Journal article
Deep sequencing analysis of individual HIV-1 proviruses reveals frequent asymmetric long terminal repeats
Journal of Virology, Vol.96(13)
2022
Abstract
Effective strategies to eliminate human immunodeficiency virus type 1 (HIV-1) reservoirs are likely to require more thorough characterizations of proviruses that persist on antiretroviral therapy (ART). The rarity of infected CD4+ T-cells and related technical challenges have limited the characterization of integrated proviruses. Current approaches using next-generation sequencing can be inefficient and limited sequencing depth can make it difficult to link proviral sequences to their respective integration sites. Here, we report on an efficient method by which HIV-1 proviruses and their sites of integration are amplified and sequenced. Across five HIV-1-positive individuals on clinically effective ART, a median of 41.2% (n = 88 of 209) of amplifications yielded near-full-length proviruses and their 5′-host-virus junctions containing a median of 430 bp (range, 18 to 1,363 bp) of flanking host sequence. Unexpectedly, 29.5% (n = 26 of 88) of the sequenced proviruses had structural asymmetries between the 5′ and 3′ long terminal repeats (LTRs), commonly in the form of major 3′ deletions. Sequence-intact proviruses were detected in 3 of 5 donors, and infected CD4+ T-cell clones were detected in 4 of 5 donors. The accuracy of the method was validated by amplifying and sequencing full-length proviruses and flanking host sequences directly from peripheral blood mononuclear cell DNA. The individual proviral sequencing assay (IPSA) described here can provide an accurate, in-depth, and longitudinal characterization of HIV-1 proviruses that persist on ART, which is important for targeting proviruses for elimination and assessing the impact of interventions designed to eradicate HIV-1.
Details
- Title
- Deep sequencing analysis of individual HIV-1 proviruses reveals frequent asymmetric long terminal repeats
- Authors/Creators
- K.W. Joseph (Author/Creator) - University of PittsburghE.K. Halvas (Author/Creator) - University of PittsburghL.D. Brandt (Author/Creator) - University of PittsburghS.C. Patro (Author/Creator) - National Cancer InstituteJ.W. Rausch (Author/Creator) - Basic Research Laboratory, Center for Cancer Research, National Cancer Institutegrid.48336.3a, Frederick, Maryland, USA.A. Chopra (Author/Creator) - Murdoch UniversityS. Mallal (Author/Creator) - Murdoch UniversityM.F. Kearney (Author/Creator) - National Cancer InstituteJ.M. Coffin (Author/Creator) - Tufts UniversityJ.W. Mellors (Author/Creator) - University of PittsburghF. Kirchhoff (Author/Creator)
- Publication Details
- Journal of Virology, Vol.96(13)
- Publisher
- American Society for Microbiology
- Identifiers
- 991005542628007891
- Copyright
- © 2022 Joseph et al.
- Murdoch Affiliation
- Institute for Immunology and Infectious Diseases
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.66 HIV
- 1.66.46 HIV Pathogenesis
- Web Of Science research areas
- Virology
- ESI research areas
- Microbiology