Genetic Diversity, Compartmentalization, and Age of HIV Proviruses Persisting in CD4 + T Cell Subsets during Long-Term Combination Antiretroviral Therapy

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Genetic Evidence That Naive T Cells Can Contribute Significantly to the Human Immunodeficiency Virus Intact Reservoir: Time to Re-evaluate Their Role

Rullo, E. V., Cannon, L., Pinzone, M. R., Ceccarelli, M., Nunnari, G., & O’Doherty, U. (2019) · Clinical Infectious Diseases · doi:10.1093/cid/ciz378 · Cited by 38 · see citing works

Clonal Expansion of Human Immunodeficiency Virus–Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy

Mullins, J. I., & Frenkel, L. M. (2017) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiw636 · Cited by 29 · see citing works

Patterns and rates of viral evolution in HIV-1 subtype B infected females and males

Dapp, M. J., Kober, K. M., Chen, L., Westfall, D. H., Wong, K., Zhao, H. C., Hall, B., Deng, W., Sibley, T. R., Ghorai, S., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182443 · Cited by 21 · see citing works

HIV-1 variants are archived throughout infection and persist in the reservoir

Brooks, K., Jones, B. R., Dilernia, D. A., Wilkins, D. J., Claiborne, D. T., McInally, S., Gilmour, J. W., Kilembe, W., Joy, J. B., Allen, S. A., et al. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008378 · Cited by 51 · see citing works

Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection

Lau, C., Adan, M. A., & Maldarelli, F. M. (2021) · Viruses · doi:10.3390/v13122512 · Cited by 44 · see citing works

IFI27 is a potential therapeutic target for HIV infection

Huang, H., Lv, J., Huang, Y., Mo, Z., Xu, H.-S., Huang, Y., Yang, L., Wu, Z., Li, H., & Qin, Y. (2022) · Annals of Medicine · doi:10.1080/07853890.2021.1995624 · Cited by 23 · see citing works

HIV reservoirs are dominated by genetically younger and clonally enriched proviruses

Kinloch, N. N., Shahid, A., Dong, W., Kirkby, D., Jones, B. R., Beelen, C. J., MacMillan, D., Lee, G. Q., Mota, T. M., Sudderuddin, H., et al. (2023) · mBio · doi:10.1128/mbio.02417-23 · Cited by 21 · see citing works

Assessment of HIV-1 integration in tissues and subsets across infection stages

Wu, V. H., Nobles, C. L., Kuri-Cervantes, L., McCormick, K., Everett, J. K., Nguyen, S., Estrada, P. M. D. R., González-Navarro, M., Torres-Ruiz, F., Ávila‐Ríos, S., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.139783 · Cited by 19 · see citing works

Could gene therapy cure HIV?

Sheykhhasan, M., Foroutan, A., Manoochehri, H., Khoei, S. G., Poondla, N., & Saidijam, M. (2021) · Life Sciences · doi:10.1016/j.lfs.2021.119451 · Cited by 20 · see citing works

Addressing an HIV cure in LMIC

Ismail, S. D., Pankrac, J., Ndashimye, E., Prodger, J. L., Abrahams, M.-R., Mann, J. F. S., Redd, A. D., & Arts, E. J. (2021) · Retrovirology · doi:10.1186/s12977-021-00565-1 · Cited by 18 · see citing works

HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy

Omondi, F. H., Sudderuddin, H., Shahid, A., Kinloch, N. N., Jones, B. R., Miller, R. L., Tsai, O., MacMillan, D., Piechocka‐Trocha, A., Brockman, M. A., et al. (2021) · mBio · doi:10.1128/mbio.02490-21 · Cited by 17 · see citing works

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, B. R., Sudderuddin, H., Dang, Z., Cobarrubias, K. D., Duncan, M. C., Kinloch, N. N., Dapp, M. J., Archin, N. M., et al. (2024) · Journal of Virology · doi:10.1128/jvi.01655-23 · Cited by 16 · see citing works

HIV-1 infection of genetically engineered iPSC-derived central nervous system-engrafted microglia in a humanized mouse model

Min, A. K., Javidfar, B., Missall, R. D., Doanman, D., Durens, M., Vil, S. S., Masih, Z., Graziani, M., Mordelt, A., Marro, S. G., et al. (2023) · Journal of Virology · doi:10.1128/jvi.01595-23 · Cited by 16 · see citing works

Identifying physiological tissue niches that support the HIV reservoir in T cells

Ikeogu, N. M., Ajibola, O., Zayats, R., & Murooka, T. T. (2023) · mBio · doi:10.1128/mbio.02053-23 · Cited by 15 · see citing works

HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy

Shahid, A., Jones, B. R., Yang, J. S. W., Dong, W. W. Y., Shaipanich, T., Donohoe, K., Brumme, C. J., Joy, J. B., Leung, J. M., & Brumme, Z. L. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010613 · Cited by 10 · see citing works

Principal component analysis of early immune cell dynamics during pembrolizumab treatment of advanced urothelial carcinoma

Teshima, T., Kobayashi, Y., Kawai, T., Kushihara, Y., Nagaoka, K., Miyakawa, J., Akiyama, Y., Yamada, Y., Sato, Y., Yamada, D., et al. (2022) · Oncology Letters · doi:10.3892/ol.2022.13384 · Cited by 7 · see citing works

Combination therapies currently under investigation in phase I and phase II clinical trials for HIV-1

Pham, H. T., Yoo, S., & Mésplède, T. (2020) · Expert Opinion on Investigational Drugs · doi:10.1080/13543784.2020.1724281 · Cited by 8 · see citing works

Limited HIV-1 Subtype C nef 3′PPT Variation in Combination Antiretroviral Therapy Naïve and Experienced People Living with HIV in Botswana

Seatla, K. K., Maruapula, D., Choga, W. T., Morerinyane, O., Lockman, S., Novitsky, V., Kasvosve, I., Moyo, S. M., & Gaseitsiwe, S. (2021) · Pathogens · doi:10.3390/pathogens10081027 · Cited by 7 · see citing works

A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy

Shahid, A., Jones, B. R., Duncan, M. C., MacLennan, S., Dapp, M. J., Kuniholm, M. H., Aouizerat, B. E., Archin, N. M., Gange, S. J., Ofotokun, I., et al. (2024) · Virus Evolution · doi:10.1093/ve/veae094 · Cited by 6 · see citing works

Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir

Jones, B. R., & Joy, J. B. (2020) · Virus Evolution · doi:10.1093/ve/veaa089 · Cited by 6 · see citing works

Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods

Otte, F., Zhang, Y., Spagnuolo, J., Thielen, A., Däumer, M., Wiethe, C., Stoeckle, M., Kusejko, K., Klein, F., Metzner, K. J., et al. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100485 · Cited by 4 · see citing works

Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference

Jones, B. R., & Joy, J. B. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad156 · Cited by 3 · see citing works

Distinct HIV-1 Population Structure across Meningeal and Peripheral T Cells and Macrophage Lineage Cells

Rose, R., Gonzalez-Perez, M. P., Nolan, D. J., Ganta, K. K., LaFleur, T. M., Cross, S., Brody, R., Lamers, S. L., & Luzuriaga, K. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02508-22 · Cited by 3 · see citing works

SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells

Sambaturu, N., Fray, E. J., Hariharan, V., Wu, F., Zitzmann, C., Simonetti, F. R., Barouch, D. H., Siliciano, J. D., Siliciano, R. F., Ribeiro, R. M., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115663 · Cited by 3 · see citing works

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 timePreprint

Shahid, A., MacLennan, S., Jones, B. R., Sudderuddin, H., Dang, Z., Cobarrubias, K. D., Duncan, M. C., Kinloch, N. N., Dapp, M. J., Archin, N. M., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3259040/v1 · Cited by 3 · see citing works

Single genome amplification and molecular cloning of HIV-1 populations in acute HIV-1 infection: implications for studies on HIV-1 diversity and evolutionary rate

Hsieh, A. Y. Y., Hassan, A. S., Nazziwa, J., Lindquist, L., Karlson, S., Hare, J., Kamali, A., Karita, E., Kilembe, W., Price, M. A., et al. (2025) · Virus Evolution · doi:10.1093/ve/veaf099 · Cited by 2 · see citing works

Non-suppressible HIV viremia sustained by clonally expanded CD4+ T cells harboring a genomically defective provirus with an immune-evasive protein expression profile

Omondi, F. H., Sang, Y., Dong, W. W. Y., Mwimanzi, F. M., Cheung, P. K., Barad, E., Derza, Z., Anderson, K., Shahid, A., Mysak, V., et al. (2026) · mBio · doi:10.1128/mbio.03909-25 · Cited by 2 · see citing works

The persistent pool of HIV-1-infected cells is formed episodically during untreated infection

Tyers, L., Moeser, M., Sondgeroth, A., Spielvogel, E., Richardson, B., Doolabh, D., Zhou, S., Emery, A., Archin, N. M., Shook‐Sa, B. E., et al. (2024) · Journal of Virology · doi:10.1128/jvi.00979-24 · Cited by 2 · see citing works

Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4 + T cellsPreprint

Sambaturu, N., Fray, E. J., Wu, F., Zitzmann, C., Simonetti, F. R., Barouch, D. H., Siliciano, J. D., Siliciano, R. F., Ribeiro, R. M., Perelson, A. S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.03.565539

A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapyPreprint

Shahid, A., Jones, B. R., Duncan, M. C., MacLennan, S., Dapp, M. J., Kuniholm, M. H., Aouizerat, B. E., Archin, N. M., Gange, S. J., Ofotokun, I., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4549934/v1

The rebound-initiating viral reservoir (RIVR) in SIV/SHIV infection is dominated by plasma virus sequences present at the time of ART initiation

Pinkevych, M., Docken, S. S., Wu, Y., Schlub, T. E., Harper, J. L., Viox, E. G., Samer, S., Kulpa, D. A., Betts, M. R., Keele, B. F., et al. (2026) · Journal of Virology · doi:10.1128/jvi.00366-26

The pitfalls of HIV-1 DNA resistance genotyping: What it can and cannot tell us

Mchantaf, G., Morand‐Joubert, L., Chéret, A., Hocqueloux, L., & Avettand-Fènoël, V. (2026) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2026.108026

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 timePreprint

Shahid, A., MacLennan, S., Jones, B. R., Sudderuddin, H., Dang, Z., Cobarrubias, K. D., Duncan, M. C., Kinloch, N. N., Dapp, M. J., Archin, N. M., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3259040/v1 · Cited by 3 · see citing works

HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy

Shahid, A., Jones, B. R., Yang, J. S. W., Dong, W. W. Y., Shaipanich, T., Donohoe, K., Brumme, C. J., Joy, J. B., Leung, J. M., & Brumme, Z. L. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010613 · Cited by 10 · see citing works

HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy

Omondi, F. H., Sudderuddin, H., Shahid, A., Kinloch, N. N., Jones, B. R., Miller, R. L., Tsai, O., MacMillan, D., Piechocka‐Trocha, A., Brockman, M. A., et al. (2021) · mBio · doi:10.1128/mbio.02490-21 · Cited by 17 · see citing works

PP 1.16 – 00100 Single-cell multiomics analysis reveals distinct mechanisms of HIV persistence in memory CD4+ T cell subsets from tissues

Frouard, J., Luo, X., & Roan, N. R. (2022) · Journal of Virus Eradication · doi:10.1016/j.jve.2022.100121

Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4 + T cellsPreprint

Sambaturu, N., Fray, E. J., Wu, F., Zitzmann, C., Simonetti, F. R., Barouch, D. H., Siliciano, J. D., Siliciano, R. F., Ribeiro, R. M., Perelson, A. S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.03.565539