Guinevere Q. Lee

This session addressed novel methods at the forefront of characterizing HIV persistence. Advances reported includes a method to study reservoir age, technologies to capture viral genome sequences, integration sites and viral transcripts, and an overview of single cell methods for reservoir studies.

Dr. Zabrina Brumme (Simon Fraser University) described a method to infer the date of when a cell was infected with HIV. Before ART initiation, reservoir turnover time during viremic infection was shorter relative to the turnover time post-treatment initiation. She also reported that early treatment limits the genetic diversity and complexity of the reservoir. Dr. Mathias Lichterfeld (Brigham and Women’s Hospital) described a series of methods (FLIP-seq, MIP-seq and PRIP-seq) to sequence proviral genomes, identify integration sites, and detect viral transcription activity from the same infected cell. His team found that proviral integration site profiles evolve over time and become enriched in centromeric integrations, and share similar integration profiles detected in elite controllers. Dr. Linos Vandekerckhove (UZ Gent) provided a critical assessment of current limiting dilution and single cell approaches to study the reservoir. Techniques discussed included FLIP-Seq, MIP-seq, Sort-Seq, LURE, PP-SLIDE and ECCITE-seq. Sort-Seq and LURE requires stimulation and alters the transcription profiles of infected cells, CyTOF-based PP-SLIDE enables multi-dimension analyses but is bioinformatically intense, while ECCITE-seq achieves high resolution but requires processing a large number of cells. Their team is testing a compound that would stimulate HIV transcription while minimally affecting the state of infected cells (Abstract 6473).

Dr. Zabrina Brumme’s presentation reaffirms the importance of early ART and limiting viral diversity before treatment initiation as a strategy to reduce viral diversity in the reservoir. Dr. Mathias Lichterfeld’s methods enables high resolution interrogation of viral reservoir composition in terms of genetic content, integration sites and transcription activities. Dr. Linos Vandekerckhove showed that single cell methodologies provide a powerful tool for studying conditions that facilitate persistence of HIV. Their team is also tackling a long-standing challenge: to achieve a high throughput method to study HIV-infected cells without altering the profiles of infected cells.