Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART
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Significance: Previously, we showed that the virus that persists in human immunodeficiency virus (HIV)-infected individuals on antiretroviral therapy (ART) is derived from cells infected prior to initiating treatment. We also showed that HIV-infected cells can undergo cellular proliferation during ART. However, it is not known what fraction of infected cells that persist during ART are latent and what fraction are actively producing HIV RNA. The method described here was developed to determine the fraction of infected cells that produce HIV RNA and the levels of HIV RNA in single cells, including cells that have undergone cellular proliferation. Additionally, the method can be used to identify the sources of rebound virus after stopping ART and the efficacy of experimental interventions designed to cure HIV infection.
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A multitude of studies showed that defective HIV-1 genomes inside cells may still produce individual viral transcripts or proteins, which could be mistaken as indicators of a functional reservoir of infectious virus.
“Conversely, a multitude of studies showed that defective HIV-1 genomes inside cells may still produce individual viral transcripts or proteins, 33-35,55 which could be mistaken as indicators of a functional reservoir of infectious virus.”
From Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods (2023) · cites this paper as [55]
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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013) · Molecular biology and evolution · doi:10.1093/molbev/mst197 · Cited by 41,174 · see citing works
Keele, B. F., Giorgi, E. E., Salazar-Gonzalez, J. F., Decker, J. M., Pham, K. T., Salazar, M. G., Sun, C., Grayson, T. B., Wang, S., Li, H., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802203105 · Cited by 1,913 · see citing works
Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure
Ho, Y.-C., Shan, L., Hosmane, N. N., Wang, J., Laskey, S. B., Rosenbloom, D. I. S., Lai, J., Blankson, J. N., Siliciano, J. D., & Siliciano, R. F. (2013) · Cell · doi:10.1016/j.cell.2013.09.020 · Cited by 1,405 · see citing works
Specific HIV integration sites are linked to clonal expansion and persistence of infected cells
Maldarelli, F., Wu, X., Su, L., Simonetti, F. R., Shao, W., Hill, S., Spindler, J., Ferris, A. L., Mellors, J. W., Kearney, M. F., et al. (2014) · Science · doi:10.1126/science.1254194 · Cited by 849 · see citing works
Self-citationDefective proviruses rapidly accumulate during acute HIV-1 infection
Bruner, K. M., Murray, A. J., Pollack, R. A., Soliman, M. G., Laskey, S. B., Capoferri, A. A., Lai, J., Strain, M. C., Lada, S. M., Hoh, R., et al. (2016) · Nature Medicine · doi:10.1038/nm.4156 · Cited by 737 · see citing works
Folks, T. M., Clouse, K. A., Justement, J. S., Rabson, A. B., Duh, E. J., Kehrl, J. H., & Fauci, A. S. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.7.2365 · Cited by 701 · see citing works
Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection
Wagner, T. A., McLaughlin, S., Garg, K., Cheung, C. Y. K., Larsen, B. B., Styrchak, S., Huang, H. C., Edlefsen, P. T., Mullins, J. I., & Frenkel, L. M. (2014) · Science · doi:10.1126/science.1256304 · Cited by 677 · see citing works
Palmer, S., Kearney, M., Maldarelli, F., Halvas, E. K., Bixby, C. J., Bazmi, H., Rock, D., Falloon, J., Davey, R. T., Dewar, R. L., et al. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.1.406-413.2005 · Cited by 506 · see citing works
Self-citationDinoso, J. B., Kim, S. Y., Wiegand, A. P., Palmer, S., Gange, S. J., Cranmer, L. M., O'Shea, A., Callender, M., Spivak, A. M., Brennan, T. P., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903107106 · Cited by 439 · see citing works
Self-citationHIV-1 Integration Landscape during Latent and Active Infection
Cohn, L. B., da Silva, I. T., Oliveira, T. Y., Rosales, R., Parrish, E. H., Learn, G. H., Hahn, B. H., Czartoski, J., McElrath, M. J., Lehmann, C., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.020 · Cited by 438 · see citing works
Bailey, J. R., Sedaghat, A. R., Kieffer, T. L., Brennan, T. P., Lee, P. K., Wind‐Rotolo, M., Haggerty, C. M., Kamireddi, A. R., Liu‐Chittenden, Y., Lee, J., et al. (2006) · Journal of Virology · doi:10.1128/jvi.00591-06 · Cited by 417 · see citing works
Clonally expanded CD4 <sup>+</sup> T cells can produce infectious HIV-1 in vivo
Simonetti, F. R., Sobolewski, M. D., Fyne, E., Shao, W., Spindler, J., Hattori, J., Anderson, E. M., Watters, S. A., Hill, S., Wu, X., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1522675113 · Cited by 372 · see citing works
Self-citationPomerantz, R. J., Trono, D., Feinberg, M. B., & Baltimore, D. (1990) · Cell · doi:10.1016/0092-8674(90)90691-7 · Cited by 365 · see citing works
Imamichi, H., Dewar, R. L., Adelsberger, J. W., Rehm, C. A., O’Doherty, U., Paxinos, E. E., Fauci, A. S., & Lane, H. C. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1609057113 · Cited by 344 · see citing works
Gandhi, R. T., Zheng, L., Bosch, R. J., Chan, E. S., Margolis, D. M., Read, S., Kallungal, B., Palmer, S., Medvik, K., Lederman, M. M., et al. (2010) · PLoS Medicine · doi:10.1371/journal.pmed.1000321 · Cited by 305 · see citing works
Self-citationMaldarelli, F. M., Wu, X., Su, L., Simonetti, F. R., Wells, D. W., Shao, W., Spindler, J., Ferris, A. L., Mellors, J. W., Kearney, M. F., et al. (2016) · JAIDS Journal of Acquired Immune Deficiency Syndromes · doi:10.1097/01.qai.0000479721.09749.2d · Cited by 294 · see citing works
Self-citationRothenberger, M. K., Keele, B. F., Wietgrefe, S. W., Fletcher, C. V., Beilman, G. J., Chipman, J. G., Khoruts, A., Estes, J. D., Anderson, J. L., Callisto, S. P., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414926112 · Cited by 276 · see citing works
Defining HIV and SIV Reservoirs in Lymphoid Tissues
Deleage, C., Wietgrefe, S., Prete, G. D. D., Morcock, D. R., Hao, X.-P., Piatak, M., Bess, J., Anderson, J. L., Perkey, K. E., Reilly, C., et al. (2016) · Pathogens and Immunity · doi:10.20411/pai.v1i1.100 · Cited by 256 · see citing works
Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy
Kearney, M. F., Spindler, J., Shao, W., Yu, S. S., Anderson, E. M., O'Shea, A., Rehm, C. A., Poethke, C., Kovacs, N., Mellors, J. W., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004010 · Cited by 235 · see citing works
Self-citationArchin, N. M., Vaidya, N. K., Kuruc, J. D., Liberty, A. L., Wiegand, A. P., Kearney, M. F., Cohen, M. S., Coffin, J. M., Bosch, R. J., Gay, C. L., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120248109 · Cited by 220 · see citing works
Self-citationHIV-1 DNA Decay Dynamics in Blood During More Than a Decade of Suppressive Antiretroviral Therapy
Besson, G. J., Lalama, C. M., Bosch, R. J., Gandhi, R. T., Bedison, M. A., Aga, E., Riddler, S. A., McMahon, D. K., Hong, F. F., & Mellors, J. W. (2014) · Clinical Infectious Diseases · doi:10.1093/cid/ciu585 · Cited by 217 · see citing works
Self-citationSingle-Cell Characterization of Viral Translation-Competent Reservoirs in HIV-Infected Individuals
Baxter, A. E., Niessl, J., Fromentin, R., Richard, J., Porichis, F., Charlebois, R., Massanella, M., Brassard, N., Alsahafi, N., Ortega-Delgado, G.-G., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.07.015 · Cited by 187 · see citing works
Lorenzi, J. C. C., Cohen, Y. Z., Cohn, L. B., Kreider, E. F., Barton, J. P., Learn, G. H., Oliveira, T. Y., Lavine, C. L., Horwitz, J. A., Settler, A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617789113 · Cited by 172 · see citing works
Human Immunodeficiency Virus Type 1 Population Genetics and Adaptation in Newly Infected Individuals
Kearney, M. F., Maldarelli, F. M., Shao, W., Margolick, J. B., Daar, E. S., Mellors, J. W., Rao, V. B., Coffin, J. M., & Palmer, S. (2008) · Journal of Virology · doi:10.1128/jvi.01960-08 · Cited by 170 · see citing works
Self-citationThe role of unintegrated DNA in HIV infection
Sloan, R. D., & Wainberg, M. A. (2011) · Retrovirology · doi:10.1186/1742-4690-8-52 · Cited by 155 · see citing works
Kearney, M. F., Wiegand, A. P., Shao, W., Coffin, J. M., Mellors, J. W., Lederman, M. M., Gandhi, R. T., Keele, B. F., & Li, J. Z. (2015) · Journal of Virology · doi:10.1128/jvi.02139-15 · Cited by 149 · see citing works
Self-citationHIV Populations Are Large and Accumulate High Genetic Diversity in a Nonlinear Fashion
Maldarelli, F. M., Kearney, M. F., Palmer, S., Stephens, R. M., Mican, J. M., Polis, M. A., Davey, R. T., Kovacs, J. A., Shao, W., Rock-Kress, D., et al. (2013) · Journal of Virology · doi:10.1128/jvi.01225-12 · Cited by 130 · see citing works
Self-citationJosefsson, L., Palmer, S., Faria, N. R., Lemey, P., Casazza, J. P., Ambrozak, D. R., Kearney, M. F., Shao, W., Kottilil, S., Sneller, M. C., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003432 · Cited by 112 · see citing works
Self-citationCillo, A. R., Vagratian, D., Bedison, M. A., Anderson, E. M., Kearney, M. F., Fyne, E., Koontz, D. L., Coffin, J. M., Piatak, M., & Mellors, J. W. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.02060-14 · Cited by 109 · see citing works
Self-citationGandhi, R. T., Coombs, R. W., Chan, E. S., Bosch, R. J., Zheng, L., Margolis, D. M., Read, S., Kallungal, B., Chang, M., Goecker, E. A., et al. (2011) · JAIDS Journal of Acquired Immune Deficiency Syndromes · doi:10.1097/qai.0b013e31823fd1f2 · Cited by 107 · see citing works
Self-citationNovel Assays for Measurement of Total Cell-Associated HIV-1 DNA and RNA
Hong, F. F., Aga, E., Cillo, A. R., Yates, A. L., Besson, G. J., Fyne, E., Koontz, D. L., Jennings, C., Zheng, L., & Mellors, J. W. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.02904-15 · Cited by 100 · see citing works
Self-citationFrequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase
Kearney, M. F., Palmer, S., Maldarelli, F. M., Shao, W., Polis, M. A., Mican, J. M., Rock-Kress, D., Margolick, J. B., Coffin, J. M., & Mellors, J. W. (2008) · AIDS · doi:10.1097/qad.0b013e3282f29478 · Cited by 80 · see citing works
Self-citationAccumulation and Intranuclear Distribution of Unintegrated Human Immunodeficiency Virus Type 1 DNA
Bell, P., Montaner, L. J., & Maul, G. G. (2001) · Journal of Virology · doi:10.1128/jvi.75.16.7683-7691.2001 · Cited by 63 · see citing works
Assays for precise quantification of total (including short) and elongated HIV-1 transcripts
Kaiser, P. D., Joshi, S. K., Kim, P., Li, P., Liu, H., Rice, A. P., Wong, J. K., & Yukl, S. A. (2016) · Journal of Virological Methods · doi:10.1016/j.jviromet.2016.12.017 · Cited by 40 · see citing works
Cillo, A. R., Krishnan, S., McMahon, D. K., Mitsuyasu, R. T., Para, M. F., & Mellors, J. W. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092118 · Cited by 29 · see citing works
Self-citationKearney, M. F., Anderson, E. M., Coomer, C. A., Smith, L., Shao, W., Johnson, N., Kline, C. E., Spindler, J., Mellors, J. W., Coffin, J. M., et al. (2015) · Retrovirology · doi:10.1186/s12977-015-0212-2 · Cited by 27 · see citing works
Self-citationKiselinova, M., Geretti, A. M., Malatinková, E., Vervisch, K., Beloukas, A. I., Messiaen, P., Bonczkowski, P., Trypsteen, W., Callens, S. F. J., Verhofstede, C., et al. (2015) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkv250 · Cited by 22 · see citing works
Panther, L., Coombs, R. W., Zeh, J. E., Collier, A. C., & Corey, L. (1998) · Journal of Acquired Immune Deficiency Syndromes & Human Retrovirology · doi:10.1097/00042560-199804010-00003 · Cited by 22 · see citing works
Recent developments in human immunodeficiency virus-1 latency research
Chan, C. N., Dietrich, I., Hosie, M. J., & Willett, B. J. (2013) · Journal of General Virology · doi:10.1099/vir.0.049296-0 · Cited by 21 · see citing works
Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells
Althaus, C. L., Joos, B., Perelson, A. S., & Günthard, H. F. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003871 · Cited by 19 · see citing works
Sharkey, M. E. (2013) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0b013e32835d08c2 · Cited by 10 · see citing works
McDermott, J. L., Martini, I., Ferrari, D., Bertolotti, F., Giacomazzi, C., Murdaca, G., Puppo, F., Indiveri, F., & Varnier, O. E. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.10.5272-5274.2005 · Cited by 10 · see citing works
Contribution of HIV-1 genomes that do not integrate to the basic reproductive ratio of the virus
Lau, J. W., Levy, D. N., & Wodarz, D. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.12.004 · Cited by 4 · see citing works
Molecular mechanism of HIV-1 resistance to 3′-azido-2′,3′-dideoxyguanosine
Meteer, J. D., Schinazi, R. F., Mellors, J. W., & Sluis‐Cremer, N. (2013) · Antiviral Research · doi:10.1016/j.antiviral.2013.10.017 · Cited by 3 · see citing works
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Ganor, Y., Real, F., Sennepin, A., Dutertre, C., Prevedel, L., Xu, L., Tudor, D., Muylder, B. C.-D., Couëdel-Courteille, A., Marion, S., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0335-z · Cited by 295 · see citing works
The Biology of the HIV-1 Latent Reservoir and Implications for Cure Strategies
Cohn, L. B., Chomont, N., & Deeks, S. G. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.03.014 · Cited by 280 · see citing works
Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses
Einkauf, K. B., Osborn, M. R., Gao, C., Sun, W., Sun, X., Lian, X., Parsons, E. M., Gladkov, G. T., Seiger, K. W., Blackmer, J. E., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.011 · Cited by 260 · see citing works
Pinzone, M. R., VanBelzen, J., Weissman, S., Bertuccio, M. P., Cannon, L., Rullo, E. V., Migueles, S. A., Jones, R. B., Mota, T. M., Joseph, S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08431-7 · Cited by 175 · see citing works
Why and where an HIV cure is needed and how it might be achieved
Ndung’u, T., McCune, J. M., & Deeks, S. G. (2019) · Nature · doi:10.1038/s41586-019-1841-8 · Cited by 144 · see citing works
Halvas, E. K., Joseph, K. W., Brandt, L. D., Guo, S., Sobolewski, M. D., Jacobs, J. L., Tumiotto, C., Bui, J. K., Cyktor, J. C., Keele, B. F., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci138099 · Cited by 141 · see citing works
Self-citationMukhamedova, N., Hoang, A., Dragoljevic, D., Dubrovsky, L., Pushkarsky, T., Low, H., Ditiatkovski, M., Fu, Y., Ohkawa, R., Meikle, P. J., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007907 · Cited by 132 · see citing works
Barriers and strategies to achieve a cure for HIV
Pitman, M. C., Lau, J. S. Y., McMahon, J. H., & Lewin, S. R. (2018) · The Lancet HIV · doi:10.1016/s2352-3018(18)30039-0 · Cited by 124 · see citing works
García‐Broncano, P., Maddali, S., Einkauf, K. B., Jiang, C., Gao, C., Chevalier, J. M., Chowdhury, F. Z., Maswabi, K., Ajibola, G., Moyo, S. M., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aax7350 · Cited by 120 · see citing works
Antigen-responsive CD4+ T cell clones contribute to the HIV-1 latent reservoir
Mendoza, P., Jackson, J., Oliveira, T. Y., Gaebler, C., Ramos, V., Caskey, M. F., Janković, M., Nussenzweig, M. C., & Cohn, L. B. (2020) · The Journal of Experimental Medicine · doi:10.1084/jem.20200051 · Cited by 119 · see citing works
HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy
McManus, W. R., Bale, M. J., Spindler, J., Wiegand, A. P., Musick, A., Patro, S. C., Sobolewski, M. D., Musick, V. K., Anderson, E. M., Cyktor, J. C., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci126714 · Cited by 112 · see citing works
Self-citationLeyre, L., Kroon, E. D. M. B., Vandergeeten, C., Sacdalan, C., Colby, D. J., Buranapraditkun, S., Schuetz, A., Chomchey, N., de Souza, M. S., Bakeman, W., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aav3491 · Cited by 108 · see citing works
Bradley, T., Ferrari, G., Haynes, B. F., Margolis, D. M., & Browne, E. P. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.09.020 · Cited by 103 · see citing works
Gantner, P., Pagliuzza, A., Pardons, M., Ramgopal, M. N., Routy, J., Fromentin, R., & Chomont, N. (2020) · Nature Communications · doi:10.1038/s41467-020-17898-8 · Cited by 99 · see citing works
A highly multiplexed droplet digital PCR assay to measure the intact HIV-1 proviral reservoir
Levy, C., Hughes, S. M., Roychoudhury, P., Reeves, D. B., Amstuz, C., Zhu, H., Huang, M.-L. W., Wei, Y., Bull, M. E., Cassidy, N. A. J., et al. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100243 · Cited by 94 · see citing works
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Dufour, C., Gantner, P., Fromentin, R., & Chomont, N. (2020) · Journal of Clinical Investigation · doi:10.1172/jci136227 · Cited by 94 · see citing works
Pasternak, A. O., Grijsen, M. L., Wit, F. W. N. M., Bakker, M. E., Jurriaans, S., Prins, J. M., & Berkhout, B. (2020) · JCI Insight · doi:10.1172/jci.insight.134196 · Cited by 92 · see citing works
White, J. A., Simonetti, F. R., Beg, S. A., McMyn, N. F., Dai, W., Bachmann, N., Lai, J., Ford, W. C., Bunch, C., Jones, J. L., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2120326119 · Cited by 90 · see citing works
White, J. A., Wu, F., Yasin, S., Moskovljevic, M., Varriale, J., Dragoni, F., Camilo-Contreras, A., Duan, J., Zheng, M. Y., Tadzong, N. F., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci165245 · Cited by 86 · see citing works
Dubé, M., Tastet, O., Dufour, C., Sannier, G., Brassard, N., Ortega-Delgado, G.-G., Pagliuzza, A., Richard, C., Nayrac, M., Routy, J., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.08.006 · Cited by 87 · see citing works
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McCauley, S. M., Kim, K., Nowosielska, A., Dauphin, A., Yurkovetskiy, L., Diehl, W. E., & Luban, J. (2018) · Nature Communications · doi:10.1038/s41467-018-07753-2 · Cited by 78 · see citing works
Antar, A. A. R., Jenike, K. M., Jang, S., Rigau, D. N., Reeves, D. B., Hoh, R., Krone, M., Keruly, J. C., Moore, R. D., Schiffer, J. T., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci135953 · Cited by 81 · see citing works
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Sharaf, R. R., Lee, G. Q., Sun, X., Etemad, B., Aboukhater, L. M., Hu, Z., Brumme, Z. L., Aga, E., Bosch, R. J., Wen, Y., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci120549 · Cited by 79 · see citing works
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van Zyl, G. U., Katusiime, M. G., Wiegand, A. P., McManus, W. R., Bale, M. J., Halvas, E. K., Luke, B. T., Boltz, V. F., Spindler, J., Laughton, B., et al. (2017) · Journal of Clinical Investigation · doi:10.1172/jci94582 · Cited by 75 · see citing works
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The multifaceted nature of HIV latency
Dufour, C., Gantner, P., Fromentin, R., & Chomont, N. (2021) · Journal of Clinical Investigation · doi:10.1172/jci151380 · Cited by 63 · see citing works
Singh, K., Natarajan, V., Dewar, R. L., Rupert, A. W., Badralmaa, Y., Zhai, T., Winchester, N., Scrimieri, F., Smith, M., Davis, I., et al. (2023) · AIDS · doi:10.1097/qad.0000000000003667 · Cited by 60 · see citing works
HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus
Musick, A., Spindler, J., Boritz, E., Pérez, L., Crespo-Vélez, D., Patro, S. C., Sobolewski, M. D., Bale, M. J., Reid, C., Keele, B. F., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02204 · Cited by 57 · see citing works
Self-citationBalasubramaniam, M., Pandhare, J., & Dash, C. (2019) · JoLS Journal of Life Sciences · doi:10.36069/jols/20190603 · Cited by 53 · see citing works
Jefferys, S. R., Burgos, S. D., Peterson, J. J., Selitsky, S. R., Turner, A. W., James, L. I., Tsai, Y., Coffey, A. R., Margolis, D. M., Parker, J. S., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009346 · Cited by 47 · see citing works
The cell biology of HIV-1 latency and rebound
Mbonye, U. R., & Karn, J. (2024) · Retrovirology · doi:10.1186/s12977-024-00639-w · Cited by 51 · see citing works
Zerbato, J. M., Khoury, G., Zhao, W. D., Gartner, M. J., Pascoe, R. D., Rhodes, A., Dantanarayana, A., Gooey, M., Anderson, J. L., Bacchetti, P., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103241 · Cited by 44 · see citing works
Bispecific antibodies promote natural killer cell-mediated elimination of HIV-1 reservoir cells
Nathan L. Board, Yuan, Z., Wu, F., Moskovljevic, M., Ravi, M., Sengupta, S., Mun, S. S., Simonetti, F. R., Lai, J., Tebas, P., et al. (2024) · Nature Immunology · doi:10.1038/s41590-023-01741-5 · Cited by 46 · see citing works
Persistent HIV-1 Viremia on Antiretroviral Therapy: Measurement and Mechanisms
Jacobs, J. L., Halvas, E. K., Tosiano, M. A., & Mellors, J. W. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02383 · Cited by 46 · see citing works
Self-citationWells, D., Guo, S., Shao, W., Bale, M. J., Coffin, J. M., Hughes, S. H., & Wu, X. (2020) · BMC Genomics · doi:10.1186/s12864-020-6647-4 · Cited by 45 · see citing works
Self-citationDefective HIV-1 genomes and their potential impact on HIV pathogenesis
Kuniholm, J., Coote, C., & Henderson, A. J. (2022) · Retrovirology · doi:10.1186/s12977-022-00601-8 · Cited by 45 · see citing works
Lau, C., Adan, M. A., & Maldarelli, F. M. (2021) · Viruses · doi:10.3390/v13122512 · Cited by 44 · see citing works
HIV Reservoirs and Treatment Strategies toward Curing HIV Infection
Matsuda, K., & Maeda, K. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25052621 · Cited by 43 · see citing works
Wonderlich, E. R., Subramanian, K., Cox, B. D., Wiegand, A. P., Lackman-Smith, C., Bale, M. J., Stone, M., Hoh, R., Kearney, M. F., Maldarelli, F. M., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1008074 · Cited by 42 · see citing works
Self-citationCD32+CD4+ T Cells Are Highly Enriched for HIV DNA and Can Support Transcriptional Latency
Darcis, G., Kootstra, N. A., Hooibrink, B., van Montfort, T., Maurer, I., Groen, K., Jurriaans, S., Bakker, M. E., Lint, C. M. V., Berkhout, B., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.071 · Cited by 43 · see citing works
Sun, C., Liu, L., Pérez, L., Li, X., Liu, Y., Xu, P., Boritz, E., Mullins, J. I., & Abate, A. R. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00864-8 · Cited by 43 · see citing works
Weymar, G. H. J., Bar‐On, Y., Oliveira, T. Y., Gaebler, C., Ramos, V., Hartweger, H., Breton, G., Caskey, M. F., Cohn, L. B., Janković, M., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111311 · Cited by 41 · see citing works
HIV integration sites and implications for maintenance of the reservoir
Symons, J., Cameron, P. U., & Lewin, S. R. (2017) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000438 · Cited by 41 · see citing works
Ferris, A. L., Wells, D. W., Guo, S., Prete, G. Q. D., Swanstrom, A. E., Coffin, J. M., Wu, X., Lifson, J. D., & Hughes, S. H. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007869 · Cited by 41 · see citing works
Self-citationAnderson, E. M., Simonetti, F. R., Gorelick, R. J., Hill, S., Gouzoulis, M. A., Bell, J., Rehm, C. A., Pérez, L., Boritz, E., Wu, X., et al. (2020) · Viruses · doi:10.3390/v12020136 · Cited by 41 · see citing works
Self-citationPersistence of viral RNA in lymph nodes in ART-suppressed SIV/SHIV-infected Rhesus Macaques
Cadena, A. M., Ventura, J. D., Abbink, P., Borducchi, E. N., Tuyishime, H., Mercado, N. B., Walker-Sperling, V. E. K., Siamatu, M., Liu, P.-T., Chandrashekar, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21724-0 · Cited by 37 · see citing works
An ordeal that does not heal: understanding barriers to a cure for HIV-1 infection
Lichterfeld, M. D., Gao, C., & Yu, X. G. (2022) · Trends in Immunology · doi:10.1016/j.it.2022.06.002 · Cited by 38 · see citing works
Hikichi, Y., Duyne, R. V., Pham, P., Groebner, J. L., Wiegand, A. P., Mellors, J. W., Kearney, M. F., & Freed, E. O. (2021) · mBio · doi:10.1128/mbio.03134-20 · Cited by 39 · see citing works
Self-citationHIV persistence: silence or resistance?
Pasternak, A. O., & Berkhout, B. (2023) · Current Opinion in Virology · doi:10.1016/j.coviro.2023.101301 · Cited by 37 · see citing works
Riddler, S. A., Zheng, L., Durand, C. M., Ritz, J., Koup, R. A., Ledgerwood, J. E., Bailer, R. T., Koletar, S. L., Eron, J. J., Keefer, M. C., et al. (2018) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofy242 · Cited by 37 · see citing works
Self-citationLeón‐Rivera, R., Morsey, B., Niu, M., Fox, H. S., & Berman, J. W. (2020) · mBio · doi:10.1128/mbio.01037-20 · Cited by 33 · see citing works
Obregon-Perko, V., Bricker, K. M., Mensah, G., Uddin, F., Kumar, M. R., Fray, E. J., Siliciano, R. F., Schoof, N., Horner, A. M., Mavigner, M., et al. (2020) · Journal of Virology · doi:10.1128/jvi.01669-20 · Cited by 33 · see citing works
Guney, M. H., Nagalekshmi, K., McCauley, S. M., Carbone, C., Aydemir, Ö., & Luban, J. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2404349121 · Cited by 28 · see citing works
Next-generation bNAbs for HIV-1 cure strategies
Schriek, A. I., Aldon, Y., van Gils, M. J., & de Taeye, S. W. (2023) · Antiviral Research · doi:10.1016/j.antiviral.2023.105788 · Cited by 27 · see citing works
Jean, M. J., Fiches, G. N., Hayashi, T., & Zhu, J. K. (2018) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2018.0153 · Cited by 29 · see citing works
Clonal Expansion of Infected CD4+ T Cells in People Living with HIV
Coffin, J. M., & Hughes, S. H. (2021) · Viruses · doi:10.3390/v13102078 · Cited by 24 · see citing works
Self-citationBrandt, L., Cristinelli, S., & Ciuffi, A. (2020) · Annual Review of Virology · doi:10.1146/annurev-virology-021820-102458 · Cited by 25 · see citing works
Persistent HIV-1 transcription during ART: time to reassess its significance?
Fombellida-Lopez, C., Berkhout, B., Darcis, G., & Pasternak, A. O. (2024) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000849 · Cited by 24 · see citing works
Dragoni, F., Kwaa, A. K., Traut, C. C., Veenhuis, R. T., Woldemeskel, B. A., Camilo-Contreras, A., Raymond, H. E., Dykema, A. G., Scully, E. P., Rosecrans, A. M., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci171097 · Cited by 24 · see citing works
Differentiating Immune Cell Targets in Gut-Associated Lymphoid Tissue for HIV Cure
Khan, S., Telwatte, S., Trapečar, M., Yukl, S. A., & Sanjabi, S. (2017) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2017.0153 · Cited by 24 · see citing works
Single-molecule techniques to quantify and genetically characterise persistent HIV
Wang, X. Q., & Palmer, S. (2018) · Retrovirology · doi:10.1186/s12977-017-0386-x · Cited by 23 · see citing works
Bale, M. J., & Kearney, M. F. (2019) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000535 · Cited by 23 · see citing works
Self-citationDetection of HPV E7 Transcription at Single-Cell Resolution in Epidermis
Lukowski, S. W., Tuong, Z. K., Nöske, K., Senabouth, A., Nguyen, Q. H., Andersen, S. B., Soyer, H. P., Frazer, I. H., & Powell, J. E. (2018) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2018.06.169 · Cited by 23 · see citing works
Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity
Sannier, G., Dubé, M., & Kaufmann, D. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00297 · Cited by 21 · see citing works
Latency Reversing Agents and the Road to an HIV Cure
Tioka, L., Diez, R. C., Sönnerborg, A., & van de Klundert, M. (2025) · Pathogens · doi:10.3390/pathogens14030232 · Cited by 20 · see citing works
Hong, F. F., Jacobs, J. L., Aga, E., Cillo, A. R., Fyne, E., Koontz, D. L., Zheng, L., & Mellors, J. W. (2018) · Virology · doi:10.1016/j.virol.2018.05.018 · Cited by 20 · see citing works
Self-citationThe Splice of Life: Does RNA Processing Have a Role in HIV-1 Persistence?
Pasternak, A. O., & Berkhout, B. (2021) · Viruses · doi:10.3390/v13091751 · Cited by 20 · see citing works
HibeRNAtion: HIV-1 RNA Metabolism and Viral Latency
Crespo, R., Rao, S., & Mahmoudi, T. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.855092 · Cited by 19 · see citing works
The latent HIV reservoir: current advances in genetic sequencing approaches
Moar, P., Premeaux, T. A., Atkins, A., & Ndhlovu, L. C. (2023) · mBio · doi:10.1128/mbio.01344-23 · Cited by 19 · see citing works
Schwarzer, R., Gramatica, A., & Greene, W. C. (2020) · Viruses · doi:10.3390/v12020188 · Cited by 21 · see citing works
Structural and computational studies of HIV-1 RNA
Levintov, L., & Vashisth, H. (2023) · RNA Biology · doi:10.1080/15476286.2023.2289709 · Cited by 17 · see citing works
Joussef-Piña, S., Nankya, I., Nalukwago, S., Baseke, J., Rwambuya, S., Winner, D., Kyeyune, F., Chervenak, K. A., Thiel, B., Asaad, R. J., et al. (2022) · Retrovirology · doi:10.1186/s12977-022-00587-3 · Cited by 17 · see citing works
HIV-1 reservoir dynamics in CD4+ T cells
Bruner, K. M., & Cohn, L. B. (2018) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000521 · Cited by 15 · see citing works
Prator, C. A., Thanh, C., Kumar, S., Pan, T., Peluso, M. J., Bosch, R. J., Jones, N. G., Milush, J. M., Bakkour, S., Stone, M., et al. (2019) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiz572 · Cited by 16 · see citing works
Silencing the transcriptionally active HIV reservoir to improve treatment outcomes
Kazmierski, J., Tavora, R., O’Brien, R. L. F., Schulze‐Gahmen, U., Boehm, D., Roan, N. R., Nixon, D. F., Ndhlovu, L. C., Valente, S. T., & Ott, M. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01816-5 · Cited by 15 · see citing works
A widely distributed HIV-1 provirus elimination assay to evaluate latency-reversing agents in vitro
Matsuda, K., Islam, S., Takada, T., Tsuchiya, K., Tan, B. J. Y., Hattori, S.-I., Katsuya, H., Kitagawa, K., Kim, K. S., Matsuo, M., et al. (2021) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100122 · Cited by 15 · see citing works
HIV-1 activates oxidative phosphorylation in infected CD4 T cells in a human tonsil explant model
Swartz, T. H., Freeman, T., Zhao, C., Schrode, N., Beaumont, K. G., Tweel, B. C., Fortune, T., & Schroff, S. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1172938 · Cited by 14 · see citing works
Astorga-Gamaza, A., & Buzón, M. J. (2021) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000685 · Cited by 14 · see citing works
HIV reservoir quantification by five-target multiplex droplet digital PCR
Levy, C., Hughes, S. M., Roychoudhury, P., Amstuz, C., Zhu, H., Huang, M.-L. W., Lehman, D. A., Jerome, K. R., & Hladik, F. (2021) · STAR Protocols · doi:10.1016/j.xpro.2021.100885 · Cited by 14 · see citing works
Moskovljevic, M., Dragoni, F., Nathan L. Board, Wu, F., Lai, J., Zhang, H., White, J. R., Hoh, R., Lynn, K., Tebas, P., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.11.002 · Cited by 15 · see citing works
Strategies for an HIV cure: progress and challenges
Wang, F. S., Zhang, L., Douek, D. C., McMichael, A. J., Xu, X., & Lewin, S. R. (2018) · Nature Immunology · doi:10.1038/s41590-018-0242-8 · Cited by 13 · see citing works
Copertino, D. C., Holmberg, C. S., Weiler, J., Ward, A. R., Howard, J. N., Levinger, C., Pang, A. P. S., Corley, M. J., Dündar, F., Zumbo, P., et al. (2023) · JCI Insight · doi:10.1172/jci.insight.169028 · Cited by 12 · see citing works
Self-citationWang, X., & Xu, H. (2021) · Viruses · doi:10.3390/v13020335 · Cited by 12 · see citing works
An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review
Ramirez, P. W., Pantoja, C., & Beliakova‐Bethell, N. (2023) · HIV/AIDS - Research and Palliative Care · doi:10.2147/hiv.s383347 · Cited by 12 · see citing works
Fish, C. S., Cassidy, N. A. J., Levy, C., Hughes, S. M., Jerome, K. R., Overbaugh, J. M., Hladik, F., & Lehman, D. A. (2022) · STAR Protocols · doi:10.1016/j.xpro.2022.101681 · Cited by 11 · see citing works
Cell Size-Based Decision-Making of a Viral Gene Circuit
Bohn-Wippert, K., Tevonian, E. N., Lu, Y., Huang, M.-Y., Megaridis, M. R., & Dar, R. D. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.12.009 · Cited by 11 · see citing works
Cure and Long-Term Remission Strategies
Mori, L., & Valente, S. T. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-1871-4_26 · Cited by 10 · see citing works
Challenges and Promise of Human Immunodeficiency Virus Remission
Li, Y., Mohammadi, A., & Li, J. Z. (2020) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiaa568 · Cited by 10 · see citing works
Karuppusamy, K. V., Babu, P., & Thangavel, S. (2021) · Stem Cell Reviews and Reports · doi:10.1007/s12015-021-10145-7 · Cited by 10 · see citing works
Genetically intact but functionally impaired HIV-1 env glycoproteins in the T-cell reservoir
de Verneuil, A., Migraine, J., Mammano, F., Molina, J.-M., Gallien, S., Mouquet, H., Hance, A. J., Clavel, F., & Dutrieux, J. (2018) · Journal of Virology · doi:10.1128/jvi.01684-17 · Cited by 10 · see citing works
Wang, X., Vincent, E., Siddiqui, S., Turnbull, K., Lü, H., Blair, R. V., Wu, X., Watkins, M., Ziani, W., Shao, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32554-z · Cited by 9 · see citing works
Joseph, S., Abrahams, M.-R., Moeser, M., Tyers, L., Archin, N. M., Sondgeroth, A., Spielvogel, E., Emery, A., Zhou, S., Doolabh, D., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1011974 · Cited by 9 · see citing works
- Authors
- Wiegand, A., Spindler, J., Hong, F. F., Shao, W., Cyktor, J. C., Cillo, A. R., Halvas, E. K., Coffin, J. M., Mellors, J. W., & Kearney, M. F.
- Affiliations
- National Cancer Institute (US)
- University of Pittsburgh (US)
- Frederick National Laboratory for Cancer Research (US)
- Tufts University (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2017-04-17
- Volume
- 114
- Issue
- 18
- Pages
- E3659-E3668
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC5422779
- OpenAlex
- W2606857030
- Cited by
- 165
- References
- 44
- Citations by year
- 2026: 8 · 2025: 19 · 2024: 15 · 2023: 17 · 2022: 15 · 2021: 19 · 2020: 25 · 2019: 19 · 2018: 23 · 2017: 4
- FWCI
- 10.57
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- HHS | NIH | National Cancer Institute (Intramural Funding, 1U01CA200441)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Keywords
- HIV-1, unspliced viral RNA, single-genome sequencing, antiretroviral therapy, viral reservoir, defective proviruses, HIV transcription, viremia, blood mononuclear cells
- MeSH terms
- Female, Humans, Leukocytes, Mononuclear, Male, Proviruses, RNA, Viral, Transcription, Genetic, HIV-1, Gene Expression Regulation, Viral, Anti-Retroviral Agents
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