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A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy.
Shahid A, Jones BR, Duncan MC, MacLennan S, Dapp MJ, Kuniholm MH, Aouizerat B, Archin NM, Gange S, Ofotokun I, Fischl MA, Kassaye S, Goldstein H, Anastos K, Joy JB, Brumme ZL. Shahid A, et al. Among authors: joy jb. Virus Evol. 2024 Nov 11;11(1):veae094. doi: 10.1093/ve/veae094. eCollection 2025. Virus Evol. 2024. PMID: 39802824 Free PMC article.
The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time.
Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobamibias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. Shahid A, et al. Among authors: joy jb. Res Sq [Preprint]. 2023 Aug 16:rs.3.rs-3259040. doi: 10.21203/rs.3.rs-3259040/v1. Res Sq. 2023. Update in: J Virol. 2024 Feb 20;98(2):e0165523. doi: 10.1128/jvi.01655-23 PMID: 37645749 Free PMC article. Updated. Preprint.
Phylogenetic approach to recover integration dates of latent HIV sequences within-host.
Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman MA, Joy JB, Poon AFY, Brumme ZL. Jones BR, et al. Among authors: joy jb. Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8958-E8967. doi: 10.1073/pnas.1802028115. Epub 2018 Sep 5. Proc Natl Acad Sci U S A. 2018. PMID: 30185556 Free PMC article.
Genetic Diversity, Compartmentalization, and Age of HIV Proviruses Persisting in CD4+ T Cell Subsets during Long-Term Combination Antiretroviral Therapy.
Jones BR, Miller RL, Kinloch NN, Tsai O, Rigsby H, Sudderuddin H, Shahid A, Ganase B, Brumme CJ, Harris M, Poon AFY, Brockman MA, Fromentin R, Chomont N, Joy JB, Brumme ZL. Jones BR, et al. Among authors: joy jb. J Virol. 2020 Feb 14;94(5):e01786-19. doi: 10.1128/JVI.01786-19. Print 2020 Feb 14. J Virol. 2020. PMID: 31776273 Free PMC article.
HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy.
Omondi FH, Sudderuddin H, Shahid A, Kinloch NN, Jones BR, Miller RL, Tsai O, MacMillan D, Trocha A, Brockman MA, Brumme CJ, Joy JB, Liang R, Walker BD, Brumme ZL. Omondi FH, et al. Among authors: joy jb. mBio. 2021 Dec 21;12(6):e0249021. doi: 10.1128/mBio.02490-21. Epub 2021 Nov 16. mBio. 2021. PMID: 34781741 Free PMC article.
HIV reservoirs are dominated by genetically younger and clonally enriched proviruses.
Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. Kinloch NN, et al. Among authors: joy jb. bioRxiv [Preprint]. 2023 Apr 13:2023.04.12.536611. doi: 10.1101/2023.04.12.536611. bioRxiv. 2023. Update in: mBio. 2023 Dec 19;14(6):e0241723. doi: 10.1128/mbio.02417-23 PMID: 37090500 Free PMC article. Updated. Preprint.
66 results