{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T20:43:06Z","timestamp":1790800986717,"version":"4.1.0"},"reference-count":161,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2020,6,30]],"date-time":"2020-06-30T00:00:00Z","timestamp":1593475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["P30AI042853"],"award-info":[{"award-number":["P30AI042853"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI064099"],"award-info":[{"award-number":["R01AI064099"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R01AG060890"],"award-info":[{"award-number":["R01AG060890"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["R21NS105837"],"award-info":[{"award-number":["R21NS105837"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["R01HD083111"],"award-info":[{"award-number":["R01HD083111"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>A hallmark of HIV-1 infection is chronic inflammation, which plays a significant role in disease pathogenesis. Acute HIV infection induces robust inflammatory responses, which are insufficient to prevent or eliminate virus in mucosal tissues. While establishment of viral set-point is coincident with downregulation of acute innate responses, systemic inflammatory responses persist during the course of chronic HIV infection. Since the introduction of combination antiviral therapy (cART), most HIV-1+ individuals can suppress viremia under detection levels for decades. However, chronic immune activation persists and has been postulated to cause HIV associated non-AIDS complications (HANA). Importantly, inflammatory cytokines and activation markers associated with macrophages are strongly and selectively correlated with the incidence of HIV-associated neurocognitive disorder (HAND), cardiovascular dysfunctions (CVD) and other HANA conditions. In this review, we discuss the roles of macrophages in facilitating viral persistence and contributing to generation of persistent inflammatory responses.<\/jats:p>","DOI":"10.3390\/v12070711","type":"journal-article","created":{"date-parts":[[2020,6,30]],"date-time":"2020-06-30T14:24:24Z","timestamp":1593527064000},"page":"711","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["HIV-1 Persistence and Chronic Induction of Innate Immune Responses in Macrophages"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9228-0465","authenticated-orcid":false,"given":"Hisashi","family":"Akiyama","sequence":"first","affiliation":[{"name":"Department of Microbiology, Boston University School of Medicine, 72 E. Concord St., R512, Boston, MA 02118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suryaram","family":"Gummuluru","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Boston University School of Medicine, 72 E. Concord St., R512, Boston, MA 02118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,6,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/nri3073","article-title":"Protective and pathogenic functions of macrophage subsets","volume":"11","author":"Murray","year":"2011","journal-title":"Nat. Rev. Immunol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2828","DOI":"10.3389\/fmicb.2019.02828","article-title":"The Role of Macrophages in HIV-1 Persistence and Pathogenesis","volume":"10","author":"Kruize","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/362359a0","article-title":"Massive covert infection of helper T lymphocytes and macrophages by HIV during the incubation period of AIDS","volume":"362","author":"Embretson","year":"1993","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.1126\/science.276.5320.1857","article-title":"Macrophages as a source of HIV during opportunistic infections","volume":"276","author":"Orenstein","year":"1997","journal-title":"Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1126\/science.3016903","article-title":"Detection of AIDS virus in macrophages in brain tissue from AIDS patients with encephalopathy","volume":"233","author":"Koenig","year":"1986","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Micci, L., Alvarez, X., Iriele, R.I., Ortiz, A.M., Ryan, E.S., McGary, C.S., Deleage, C., McAtee, B.B., He, T., and Apetrei, C. (2014). CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells. PLoS Pathog., 10.","DOI":"10.1371\/journal.ppat.1004467"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1073\/pnas.98.2.658","article-title":"Macrophage are the principal reservoir and sustain high virus loads in rhesus macaques after the depletion of CD4+ T cells by a highly pathogenic simian immunodeficiency virus\/HIV type 1 chimera (SHIV): Implications for HIV-1 infections of humans","volume":"98","author":"Igarashi","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1189\/jlb.4A0914-441R","article-title":"Increased monocyte turnover is associated with interstitial macrophage accumulation and pulmonary tissue damage in SIV-infected rhesus macaques","volume":"97","author":"Cai","year":"2015","journal-title":"J. Leukoc. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e46916","DOI":"10.7554\/eLife.46916","article-title":"Mechanisms of virus dissemination in bone marrow of HIV-1-infected humanized BLT mice","volume":"8","author":"Ladinsky","year":"2019","journal-title":"eLife"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1084\/jem.20090378","article-title":"Genetic identity, biological phenotype, and evolutionary pathways of transmitted\/founder viruses in acute and early HIV-1 infection","volume":"206","author":"Salazar","year":"2009","journal-title":"J. Exp. Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1128\/JVI.02477-13","article-title":"Quantification of entry phenotypes of macrophage-tropic HIV-1 across a wide range of CD4 densities","volume":"88","author":"Joseph","year":"2014","journal-title":"J. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"8208","DOI":"10.1128\/JVI.00296-09","article-title":"Heterosexual transmission of human immunodeficiency virus type 1 subtype C: Macrophage tropism, alternative coreceptor use, and the molecular anatomy of CCR5 utilization","volume":"83","author":"Hermann","year":"2009","journal-title":"J. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1128\/JVI.06157-11","article-title":"Generation of transmitted\/founder HIV-1 infectious molecular clones and characterization of their replication capacity in CD4 T lymphocytes and monocyte-derived macrophages","volume":"86","author":"Ochsenbauer","year":"2012","journal-title":"J. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/j.immuni.2014.08.014","article-title":"Tissue myeloid cells in SIV-infected primates acquire viral DNA through phagocytosis of infected T cells","volume":"41","author":"Calantone","year":"2014","journal-title":"Immunity"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/j.chom.2014.10.010","article-title":"Macrophage infection via selective capture of HIV-1-infected CD4+ T cells","volume":"16","author":"Baxter","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Bracq, L., Xie, M., Lambele, M., Vu, L.T., Matz, J., Schmitt, A., Delon, J., Zhou, P., Randriamampita, C., and Bouchet, J. (2017). T Cell-Macrophage Fusion Triggers Multinucleated Giant Cell Formation for HIV-1 Spreading. J. Virol., 91.","DOI":"10.1128\/JVI.01237-17"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1016\/j.chom.2016.02.013","article-title":"Macrophages and HIV-1: An Unhealthy Constellation","volume":"19","author":"Sattentau","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Dupont, M., and Sattentau, Q.J. (2020). Macrophage Cell-Cell Interactions Promoting HIV-1 Infection. Viruses, 12.","DOI":"10.3390\/v12050492"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3258","DOI":"10.1128\/JVI.01796-08","article-title":"Macrophages in vaginal but not intestinal mucosa are monocyte-like and permissive to human immunodeficiency virus type 1 infection","volume":"83","author":"Shen","year":"2009","journal-title":"J. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1038\/mi.2013.127","article-title":"Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function","volume":"7","author":"Jambo","year":"2014","journal-title":"Mucosal Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1089\/aid.2017.0004","article-title":"Brain Microglial Cells Are Highly Susceptible to HIV-1 Infection and Spread","volume":"33","author":"Cenker","year":"2017","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5643","DOI":"10.1128\/JVI.00290-16","article-title":"Quantitation of Productively Infected Monocytes and Macrophages of Simian Immunodeficiency Virus-Infected Macaques","volume":"90","author":"Avalos","year":"2016","journal-title":"J. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e01659-19","DOI":"10.1128\/mBio.01659-19","article-title":"Myeloid and CD4 T Cells Comprise the Latent Reservoir in Antiretroviral Therapy-Suppressed SIVmac251-Infected Macaques","volume":"10","author":"Abreu","year":"2019","journal-title":"mBio"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1093\/cid\/ciy1066","article-title":"Human Immunodeficiency Virus Type 1 RNA Detected in the Central Nervous System (CNS) After Years of Suppressive Antiretroviral Therapy Can Originate from a Replicating CNS Reservoir or Clonally Expanded Cells","volume":"69","author":"Joseph","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nm.4319","article-title":"HIV persistence in tissue macrophages of humanized myeloid-only mice during antiretroviral therapy","volume":"23","author":"Honeycutt","year":"2017","journal-title":"Nat. Med."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Witwer, K.W., Gama, L., Li, M., Bartizal, C.M., Queen, S.E., Varrone, J.J., Brice, A.K., Graham, D.R., Tarwater, P.M., and Mankowski, J.L. (2009). Coordinated regulation of SIV replication and immune responses in the CNS. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0008129"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1736","DOI":"10.1212\/WNL.42.9.1736","article-title":"Early viral brain invasion in iatrogenic human immunodeficiency virus infection","volume":"42","author":"Davis","year":"1992","journal-title":"Neurology"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.3389\/fimmu.2019.01435","article-title":"The HIV Reservoir in Monocytes and Macrophages","volume":"10","author":"Wong","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/j.immuni.2014.08.006","article-title":"Human dermal CD14(+) cells are a transient population of monocyte-derived macrophages","volume":"41","author":"McGovern","year":"2014","journal-title":"Immunity"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1182\/blood.V93.2.667","article-title":"Augmented proliferation of human alveolar macrophages after allogeneic bone marrow transplantation","volume":"93","author":"Nakata","year":"1999","journal-title":"Blood"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1126\/science.1194637","article-title":"Fate mapping analysis reveals that adult microglia derive from primitive macrophages","volume":"330","author":"Ginhoux","year":"2010","journal-title":"Science"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1538","DOI":"10.1038\/nn2014","article-title":"Local self-renewal can sustain CNS microglia maintenance and function throughout adult life","volume":"10","author":"Ajami","year":"2007","journal-title":"Nat. Neurosci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.immuni.2013.04.004","article-title":"Tissue-resident macrophages self-maintain locally throughout adult life with minimal contribution from circulating monocytes","volume":"38","author":"Hashimoto","year":"2013","journal-title":"Immunity"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.cell.2020.03.021","article-title":"Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development","volume":"181","author":"Utz","year":"2020","journal-title":"Cell"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1038\/s41586-020-2316-7","article-title":"Deciphering human macrophage development at single-cell resolution","volume":"582","author":"Bian","year":"2020","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.celrep.2017.07.004","article-title":"The Lifespan and Turnover of Microglia in the Human Brain","volume":"20","author":"Reu","year":"2017","journal-title":"Cell Rep."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e01186-17","DOI":"10.1128\/mBio.01186-17","article-title":"Brain Macrophages in Simian Immunodeficiency Virus-Infected, Antiretroviral-Suppressed Macaques: A Functional Latent Reservoir","volume":"8","author":"Avalos","year":"2017","journal-title":"mBio"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.3390\/v6041837","article-title":"HIV-1 latency in monocytes\/macrophages","volume":"6","author":"Kumar","year":"2014","journal-title":"Viruses"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1182\/blood-2005-04-1390","article-title":"Human herpesvirus 8 enhances human immunodeficiency virus replication in acutely infected cells and induces reactivation in latently infected cells","volume":"106","author":"Caselli","year":"2005","journal-title":"Blood"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Alvarez-Carbonell, D., Ye, F., Ramanath, N., Garcia-Mesa, Y., Knapp, P.E., Hauser, K.F., and Karn, J. (2019). Cross-talk between microglia and neurons regulates HIV latency. PLoS Pathog., 15.","DOI":"10.1371\/journal.ppat.1008249"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1189\/jlb.3HI0516-242R","article-title":"Frontline Science: HIV infection of Kupffer cells results in an amplified proinflammatory response to LPS","volume":"101","author":"Mosoian","year":"2017","journal-title":"J. Leukoc. Biol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4501","DOI":"10.1172\/JCI121678","article-title":"No recovery of replication-competent HIV-1 from human liver macrophages","volume":"128","author":"Kandathil","year":"2018","journal-title":"J. Clin. Investig."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1089\/aid.2014.0133","article-title":"Healthy HIV-1-infected individuals on highly active antiretroviral therapy harbor HIV-1 in their alveolar macrophages","volume":"31","author":"Cribbs","year":"2015","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e00065-19","DOI":"10.1128\/JVI.00065-19","article-title":"Infectious Virus Persists in CD4(+) T Cells and Macrophages in Antiretroviral Therapy-Suppressed Simian Immunodeficiency Virus-Infected Macaques","volume":"93","author":"Abreu","year":"2019","journal-title":"J. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"5772","DOI":"10.1128\/JVI.03628-14","article-title":"Detection of Simian Immunodeficiency Virus in Semen, Urethra, and Male Reproductive Organs during Efficient Highly Active Antiretroviral Therapy","volume":"89","author":"Matusali","year":"2015","journal-title":"J. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1038\/s41564-018-0335-z","article-title":"HIV-1 reservoirs in urethral macrophages of patients under suppressive antiretroviral therapy","volume":"4","author":"Ganor","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Duprez, D.A., Neuhaus, J., Kuller, L.H., Tracy, R., Belloso, W., De Wit, S., Drummond, F., Lane, H.C., Ledergerber, B., and Lundgren, J. (2012). Inflammation, coagulation and cardiovascular disease in HIV-infected individuals. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0044454"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1097\/QAD.0b013e32833ad914","article-title":"Traditional risk factors and D-dimer predict incident cardiovascular disease events in chronic HIV infection","volume":"24","author":"Ford","year":"2010","journal-title":"Aids"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/infdis\/jit147","article-title":"Association of functional impairment with inflammation and immune activation in HIV type 1-infected adults receiving effective antiretroviral therapy","volume":"208","author":"Erlandson","year":"2013","journal-title":"J. Infect. Dis."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1097\/QAD.0b013e32835f6b0c","article-title":"Predicting risk of cancer during HIV infection: The role of inflammatory and coagulation biomarkers","volume":"27","author":"Borges","year":"2013","journal-title":"Aids"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Bjerk, S.M., Baker, J.V., Emery, S., Neuhaus, J., Angus, B., Gordin, F.M., Pett, S.L., Stephan, C., Kunisaki, K.M., and Group, I.S.S. (2013). Biomarkers and bacterial pneumonia risk in patients with treated HIV infection: A case-control study. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0056249"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1089\/aid.2013.0183","article-title":"Plasma monocyte chemoattractant protein-1 and tumor necrosis factor-alpha levels predict the presence of coronary artery calcium in HIV-infected individuals independent of traditional cardiovascular risk factors","volume":"30","author":"Shikuma","year":"2014","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1097\/QAD.0000000000000893","article-title":"The metabolic and cardiovascular consequences of obesity in persons with HIV on long-term antiretroviral therapy","volume":"30","author":"Koethe","year":"2016","journal-title":"Aids"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1080\/15284336.2016.1162386","article-title":"Non-classical monocytes predict progression of carotid artery bifurcation intima-media thickness in HIV-infected individuals on stable antiretroviral therapy","volume":"17","author":"Chow","year":"2016","journal-title":"HIV Clin. Trials"},{"key":"ref_55","first-page":"383","article-title":"Reduced ovarian reserve relates to monocyte activation and subclinical coronary atherosclerotic plaque in women with HIV","volume":"30","author":"Looby","year":"2016","journal-title":"Aids"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1093\/infdis\/jiu594","article-title":"Elevated Levels of Monocyte Activation Markers Are Associated With Subclinical Atherosclerosis in Men With and Those Without HIV Infection","volume":"211","author":"McKibben","year":"2014","journal-title":"J. Infect. Dis."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1111\/hiv.12270","article-title":"The effect of initiation of antiretroviral therapy on monocyte, endothelial and platelet function in HIV-1 infection","volume":"16","author":"Dunne","year":"2015","journal-title":"HIV Med."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1093\/infdis\/jir520","article-title":"Soluble CD163, a novel marker of activated macrophages, is elevated and associated with noncalcified coronary plaque in HIV-infected patients","volume":"204","author":"Burdo","year":"2011","journal-title":"J. Infect. Dis."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1093\/infdis\/jis545","article-title":"Biomarkers of microbial translocation and macrophage activation: Association with progression of subclinical atherosclerosis in HIV-1 infection","volume":"206","author":"Kelesidis","year":"2012","journal-title":"J. Infect. Dis."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1093\/infdis\/jiq118","article-title":"Plasma levels of soluble CD14 independently predict mortality in HIV infection","volume":"203","author":"Sandler","year":"2011","journal-title":"J. Infect. Dis."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1038\/nrneurol.2016.27","article-title":"HIV-associated neurocognitive disorder--pathogenesis and prospects for treatment","volume":"12","author":"Saylor","year":"2016","journal-title":"Nat. Rev. Neurol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1111\/imr.12065","article-title":"Immune activation and HIV persistence: Implications for curative approaches to HIV infection","volume":"254","author":"Klatt","year":"2013","journal-title":"Immunol. Rev."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1097\/QAD.0b013e3283174636","article-title":"The role of HIV in serious diseases other than AIDS","volume":"22","author":"Phillips","year":"2008","journal-title":"Aids"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/nri1527","article-title":"The neuropathogenesis of AIDS","volume":"5","year":"2005","journal-title":"Nat. Rev. Immunol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"a007120","DOI":"10.1101\/cshperspect.a007120","article-title":"HIV-1-related central nervous system disease: Current issues in pathogenesis, diagnosis, and treatment","volume":"2","author":"Spudich","year":"2012","journal-title":"Cold Spring Harb Perspect. Med."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1086\/650538","article-title":"Discordance between cerebral spinal fluid and plasma HIV replication in patients with neurological symptoms who are receiving suppressive antiretroviral therapy","volume":"50","author":"Canestri","year":"2010","journal-title":"Clin. Infect. Dis."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2251","DOI":"10.1097\/QAD.0000000000000400","article-title":"Low levels of HIV-1 RNA detected in the cerebrospinal fluid after up to 10 years of suppressive therapy are associated with local immune activation","volume":"28","author":"Dahl","year":"2014","journal-title":"Aids"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1097\/QAD.0b013e32832d077c","article-title":"Detectable cerebrospinal fluid HIV RNA with associated neurological deficits, despite suppression of HIV replication in the plasma compartment","volume":"23","author":"Garvey","year":"2009","journal-title":"Aids"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1097\/QAD.0b013e328355e6b2","article-title":"Cerebrospinal fluid HIV escape associated with progressive neurologic dysfunction in patients on antiretroviral therapy with well controlled plasma viral load","volume":"26","author":"Peluso","year":"2012","journal-title":"Aids"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s40169-015-0049-2","article-title":"Understanding the MIND phenotype: Macrophage\/microglia inflammation in neurocognitive disorders related to human immunodeficiency virus infection","volume":"4","author":"Brown","year":"2015","journal-title":"Clin. Transl. Med."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/s13365-015-0346-y","article-title":"Role of the macrophage in HIV-associated neurocognitive disorders and other comorbidities in patients on effective antiretroviral treatment","volume":"21","author":"Rappaport","year":"2015","journal-title":"J. Neurovirol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1002\/glia.23081","article-title":"Fate of microglia during HIV-1 infection: From activation to senescence?","volume":"65","author":"Chen","year":"2017","journal-title":"Glia"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1016\/j.stemcr.2017.05.017","article-title":"A Highly Efficient Human Pluripotent Stem Cell Microglia Model Displays a Neuronal-Co-culture-Specific Expression Profile and Inflammatory Response","volume":"8","author":"Haenseler","year":"2017","journal-title":"Stem Cell Rep."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1016\/j.stemcr.2017.04.023","article-title":"Directed Differentiation of Human Pluripotent Stem Cells to Microglia","volume":"8","author":"Douvaras","year":"2017","journal-title":"Stem Cell Rep."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1038\/nn.4534","article-title":"Differentiation of human and murine induced pluripotent stem cells to microglia-like cells","volume":"20","author":"Pandya","year":"2017","journal-title":"Nat. Neurosci."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.immuni.2017.06.017","article-title":"Induced-Pluripotent-Stem-Cell-Derived Primitive Macrophages Provide a Platform for Modeling Tissue-Resident Macrophage Differentiation and Function","volume":"47","author":"Takata","year":"2017","journal-title":"Immunity"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1038\/nm.4189","article-title":"Efficient derivation of microglia-like cells from human pluripotent stem cells","volume":"22","author":"Muffat","year":"2016","journal-title":"Nat. Med."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.neuron.2017.03.042","article-title":"iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases","volume":"94","author":"Abud","year":"2017","journal-title":"Neuron"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1016\/j.neuron.2018.05.008","article-title":"APOE4 Causes Widespread Molecular and Cellular Alterations Associated with Alzheimer\u2019s Disease Phenotypes in Human iPSC-Derived Brain Cell Types","volume":"98","author":"Lin","year":"2018","journal-title":"Neuron"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/j.stem.2016.04.013","article-title":"Induced Pluripotent Stem Cells Meet Genome Editing","volume":"18","author":"Hockemeyer","year":"2016","journal-title":"Cell Stem Cell"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1016\/j.immuni.2017.08.008","article-title":"The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases","volume":"47","author":"Krasemann","year":"2017","journal-title":"Immunity"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Burdo, T.H., Soulas, C., Orzechowski, K., Button, J., Krishnan, A., Sugimoto, C., Alvarez, X., Kuroda, M.J., and Williams, K.C. (2010). Increased monocyte turnover from bone marrow correlates with severity of SIV encephalitis and CD163 levels in plasma. PLoS Pathog., 6.","DOI":"10.1371\/journal.ppat.1000842"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1016\/S0140-6736(96)10178-1","article-title":"Unique monocyte subset in patients with AIDS dementia","volume":"349","author":"Pulliam","year":"1997","journal-title":"Lancet"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.immuni.2013.10.001","article-title":"Systemic effects of inflammation on health during chronic HIV infection","volume":"39","author":"Deeks","year":"2013","journal-title":"Immunity"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.immuni.2012.08.011","article-title":"Innate immune recognition of HIV-1","volume":"37","author":"Iwasaki","year":"2012","journal-title":"Immunity"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1038\/ni.1863","article-title":"The role of pattern-recognition receptors in innate immunity: Update on Toll-like receptors","volume":"11","author":"Kawai","year":"2010","journal-title":"Nat. Immunol."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Brown, J.N., Kohler, J.J., Coberley, C.R., Sleasman, J.W., and Goodenow, M.M. (2008). HIV-1 activates macrophages independent of Toll-like receptors. PLoS ONE, 3.","DOI":"10.1371\/journal.pone.0003664"},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Decalf, J., Desdouits, M., Rodrigues, V., Gobert, F.X., Gentili, M., Marques-Ladeira, S., Chamontin, C., Mougel, M., Cunha de Alencar, B., and Benaroch, P. (2017). Sensing of HIV-1 Entry Triggers a Type I Interferon Response in Human Primary Macrophages. J. Virol., 91.","DOI":"10.1128\/JVI.00147-17"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1097\/COH.0000000000000129","article-title":"Innate immune sensing of HIV-1 infection","volume":"10","author":"Jakobsen","year":"2015","journal-title":"Curr. Opin. HIV AIDS"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1126\/science.1240933","article-title":"Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses","volume":"341","author":"Gao","year":"2013","journal-title":"Science"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"14391","DOI":"10.1038\/ncomms14391","article-title":"IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP","volume":"8","author":"Jonsson","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1038\/nature10195","article-title":"Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein","volume":"474","author":"Hrecka","year":"2011","journal-title":"Nature"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1038\/nature10117","article-title":"SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx","volume":"474","author":"Laguette","year":"2011","journal-title":"Nature"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"4854","DOI":"10.1128\/JVI.00187-09","article-title":"The human immunodeficiency virus type 2 Vpx protein usurps the CUL4A-DDB1 DCAF1 ubiquitin ligase to overcome a postentry block in macrophage infection","volume":"83","author":"Bergamaschi","year":"2009","journal-title":"J. Virol."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"12550","DOI":"10.1074\/jbc.M112.340711","article-title":"HIV\/simian immunodeficiency virus (SIV) accessory virulence factor Vpx loads the host cell restriction factor SAMHD1 onto the E3 ubiquitin ligase complex CRL4DCAF1","volume":"287","author":"Ahn","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/sj.gt.3302753","article-title":"With a little help from a friend: Increasing HIV transduction of monocyte-derived dendritic cells with virion-like particles of SIV(MAC)","volume":"13","author":"Goujon","year":"2006","journal-title":"Gene Ther."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Bejarano, D.A., Puertas, M.C., Borner, K., Martinez-Picado, J., Muller, B., and Krausslich, H.G. (2018). Detailed Characterization of Early HIV-1 Replication Dynamics in Primary Human Macrophages. Viruses, 10.","DOI":"10.3390\/v10110620"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"3450","DOI":"10.1038\/s41467-018-05899-7","article-title":"HIV-1 intron-containing RNA expression induces innate immune activation and T cell dysfunction","volume":"9","author":"Akiyama","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"2255","DOI":"10.1097\/QAD.0b013e328331a4ce","article-title":"HIV-1 infection of macrophages is dependent on evasion of innate immune cellular activation","volume":"23","author":"Tsang","year":"2009","journal-title":"Aids"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1038\/nature12769","article-title":"HIV-1 evades innate immune recognition through specific cofactor recruitment","volume":"503","author":"Rasaiyaah","year":"2013","journal-title":"Nature"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"7669","DOI":"10.1073\/pnas.0402431101","article-title":"HIV-1-infected monocyte-derived dendritic cells do not undergo maturation but can elicit IL-10 production and T cell regulation","volume":"101","author":"Golebiowska","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/ni.3647","article-title":"HIV-1 blocks the signaling adaptor MAVS to evade antiviral host defense after sensing of abortive HIV-1 RNA by the host helicase DDX3","volume":"18","author":"Gringhuis","year":"2017","journal-title":"Nat. Immunol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nrmicro3503","article-title":"HIV-1 capsid: The multifaceted key player in HIV-1 infection","volume":"13","author":"Campbell","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1016\/j.tim.2017.04.004","article-title":"Capsid-Dependent Host Factors in HIV-1 Infection","volume":"25","author":"Yamashita","year":"2017","journal-title":"Trends Microbiol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1038\/ni.1941","article-title":"The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1","volume":"11","author":"Yan","year":"2010","journal-title":"Nat. Immunol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"5486","DOI":"10.1073\/pnas.1920631117","article-title":"HIV-1 uncoats in the nucleus near sites of integration","volume":"117","author":"Burdick","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Dharan, A., Bachmann, N., Talley, S., Zwikelmaier, V., and Campbell, E.M. (2020). Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus. Nat. Microbiol.","DOI":"10.1038\/s41564-020-0735-8"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"E1773","DOI":"10.1073\/pnas.1424637112","article-title":"cGAS-mediated stabilization of IFI16 promotes innate signaling during herpes simplex virus infection","volume":"112","author":"Orzalli","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"10558","DOI":"10.1073\/pnas.1203447109","article-title":"Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16","volume":"109","author":"Li","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"2377","DOI":"10.1016\/j.celrep.2019.01.105","article-title":"The N-Terminal Domain of cGAS Determines Preferential Association with Centromeric DNA and Innate Immune Activation in the Nucleus","volume":"26","author":"Gentili","year":"2019","journal-title":"Cell Rep."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"13588","DOI":"10.1073\/pnas.1308673110","article-title":"Induction of IL-17 and nonclassical T-cell activation by HIV-Tat protein","volume":"110","author":"Johnson","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1006\/clim.2000.4905","article-title":"Activation of human microglial cells by HIV-1 gp41 and Tat proteins","volume":"96","author":"Sheng","year":"2000","journal-title":"Clin. Immunol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/s12977-017-0370-5","article-title":"Reduced antiretroviral drug efficacy and concentration in HIV-infected microglia contributes to viral persistence in brain","volume":"14","author":"Asahchop","year":"2017","journal-title":"Retrovirology"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/S0165-5728(01)00413-1","article-title":"The regulation of alpha chemokines during HIV-1 infection and leukocyte activation: Relevance for HIV-1-associated dementia","volume":"120","author":"Poluektova","year":"2001","journal-title":"J. Neuroimmunol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"4892","DOI":"10.4049\/jimmunol.174.8.4892","article-title":"Roles for CXC chemokine ligands 10 and 11 in recruiting CD4+ T cells to HIV-1-infected monocyte-derived macrophages, dendritic cells, and lymph nodes","volume":"174","author":"Foley","year":"2005","journal-title":"J. Immunol."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.virol.2006.02.031","article-title":"Macrophage activation and human immunodeficiency virus infection: HIV replication directs macrophages towards a pro-inflammatory phenotype while previous activation modulates macrophage susceptibility to infection and viral production","volume":"349","author":"Porcheray","year":"2006","journal-title":"Virology"},{"key":"ref_117","doi-asserted-by":"crossref","unstructured":"Nasr, N., Alshehri, A.A., Wright, T.K., Shahid, M., Heiner, B.M., Harman, A.N., Botting, R.A., Helbig, K.J., Beard, M.R., and Suzuki, K. (2017). Mechanism of Interferon-Stimulated Gene Induction in HIV-1-Infected Macrophages. J. Virol., 91.","DOI":"10.1128\/JVI.00744-17"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1182\/blood-2012-01-407395","article-title":"HIV-1 infection of human macrophages directly induces viperin which inhibits viral production","volume":"120","author":"Nasr","year":"2012","journal-title":"Blood"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.antiviral.2016.08.004","article-title":"Long-term HIV-1 infection induces an antiviral state in primary macrophages","volume":"133","author":"Pujantell","year":"2016","journal-title":"Antivir. Res."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1016\/j.celrep.2013.03.017","article-title":"Phosphorylation of SAMHD1 by cyclin A2\/CDK1 regulates its restriction activity toward HIV-1","volume":"3","author":"Cribier","year":"2013","journal-title":"Cell Rep."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/j.chom.2013.03.005","article-title":"The retroviral restriction ability of SAMHD1, but not its deoxynucleotide triphosphohydrolase activity, is regulated by phosphorylation","volume":"13","author":"White","year":"2013","journal-title":"Cell Host Microbe"},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Badia, R., Pujantell, M., Riveira-Munoz, E., Puig, T., Torres-Torronteras, J., Marti, R., Clotet, B., Ampudia, R.M., Vives-Pi, M., and Este, J.A. (2016). The G1\/S Specific Cyclin D2 Is a Regulator of HIV-1 Restriction in Non-proliferating Cells. PLoS Pathog., 12.","DOI":"10.1371\/journal.ppat.1005829"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"604","DOI":"10.15252\/embj.201696025","article-title":"A G1-like state allows HIV-1 to bypass SAMHD1 restriction in macrophages","volume":"36","author":"Mlcochova","year":"2017","journal-title":"EMBO J."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.coi.2008.01.002","article-title":"MDA5\/RIG-I and virus recognition","volume":"20","author":"Takeuchi","year":"2008","journal-title":"Curr. Opin. Immunol."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1016\/j.immuni.2011.05.003","article-title":"Immune signaling by RIG-I-like receptors","volume":"34","author":"Loo","year":"2011","journal-title":"Immunity"},{"key":"ref_126","doi-asserted-by":"crossref","unstructured":"Berg, R.K., Melchjorsen, J., Rintahaka, J., Diget, E., Soby, S., Horan, K.A., Gorelick, R.J., Matikainen, S., Larsen, C.S., and Ostergaard, L. (2012). Genomic HIV RNA induces innate immune responses through RIG-I-dependent sensing of secondary-structured RNA. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0029291"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1128\/JVI.01635-10","article-title":"RIG-I-mediated antiviral signaling is inhibited in HIV-1 infection by a protease-mediated sequestration of RIG-I","volume":"85","author":"Solis","year":"2011","journal-title":"J. Virol."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"165","DOI":"10.3390\/biology1020165","article-title":"Multi-Faceted Post-Transcriptional Functions of HIV-1 Rev","volume":"1","author":"Jeang","year":"2012","journal-title":"Biology"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"5305","DOI":"10.1038\/s41467-018-07753-2","article-title":"Intron-containing RNA from the HIV-1 provirus activates type I interferon and inflammatory cytokines","volume":"9","author":"McCauley","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/nar\/28.4.901","article-title":"Multiple copies of the Mason-Pfizer monkey virus constitutive RNA transport element lead to enhanced HIV-1 Gag expression in a context-dependent manner","volume":"28","author":"Wodrich","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.it.2015.02.001","article-title":"RNA degradation in antiviral immunity and autoimmunity","volume":"36","author":"Rigby","year":"2015","journal-title":"Trends Immunol."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1038\/nm.4411","article-title":"Defining total-body AIDS-virus burden with implications for curative strategies","volume":"23","author":"Estes","year":"2017","journal-title":"Nat. Med."},{"key":"ref_133","doi-asserted-by":"crossref","unstructured":"Mavigner, M., Habib, J., Deleage, C., Rosen, E., Mattingly, C., Bricker, K., Kashuba, A., Amblard, F., Schinazi, R.F., and Lawson, B. (2018). Simian Immunodeficiency Virus Persistence in Cellular and Anatomic Reservoirs in Antiretroviral Therapy-Suppressed Infant Rhesus Macaques. J. Virol., 92.","DOI":"10.1128\/JVI.00562-18"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1007\/s11481-018-9809-2","article-title":"Macrophages but not Astrocytes Harbor HIV DNA in the Brains of HIV-1-Infected Aviremic Individuals on Suppressive Antiretroviral Therapy","volume":"14","author":"Ko","year":"2019","journal-title":"J. Neuroimmune Pharm."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1007\/s13365-015-0399-y","article-title":"The meningeal lymphatic system: A route for HIV brain migration?","volume":"22","author":"Lamers","year":"2016","journal-title":"J. Neurovirol."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1097\/COH.0000000000000293","article-title":"Tissue reservoirs of HIV","volume":"11","author":"Wong","year":"2016","journal-title":"Curr. Opin. HIV AIDS"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.cell.2013.09.020","article-title":"Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure","volume":"155","author":"Ho","year":"2013","journal-title":"Cell"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1038\/nm.4156","article-title":"Defective proviruses rapidly accumulate during acute HIV-1 infection","volume":"22","author":"Bruner","year":"2016","journal-title":"Nat. Med."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1016\/j.chom.2017.03.008","article-title":"Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape","volume":"21","author":"Pollack","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"3704","DOI":"10.1073\/pnas.1917876117","article-title":"Defective HIV-1 proviruses produce viral proteins","volume":"117","author":"Imamichi","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1084\/jem.167.4.1428","article-title":"Efficient isolation and propagation of human immunodeficiency virus on recombinant colony-stimulating factor 1-treated monocytes","volume":"167","author":"Gendelman","year":"1988","journal-title":"J. Exp. Med."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.cyto.2018.11.018","article-title":"IP-10 is highly involved in HIV infection","volume":"115","author":"Lei","year":"2019","journal-title":"Cytokine"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"16934","DOI":"10.1073\/pnas.1002894107","article-title":"Establishment of HIV-1 latency in resting CD4+ T cells depends on chemokine-induced changes in the actin cytoskeleton","volume":"107","author":"Cameron","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_144","doi-asserted-by":"crossref","unstructured":"Van der Sluis, R.M., Zerbato, J.M., Rhodes, J.W., Pascoe, R.D., Solomon, A., Kumar, N.A., Dantanarayana, A.I., Tennakoon, S., Dufloo, J., and McMahon, J. (2020). Diverse effects of interferon alpha on the establishment and reversal of HIV latency. PLoS Pathog., 16.","DOI":"10.1371\/journal.ppat.1008151"},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/ni.2035","article-title":"T cell exhaustion","volume":"12","author":"Wherry","year":"2011","journal-title":"Nat. Immunol."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1172\/JCI89488","article-title":"Targeting type I interferon-mediated activation restores immune function in chronic HIV infection","volume":"127","author":"Zhen","year":"2017","journal-title":"J. Clin. Investig."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1172\/JCI90745","article-title":"Blocking type I interferon signaling enhances T cell recovery and reduces HIV-1 reservoirs","volume":"127","author":"Cheng","year":"2017","journal-title":"J. Clin. Investig."},{"key":"ref_148","first-page":"333","article-title":"Macrophage Polarization in AIDS: Dynamic Interface between Anti-Viral and Anti-Inflammatory Macrophages during Acute and Chronic Infection","volume":"6","author":"Burdo","year":"2015","journal-title":"J. Clin. Cell Immunol."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.immuni.2014.06.008","article-title":"Macrophage activation and polarization: Nomenclature and experimental guidelines","volume":"41","author":"Murray","year":"2014","journal-title":"Immunity"},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13024-017-0200-1","article-title":"Absence of CX3CR1 impairs the internalization of Tau by microglia","volume":"12","author":"Bolos","year":"2017","journal-title":"Mol. Neurodegener."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1097\/QAD.0000000000000303","article-title":"Cerebrospinal fluid metabolomics reveals altered waste clearance and accelerated aging in HIV patients with neurocognitive impairment","volume":"28","author":"Cassol","year":"2014","journal-title":"Aids"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1093\/brain\/awh130","article-title":"CSF quinolinic acid levels are determined by local HIV infection: Cross-sectional analysis and modelling of dynamics following antiretroviral therapy","volume":"127","author":"Valle","year":"2004","journal-title":"Brain"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1093\/infdis\/jix082","article-title":"Association of Macrophage Inflammation Biomarkers With Progression of Subclinical Carotid Artery Atherosclerosis in HIV-Infected Women and Men","volume":"215","author":"Hanna","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"E11341","DOI":"10.1073\/pnas.1813512115","article-title":"Relationship between intact HIV-1 proviruses in circulating CD4(+) T cells and rebound viruses emerging during treatment interruption","volume":"115","author":"Lu","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"3102","DOI":"10.1172\/JCI120194","article-title":"HIV-1 latent reservoir size and diversity are stable following brief treatment interruption","volume":"128","author":"Salantes","year":"2018","journal-title":"J. Clin. Investig."},{"key":"ref_156","doi-asserted-by":"crossref","unstructured":"Vibholm, L.K., Lorenzi, J.C.C., Pai, J.A., Cohen, Y.Z., Oliveira, T.Y., Barton, J.P., Garcia Noceda, M., Lu, C.L., Ablanedo-Terrazas, Y., and Del Rio Estrada, P.M. (2019). Characterization of Intact Proviruses in Blood and Lymph Node from HIV-Infected Individuals Undergoing Analytical Treatment Interruption. J. Virol., 93.","DOI":"10.1128\/JVI.01920-18"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1038\/s41577-018-0054-y","article-title":"Studying tissue macrophages in vitro: Are iPSC-derived cells the answer?","volume":"18","author":"Lee","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/nature17982","article-title":"Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis","volume":"536","author":"Takasato","year":"2016","journal-title":"Nature"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.tcb.2019.11.004","article-title":"Organoid and Assembloid Technologies for Investigating Cellular Crosstalk in Human Brain Development and Disease","volume":"30","author":"Marton","year":"2019","journal-title":"Trends Cell Biol."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/nature12271","article-title":"Vascularized and functional human liver from an iPSC-derived organ bud transplant","volume":"499","author":"Takebe","year":"2013","journal-title":"Nature"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nature09691","article-title":"Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro","volume":"470","author":"Spence","year":"2011","journal-title":"Nature"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/7\/711\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:45:23Z","timestamp":1760175923000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/7\/711"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,30]]},"references-count":161,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2020,7]]}},"alternative-id":["v12070711"],"URL":"https:\/\/doi.org\/10.3390\/v12070711","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,30]]}}}