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HIV reservoir quantification using cross-subtype multiplex ddPCR.

Noah A J Cassidy1, Carolyn S Fish1, Claire N Levy2

  • 1Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Iscience
|February 2, 2022
PubMed
Summary
This summary is machine-generated.

Developing a new assay to measure intact HIV DNA across diverse subtypes is crucial for HIV cure research. This tool accurately quantifies the HIV reservoir, aiding studies in high-burden regions.

Keywords:
GenotypingVirology

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Area of Science:

  • Virology
  • Immunology
  • Infectious Diseases

Background:

  • Accurate quantification of the replication-competent HIV-1 reservoir is essential for cure research, particularly in regions with high HIV burden.
  • Existing assays often lack the ability to detect diverse global HIV-1 subtypes, limiting their applicability in widespread research.
  • The presence of intact proviral DNA is a key indicator of the persistent viral reservoir.

Purpose of the Study:

  • To modify and validate a cross-subtype assay for quantifying intact and defective HIV-1 proviral DNA.
  • To assess the assay's performance across major global HIV-1 subtypes (A, B, C, D, CRF01_AE).
  • To evaluate the assay's utility in longitudinal samples from infants undergoing antiretroviral therapy.

Main Methods:

  • Adaptation of a subtype B HIV-1 assay to accommodate cross-subtype sequence diversity.
  • Validation of the modified assay's ability to detect intact provirus down to a single copy.
  • Application of the assay to longitudinal blood samples from Kenyan infants infected with HIV-1 subtypes A and D.

Main Results:

  • The developed cross-subtype assay accurately quantifies intact and defective HIV-1 DNA across subtypes A, B, C, D, and CRF01_AE.
  • The assay demonstrated sensitivity to detect a single copy of intact provirus.
  • In infants on antiretroviral therapy, intact HIV DNA constituted 7% (range 1%-33%) of total HIV DNA during viral suppression, mirroring plasma viral load decay.

Conclusions:

  • This high-throughput, cross-subtype HIV reservoir assay is a valuable tool for HIV cure research.
  • The assay's ability to work across diverse subtypes makes it suitable for application in Africa and Asia, regions with the highest HIV prevalence.
  • The findings support the use of this assay to monitor reservoir dynamics during treatment and in potential cure strategies.