Deep Sequencing Analysis of Individual HIV-1 Proviruses Reveals Frequent Asymmetric Long Terminal Repeats
Year: 2022
Type: article
Abstract: The integration of human immunodeficiency virus type 1 (HIV-1) into chromosomal DNA establishes the long-term persistence of HIV-1 as proviruses despite effective antiretroviral therapy (ART). Characterizing proviruses is difficult because of their rarity in individuals on long-term suppressive ART, their highly polymorphic sequences and genetic structures, and the need for efficient amplification and sequencing of the provirus and its integration site. Here, we describe a novel, integrated, two-step method (individual proviral sequencing assay [IPSA]) that amplifies the host-virus junction and the full-length provirus except for the last 69 bp of the 3' long terminal repeat (LTR). Using this method, we identified the integration sites of proviruses, including those that are sequence intact and replication competent or defective. Importantly, this new method identified previously unreported asymmetries between LTRs that have implications for how proviruses are detected and quantified. The IPSA method reported is unaffected by LTR asymmetries, permitting a more accurate and comprehensive characterization of the proviral landscape.
Source: Journal of Virology
DOI: 10.1128/jvi.00122-22
Language: English
Topic: HIV Research and Treatment
Subfield: Virology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: hybrid
Funders: U.S. Department of Health and Human Services, American Cancer Society, Bill and Melinda Gates Foundation, University of Pittsburgh, Allegheny Health Network, ACT Government, Leidos, National Institutes of Health, Medical Center, University of Pittsburgh, National Cancer Institute, National Institute of Allergy and Infectious Diseases, Office of AIDS Research
Awards: G2271303644, G2415337126, G285461174, G3322579637, Retrovirus Evolution and Cancer, G4062820909, G4304622442, G4573400019, Combined Immunologic Approaches to Cure HIV-1, G4661820159, G4689185066, G4691177778, G6252953675, G632742325, G6760706999, G6852276336, G8567865963, G8734902035, REACH: Research Enterprise to Advance a Cure for HIV, AIDS Clinical Trial Group Laboratory Center, I4C 2.0: Immunotherapy for Cure, G996393186
OpenAlex ID: W4282942205