also complex recombinant forms, ensuring precise classification of HIV-1 variants based on their genomic features.
- Performance Validation with Clinical Samples
We conducted validation experiments using 35 clinical HIV-1 samples with varying viral loads, including both single subtypes and CRFs. Among them, 33 samples showed successful genome detection and accurate subtype identification. The two samples that failed detection had low viral loads (<1,000 IU/mL). Notably, the panel also achieved high coverage and consistent subtype matching for CRFs and complex recombinant forms (cpx), confirming its analytical performance and broad utility.
Impact
This Comprehensive HIV-1 Panel developed through the collaboration could contribute to improve the accuracy and reliability of Korea’s infectious disease surveillance system. With its flexible design that accommodates diverse variants, the panel could serve as a useful tool in areas such as mutation tracking, vaccine and therapeutic development, and broader infectious disease research.
