HIVE-seq: A Novel Omics Technology to Profile Thousands of Single HIV-Positive Cells

About This Grant

ABSTRACT Identifying and fully characterizing cells infected with viable HIV proviruses in diverse tissues without reactivation remains a critical barrier to developing curative strategies, particularly in people living with HIV (PLWH) who also use opioids, where the reservoir’s biology can differ. This Fast-Track SBIR aims to address this gap by building on published, rigorously tested academic protocols to create HIVE-seq: a novel platform integrating the intact proviral DNA assay (IPDA) with single-cell/nucleus multi-omic profiling. Unlike current methods that rely on virus reactivation or partial genotyping, HIVE-seq preserves the natural, unstimulated state of HIV-infected cells while capturing comprehensive viral and host information, including full-length proviral sequences, and host cell transcriptomes, and proteomes. In Phase I, we will transfer single-cell protocols to Fluid Discovery’s R&D facility, validate the workflow with known reference standards, and establish SOPs for processing blood and solid tissues. We will validate our methods using samples from diverse tissue sources, including blood, lymph nodes, brain, gut, and other clinically relevant tissues. Critically, we will prioritize access to the Last Gift cohort, a unique biorepository of tissues from PLWH who used opioids, to ensure our platform addresses this understudied population (see letters of support). In Phase II, we will first operate an in-house service laboratory to immediately process real-world samples, refining performance and demonstrating commercial feasibility. We will then enhance the platform’s throughput, automation, and data analysis pipelines, ensuring it can handle complex tissues and high sample volumes. Finally, we will integrate these improvements into a commercial-ready HIVE- seq instrument and reagent kit, enabling researchers to detect intact proviruses directly and gain unprecedented insight into how opioid use affects HIV latency. With support from expert collaborators at UCSF and the Gladstone Institutes, and leveraging our extensive prior work, this proposal will deliver a transformative, user- friendly tool to accelerate HIV research, guide targeted interventions, and advance cure efforts.