Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR

Author:

Brandt, Leah D [ORCID]

Guo,Amber [ORCID]

Joseph, Kevin W

Jacobs, Jana L

Naqvi, Asma

Coffin, John M

Kearney,Mary

Halvas, Elias K

Wu,Xiaolin

Hughes,Stephen

Mellors, John W
Author Address

Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA., Cancer Research Technology Program, Leidos Biomedical Research, Inc., 8560 Progress Drive, ATRF, Room C3004, Frederick, MD 21701, USA., Department of Molecular Biology and Microbiology, Tufts University, 145 Harrison Avenue, Jaharis 409, Boston, MA 02111, USA., HIV-Dynamics and Replication Program, National Cancer Institute, 1050 Boyles Street, Building 535, Room 308, Frederick, MD 21702, USA.,

Abstract:

Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the dynamics of repliclones are not well defined. The major challenge in tracking repliclones is the relative rarity of the cells carrying specific intact proviruses. To date, detection and accurate quantification of repliclones requires in-depth integration site sequencing. Here, we describe a simplified workflow using integration site-specific qPCR (IS-qPCR) to determine the frequencies of the proviruses integrated in individual repliclones. We designed IS-qPCR to determine the frequencies of repliclones and clones of cells that carry defective proviruses in samples from three donors. Comparing the results of IS-qPCR with deep integration site sequencing data showed that the two methods yielded concordant estimates of clone frequencies (r = 0.838). IS-qPCR is a potentially valuable tool that can be applied to multiple samples and cell types over time to measure the dynamics of individual repliclones and the efficacy of treatments designed to eliminate them.

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