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Cell Rep. 2017 Oct 17;21(3):813-822. doi: 10.1016/j.celrep.2017.09.081.

Identification of Genetically Intact HIV-1 Proviruses in Specific CD4+ T Cells from Effectively Treated Participants.

Author information

1
Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia. Electronic address: bonnie.hiener@sydney.edu.au.
2
Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia.
3
Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
4
Sydney School of Public Health, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
5
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 77, Sweden.
6
Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA.
7
Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD 20814, USA.
8
Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD 20814, USA.
9
Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H2X 0A9, Canada.

Abstract

Latent replication-competent HIV-1 persists in individuals on long-term antiretroviral therapy (ART). We developed the Full-Length Individual Proviral Sequencing (FLIPS) assay to determine the distribution of latent replication-competent HIV-1 within memory CD4+ T cell subsets in six individuals on long-term ART. FLIPS is an efficient, high-throughput assay that amplifies and sequences near full-length (∼9 kb) HIV-1 proviral genomes and determines potential replication competency through genetic characterization. FLIPS provides a genome-scale perspective that addresses the limitations of other methods that also genetically characterize the latent reservoir. Using FLIPS, we identified 5% of proviruses as intact and potentially replication competent. Intact proviruses were unequally distributed between T cell subsets, with effector memory cells containing the largest proportion of genetically intact HIV-1 proviruses. We identified multiple identical intact proviruses, suggesting a role for cellular proliferation in the maintenance of the latent HIV-1 reservoir.

KEYWORDS:

HIV; antiretroviral therapy; cellular proliferation; clonal expansion; full-length HIV sequencing; latency; replication competency; single proviral sequencing

PMID:
29045846
PMCID:
PMC5960642
DOI:
10.1016/j.celrep.2017.09.081
[Indexed for MEDLINE]
Free PMC Article

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