Barcoded HIV-1 reveals viral persistence driven by clonal proliferation and distinct epigenetic patterns

Area of Science:

• Virology
• Immunology
• Genetics

Background:

• The human immunodeficiency virus (HIV) reservoir comprises infected cells harboring persistent HIV-1 provirus, even during effective antiretroviral therapy (ART).
• Current HIV cure research often assesses intact proviral DNA, viral rebound post-ART interruption, or ex vivo assays of latently infected cells.

Purpose of the Study:

• To comprehensively analyze HIV reservoir dynamics, including viral genetic diversity, integration sites, and clonal proliferation, in vivo using a barcoded HIV model in humanized mice.
• To elucidate the role of cellular proliferation in maintaining the viral reservoir and driving viral persistence during and after ART.

Main Methods:

• Utilized barcoded HIV in humanized mice for in vivo reservoir analysis.
• Employed bulk PCR and deep sequencing to identify viral RNA and proviral barcodes, linking them to integration sites at the single-molecule level.
• Tracked viral genetic diversity, cellular clonal proliferation, and proviral dynamics throughout infection, ART, and rebound phases.

Main Results:

• Successfully retrieved 890 viral RNA barcodes and 504 proviral barcodes linked to 15,305 integration sites.
• Observed that the proviral reservoir maintains genetic diversity despite cellular proliferation and viral seeding from rebound viremia.
• Identified that proliferated, but not massively expanded, cell clones contribute significantly to proviral expansion and viremia, thus fueling viral persistence.

Conclusions:

• The study provides a comprehensive in vivo assessment of HIV reservoir characteristics, including viral levels, lineages, integration sites, and clonal proliferation.
• Findings indicate that proliferated cell clones play a crucial role in sustaining HIV persistence and driving viremia.
• This research offers novel insights into the complex dynamics of the HIV reservoir, essential for advancing HIV cure strategies.