{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T03:20:30Z","timestamp":1781580030365,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011676","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T00:00:00Z","timestamp":1696464000000}}],"reference-count":87,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2023,9,25]],"date-time":"2023-09-25T00:00:00Z","timestamp":1695600000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["P51RR000167"],"award-info":[{"award-number":["P51RR000167"]}]},{"name":"NIH","award":["P51OD011106"],"award-info":[{"award-number":["P51OD011106"]}]},{"name":"NIH","award":["R01 AI108415"],"award-info":[{"award-number":["R01 AI108415"]}]},{"name":"NIH","award":["R01 AI124965"],"award-info":[{"award-number":["R01 AI124965"]}]},{"name":"NIH","award":["T32AI55397"],"award-info":[{"award-number":["T32AI55397"]}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["75N91019D00024\/HHSN261201500003I"],"award-info":[{"award-number":["75N91019D00024\/HHSN261201500003I"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). None of the MCMs possessed MHC haplotypes previously associated with SIV control. For six months after ART withdrawal, we observed undetectable or transient viremia in seven of the eight MCMs, despite detecting replication competent SIV using quantitative viral outgrowth assays. <jats:italic>In vivo<\/jats:italic> depletion of CD8\u03b1+ cells induced rebound in all animals, indicating the observed PTC was mediated, at least in part, by CD8\u03b1+ cells. With intact proviral DNA assays, we found that MCMs had significantly smaller viral reservoirs two wpi than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. We found a similarly small viral reservoir among six additional SIV+ MCMs in which ART was initiated at eight wpi, some of whom exhibited viral rebound. These results suggest that an unusually small viral reservoir is a hallmark among SIV+ MCMs. By evaluating immunological differences between MCMs that did and did not rebound, we identified that PTC was associated with a reduced frequency of CD4+ and CD8+ lymphocyte subsets expressing exhaustion markers. Together, these results suggest a combination of small reservoirs and immune-mediated virus suppression contribute to PTC in MCMs. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011676","type":"journal-article","created":{"date-parts":[[2023,9,25]],"date-time":"2023-09-25T17:33:46Z","timestamp":1695663226000},"page":"e1011676","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["CD8+ cells and small viral reservoirs facilitate post-ART control of SIV replication in M3+ Mauritian cynomolgus macaques initiated on ART two weeks post-infection"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0315-9645","authenticated-orcid":true,"given":"Olivia E.","family":"Harwood","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lea M.","family":"Matschke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan V.","family":"Moriarty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexis J.","family":"Balgeman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail J.","family":"Weaver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy L.","family":"Ellis-Connell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea M.","family":"Weiler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lee C.","family":"Winchester","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Courtney V.","family":"Fletcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas C.","family":"Friedrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandon F.","family":"Keele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David H.","family":"O\u2019Connor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica D.","family":"Lang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew R.","family":"Reynolds","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0183-5010","authenticated-orcid":true,"given":"Shelby L.","family":"O\u2019Connor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,9,25]]},"reference":[{"issue":"12","key":"ppat.1011676.ref001","doi-asserted-by":"crossref","first-page":"1954","DOI":"10.1093\/infdis\/jiy479","article-title":"The control of HIV after antiretroviral medication pause (CHAMP) study: Posttreatment controllers identified from 14 clinical studies.","volume":"218","author":"G Namazi","year":"2018","journal-title":"J Infect Dis"},{"issue":"3","key":"ppat.1011676.ref002","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003211","article-title":"Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study.","volume":"9","author":"A S\u00e1ez-Ciri\u00f3n","year":"2013","journal-title":"PLoS Pathog."},{"issue":"4","key":"ppat.1011676.ref003","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1097\/QAD.0000000000001382","article-title":"Post-treatment control or treated controllers? Viral remission in treated and untreated primary HIV infection","volume":"31","author":"GE Martin","year":"2017","journal-title":"Aids"},{"issue":"16","key":"ppat.1011676.ref004","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1001\/archinternmed.2012.2719","article-title":"Immunovirologic control 24 months after interruption of antiretroviral therapy initiated close to HIV seroconversion","volume":"172","author":"S Lodi","year":"2012","journal-title":"Arch Intern Med"},{"issue":"10","key":"ppat.1011676.ref005","doi-asserted-by":"crossref","first-page":"5074","DOI":"10.1128\/JVI.80.10.5074-5077.2006","article-title":"The High-Frequency Major Histocompatibility Complex Class I Allele Mamu-B * 17 Is Associated with Control of Simian Immunodeficiency Virus SIVmac239 Replication","volume":"80","author":"LJ Yant","year":"2006","journal-title":"J Virol"},{"issue":"16","key":"ppat.1011676.ref006","doi-asserted-by":"crossref","first-page":"8827","DOI":"10.1128\/JVI.00895-07","article-title":"Mamu-B*08-Positive Macaques Control Simian Immunodeficiency Virus Replication","volume":"81","author":"JT Loffredo","year":"2007","journal-title":"J Virol"},{"issue":"11","key":"ppat.1011676.ref007","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1186\/s13059-014-0478-z","article-title":"Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication.","volume":"15","author":"AJ Ericsen","year":"2014","journal-title":"Genome Biol"},{"issue":"14","key":"ppat.1011676.ref008","doi-asserted-by":"crossref","first-page":"7596","DOI":"10.1128\/JVI.00716-12","article-title":"Specific CD8+ T Cell Responses Correlate with Control of Simian Immunodeficiency Virus Replication in Mauritian Cynomolgus Macaques","volume":"86","author":"ML Budde","year":"2012","journal-title":"J Virol"},{"issue":"5","key":"ppat.1011676.ref009","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1097\/COH.0000000000000748","article-title":"CD8+ T-cell responses in HIV controllers: potential implications for novel HIV remission strategies.","volume":"17","author":"RL Rutishauser","year":"2022","journal-title":"Curr Opin HIV AIDS"},{"issue":"July","key":"ppat.1011676.ref010","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.3389\/fimmu.2019.01749","article-title":"Learning From the Exceptions: HIV Remission in Post-treatment Controllers.","volume":"10","author":"B Etemad","year":"2019","journal-title":"Front Immunol."},{"issue":"11","key":"ppat.1011676.ref011","first-page":"1","article-title":"How elite controllers and posttreatment controllers inform our search for an HIV-1 cure","volume":"131","author":"JZ Li","year":"2021","journal-title":"J Clin Invest"},{"issue":"May 2014","key":"ppat.1011676.ref012","doi-asserted-by":"crossref","first-page":"S165","DOI":"10.1093\/cid\/civ069","article-title":"Efficacy of HIV postexposure prophylaxis: Systematic review and meta-analysis of nonhuman primate studies","volume":"60","author":"C Irvine","year":"2015","journal-title":"Clin Infect Dis"},{"issue":"1","key":"ppat.1011676.ref013","article-title":"Prevention of SIVmac251 reservoir seeding in rhesus monkeys by early antiretroviral therapy. Nat Commun","volume":"9","author":"JB Whitney","year":"2018","journal-title":"Internet]"},{"issue":"5","key":"ppat.1011676.ref014","doi-asserted-by":"crossref","first-page":"e198","DOI":"10.1016\/S2666-5247(21)00010-0","article-title":"Long-term effects of early antiretroviral initiation on HIV reservoir markers: a longitudinal analysis of the MERLIN clinical study","volume":"2","author":"M Massanella","year":"2021","journal-title":"The Lancet Microbe"},{"issue":"12","key":"ppat.1011676.ref015","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004543","article-title":"Initiation of ART during Early Acute HIV Infection Preserves Mucosal Th17 Function and Reverses HIV-Related Immune Activation.","volume":"10","author":"A Schuetz","year":"2014","journal-title":"PLoS Pathog."},{"issue":"377","key":"ppat.1011676.ref016","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1126\/scitranslmed.aag1809","article-title":"Delayed differentiation of potent effector CD8+ T cells reducing viremia and reservoir seeding in acute HIV infection.","volume":"9","author":"H Takata","year":"2017","journal-title":"Sci Transl Med."},{"issue":"5403","key":"ppat.1011676.ref017","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1126\/science.283.5403.857","article-title":"Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes","volume":"283","author":"JE Schmitz","year":"1999","journal-title":"Science (80-)."},{"key":"ppat.1011676.ref018","article-title":"CD8+ lymphocytes do not impact SIV reservoir establishment under ART. Nat Microbiol","author":"M Statzu","year":"2023","journal-title":"Internet]"},{"issue":"3","key":"ppat.1011676.ref019","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1016\/j.immuni.2016.08.018","article-title":"CD8+ Lymphocytes Are Required for Maintaining Viral Suppression in SIV-Infected Macaques Treated with Short-Term Antiretroviral Therapy","volume":"45","author":"EK Cartwright","year":"2016","journal-title":"Immunity"},{"issue":"7","key":"ppat.1011676.ref020","doi-asserted-by":"crossref","first-page":"3465","DOI":"10.1128\/JVI.02392-06","article-title":"Subdominant CD8 + T-Cell Responses Are Involved in Durable Control of AIDS Virus Replication","volume":"81","author":"TC Friedrich","year":"2007","journal-title":"J Virol"},{"issue":"5","key":"ppat.1011676.ref021","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.ppat.1000917","article-title":"Perforin expression directly ex vivo by HIV-specific CD8+ T-cells is a correlate of HIV elite control.","volume":"6","author":"AR Hersperger","year":"2010","journal-title":"PLoS Pathog."},{"key":"ppat.1011676.ref022","first-page":"1","article-title":"Immunological biomarkers predict HIV-1 viral rebound after treatment interruption.","volume":"6","author":"J Hurst","year":"2015","journal-title":"Nat Commun [Internet]."},{"issue":"4","key":"ppat.1011676.ref023","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01436-18","article-title":"Mechanisms of Abrupt Loss of Virus Control in a Cohort of Previous HIV Controllers. Kirchhoff F, editor","volume":"93","author":"M Ros\u00e1s-Umbert","year":"2019","journal-title":"J Virol"},{"issue":"9","key":"ppat.1011676.ref024","first-page":"e1008821","article-title":"Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription. Douek DC, editor","volume":"16","author":"M Zanoni","year":"2020","journal-title":"Internet]"},{"issue":"10","key":"ppat.1011676.ref025","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/nri2636","article-title":"Monkeying around with HIV vaccines: using rhesus macaques to define \u201cgatekeepers\u201d for clinical trials.","volume":"9","author":"DJ Shedlock","year":"2009","journal-title":"Nat Rev Immunol"},{"issue":"9","key":"ppat.1011676.ref026","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.1038\/s41591-018-0130-7","article-title":"Early antiretroviral therapy limits SIV reservoir establishment to delay or prevent post-treatment viral rebound","volume":"24","author":"AA Okoye","year":"2018","journal-title":"Nat Med"},{"key":"ppat.1011676.ref027","article-title":"Virologic and immunologic features of SIV control post ART interruption in rhesus macaques","author":"Z Strongin","year":"2020","journal-title":"J Virol"},{"issue":"1","key":"ppat.1011676.ref028","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/nature13594","article-title":"Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys","volume":"512","author":"JB Whitney","year":"2014","journal-title":"Nature"},{"issue":"3","key":"ppat.1011676.ref029","first-page":"1","article-title":"Immunotherapy with DNA vaccine and live attenuated rubella\/SIV gag vectors plus early ART can prevent SIVmac251 viral rebound in acutely infected rhesus macaques.","volume":"15","author":"K Virnik","year":"2020","journal-title":"PLoS One [Internet"},{"key":"ppat.1011676.ref030","first-page":"2","article-title":"MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques","author":"SL O\u2019Connor","year":"2010","journal-title":"Sci Transl Med"},{"issue":"5","key":"ppat.1011676.ref031","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1007\/s00251-009-0369-8","article-title":"Mhc haplotype H6 is associated with sustained control of SIVmac251 infection in Mauritian cynomolgus macaques","volume":"61","author":"ET Mee","year":"2009","journal-title":"Immunogenetics"},{"issue":"23","key":"ppat.1011676.ref032","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.01424-22","article-title":"Transient T Cell Expansion, Activation, and Proliferation in Therapeutically Vaccinated Simian Immunodeficiency Virus-Positive Macaques Treated with N-803.","volume":"96","author":"OE Harwood","year":"2022","journal-title":"J Virol"},{"issue":"11","key":"ppat.1011676.ref033","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1007\/s40262-013-0093-2","article-title":"Clinical pharmacokinetic, pharmacodynamic and drug-interaction profile of the integrase inhibitor dolutegravir.","volume":"52","author":"ML Cottrell","year":"2013","journal-title":"Clin Pharmacokinet"},{"issue":"1","key":"ppat.1011676.ref034","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1097\/QAI.0000000000001106","article-title":"Plasma and Intracellular Concentrations in HIV-Infected Patients Requiring Hemodialysis Dosed with Tenofovir Disoproxil Fumarate and Emtricitabine.","volume":"73","author":"JE Slaven","year":"2016","journal-title":"J Acquir Immune Defic Syndr."},{"key":"ppat.1011676.ref035","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7554\/eLife.49022","article-title":"Predictors of SIV recrudescence following antiretroviral treatment interruption.","volume":"8","author":"M Pinkevych","year":"2019","journal-title":"Elife."},{"issue":"17","key":"ppat.1011676.ref036","doi-asserted-by":"crossref","first-page":"5467","DOI":"10.1073\/pnas.1419162112","article-title":"Post-treatment control of HIV infection","volume":"112","author":"JM Conway","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"ppat.1011676.ref037","first-page":"1","article-title":"The size of the expressed HIV reservoir predicts timing of viral rebound after treatment interruption.","volume":"30","author":"JZ Li","year":"2015","journal-title":"AIDS"},{"key":"ppat.1011676.ref038","doi-asserted-by":"crossref","first-page":"e03821","DOI":"10.7554\/eLife.03821","article-title":"HIV-1 DNA predicts disease progression and post-treatment virological control","volume":"3","author":"JP Williams","year":"2014","journal-title":"Elife"},{"issue":"9","key":"ppat.1011676.ref039","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":"KM Bruner","year":"2016","journal-title":"Nat Med"},{"key":"ppat.1011676.ref040","article-title":"A quantitative approach for measuring the reservoir of latent HIV-1 proviruses","author":"KM Bruner","year":"2019","journal-title":"Nature"},{"key":"ppat.1011676.ref041","article-title":"Control of Simian Immunodeficiency Virus Infection in Prophylactically Vaccinated, Antiretroviral Treatment-Naive Macaques Is Required for the Most Efficacious CD8 T Cell Response during Treatment with the Interleukin-15 Superagonist N-803. Silvestri G, editor","author":"AL Ellis-Connell","year":"2022","journal-title":"J Virol"},{"issue":"10","key":"ppat.1011676.ref042","first-page":"e1008954","article-title":"Therapeutic vaccination of SIV-infected, ART-treated infant rhesus macaques using Ad48\/MVA in combination with TLR-7 stimulation. Evans DT, editor","volume":"16","author":"KM Bricker","year":"2020","journal-title":"Internet]"},{"key":"ppat.1011676.ref043","first-page":"131","article-title":"Antibody-mediated depletion of viral reservoirs is limited in SIV-infected macaques treated early with antiretroviral therapy","author":"AE Swanstrom","year":"2021","journal-title":"J Clin Invest"},{"issue":"1","key":"ppat.1011676.ref044","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-021-87872-x","article-title":"Differences in host immune populations between rhesus macaques and cynomolgus macaque subspecies in relation to susceptibility to Mycobacterium tuberculosis infection","volume":"11","author":"L Sibley","year":"2021","journal-title":"Sci Rep"},{"issue":"6","key":"ppat.1011676.ref045","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2120326119","article-title":"Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy","volume":"119","author":"JA White","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"ppat.1011676.ref046","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1093\/cid\/ciab541","article-title":"Time to Viral Rebound After Interruption of Modern Antiretroviral Therapies","volume":"74","author":"JZ Li","year":"2022","journal-title":"Clin Infect Dis"},{"issue":"1","key":"ppat.1011676.ref047","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1111\/imr.12823","article-title":"T-cell exhaustion in HIV infection","volume":"292","author":"C Fenwick","year":"2019","journal-title":"Immunol Rev"},{"issue":"523","key":"ppat.1011676.ref048","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aax4077","article-title":"Elite control of HIV is associated with distinct functional and transcriptional signatures in lymphoid tissue CD8 + T cells.","volume":"11","author":"S Nguyen","year":"2019","journal-title":"Sci Transl Med"},{"issue":"10","key":"ppat.1011676.ref049","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.1016\/j.immuni.2021.08.007","article-title":"Functional impairment of HIV-specific CD8+ T cells precedes aborted spontaneous control of viremia","volume":"54","author":"DR Collins","year":"2021","journal-title":"Immunity"},{"key":"ppat.1011676.ref050","first-page":"1","article-title":"CD8+ T cells promote HIV latency by remodeling CD4+ T cell metabolism to enhance their survival, quiescence, and stemness","author":"S Mutascio","year":"2023","journal-title":"Immunity"},{"key":"ppat.1011676.ref051","first-page":"1","article-title":"Allogeneic immunity clears latent virus following allogeneic stem cell transplantation in SIV-infected ART-suppressed macaques","author":"HL Wu","year":"2023","journal-title":"Immunity"},{"issue":"15","key":"ppat.1011676.ref052","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/JVI.00537-19","article-title":"CD8\u03b2 Depletion Does Not Prevent Control of Viral Replication or Protection from Challenge in Macaques Chronically Infected with a Live Attenuated Simian Immunodeficiency Virus.","volume":"93","author":"MS Sutton","year":"2019","journal-title":"J Virol"},{"issue":"4","key":"ppat.1011676.ref053","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1016\/j.immuni.2019.09.007","article-title":"Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields","volume":"51","author":"J Gorman","year":"2019","journal-title":"Immunity"},{"issue":"1","key":"ppat.1011676.ref054","article-title":"Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus.","volume":"13","author":"F Zhao","year":"2022","journal-title":"Nat Commun."},{"issue":"7613","key":"ppat.1011676.ref055","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1038\/nature18929","article-title":"HIV-1 antibody 3BNC117 suppresses viral rebound in humans during treatment interruption","volume":"535","author":"JF Scheid","year":"2016","journal-title":"Nature"},{"issue":"9","key":"ppat.1011676.ref056","doi-asserted-by":"crossref","first-page":"2311","DOI":"10.1084\/jem.20180936","article-title":"Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117","volume":"215","author":"YZ Cohen","year":"2018","journal-title":"J Exp Med"},{"issue":"9","key":"ppat.1011676.ref057","doi-asserted-by":"crossref","first-page":"4074","DOI":"10.1172\/JCI120549","article-title":"HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers","volume":"128","author":"R Sharaf","year":"2018","journal-title":"J Clin Invest"},{"issue":"1","key":"ppat.1011676.ref058","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-28130-0","article-title":"Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry.","volume":"13","author":"M Claireaux","year":"2022","journal-title":"Nat Commun."},{"issue":"7511","key":"ppat.1011676.ref059","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/nature13554","article-title":"Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression","volume":"511","author":"NG Sandler","year":"2014","journal-title":"Nature"},{"issue":"8","key":"ppat.1011676.ref060","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1002170","article-title":"Functional cure of sivagm infection in rhesus macaques results in complete recovery of CD4 +T cells and is reverted by CD8 + cell depletion","volume":"7","author":"I Pandrea","year":"2011","journal-title":"PLoS Pathog"},{"issue":"2\u20133","key":"ppat.1011676.ref061","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1111\/j.1600-0684.1998.tb00232.x","article-title":"SIVrcm infection of macaques","volume":"27","author":"SM Smith","year":"1998","journal-title":"J Med Primatol"},{"issue":"12","key":"ppat.1011676.ref062","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00565-18","article-title":"Preexisting simian immunodeficiency virus infection increases susceptibility to tuberculosis in mauritian cynomolgus macaques","volume":"86","author":"MA Rodgers","year":"2018","journal-title":"Infect Immun"},{"issue":"14","key":"ppat.1011676.ref063","doi-asserted-by":"crossref","first-page":"8878","DOI":"10.1128\/JVI.79.14.8878-8885.2005","article-title":"Pathogenicity of Simian-Human Immunodeficiency Virus SHIV-89.6P and SIVmac Is Attenuated in Cynomolgus Macaques and Associated with Early T-Lymphocyte Responses","volume":"79","author":"KA Reimann","year":"2005","journal-title":"J Virol"},{"issue":"1","key":"ppat.1011676.ref064","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.chom.2019.06.005","article-title":"The Landscape of Persistent Viral Genomes in ART-Treated SIV, SHIV, and HIV-2","volume":"26","author":"AM Bender","year":"2019","journal-title":"Infections. Cell Host Microbe"},{"issue":"1","key":"ppat.1011676.ref065","doi-asserted-by":"crossref","first-page":"49","DOI":"10.4049\/jimmunol.1700841","article-title":"The Role of MHC-E in T Cell Immunity Is Conserved among Humans, Rhesus Macaques, and","volume":"200","author":"HL Wu","year":"2018","journal-title":"Cynomolgus Macaques. J Immunol"},{"key":"ppat.1011676.ref066","article-title":"Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype","author":"JA Karl","year":"2023","journal-title":"Genome Res"},{"key":"ppat.1011676.ref067","first-page":"1","article-title":"Cytomegalovirus-vaccine-induced unconventional T cell priming and control of SIV replication is conserved between primate species","author":"D Malouli","year":"2022","journal-title":"Cell Host Microbe"},{"issue":"11","key":"ppat.1011676.ref068","doi-asserted-by":"crossref","first-page":"3240","DOI":"10.1002\/eji.200535343","article-title":"Identification of effector-memory CMV-specific T lymphocytes that kill CMV-infected target cells in an HLA-E-restricted fashion","volume":"35","author":"P Mazzarino","year":"2005","journal-title":"Eur J Immunol"},{"issue":"12","key":"ppat.1011676.ref069","doi-asserted-by":"crossref","first-page":"5541","DOI":"10.1128\/JVI.00192-16","article-title":"Vaccination with Live Attenuated Simian Immunodeficiency Virus (SIV) Protects from Mucosal, but Not Necessarily Intravenous, Challenge with a Minimally Heterologous SIV.","volume":"90","author":"MS Sutton","year":"2016","journal-title":"J Virol"},{"issue":"5","key":"ppat.1011676.ref070","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.ppat.1006359","article-title":"Genetically-barcoded SIV facilitates enumeration of rebound variants and estimation of reactivation rates in nonhuman primates following interruption of suppressive antiretroviral therapy.","volume":"13","author":"CM Fennessey","year":"2017","journal-title":"PLoS Pathog"},{"key":"ppat.1011676.ref071","first-page":"7","article-title":"Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection","author":"AL Bailey","year":"2015","journal-title":"Sci Transl Med"},{"issue":"5\u20136","key":"ppat.1011676.ref072","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1111\/j.1600-0684.2005.00128.x","article-title":"Highly sensitive SIV plasma viral load assay: Practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS","volume":"34","author":"AN Cline","year":"2005","journal-title":"J Med Primatol"},{"key":"ppat.1011676.ref073","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1007\/978-1-4939-3046-3_16","article-title":"Measuring the frequency of latent HIV-1 in resting CD4+ T cells using a limiting dilution coculture assay","volume":"1354","author":"GM Laird","year":"2016","journal-title":"Methods Mol Biol"},{"issue":"4","key":"ppat.1011676.ref074","first-page":"2633851","article-title":"Designing and Interpreting Limiting Dilution Assays: General Principles and Applications to the Latent Reservoir for Human Immunodeficiency Virus-1.","volume":"2","author":"DIS Rosenbloom","year":"2015","journal-title":"Open Forum Infect Dis [Internet]."},{"issue":"7","key":"ppat.1011676.ref075","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1097\/QAD.0000000000003201","article-title":"Persistent HIV transcription and variable antiretroviral drug penetration in lymph nodes during plasma viral suppression","volume":"36","author":"V. Fletcher C","year":"2022","journal-title":"Aids"},{"issue":"1","key":"ppat.1011676.ref076","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-021-21724-0","article-title":"Persistence of viral RNA in lymph nodes in ART-suppressed SIV\/SHIV-infected Rhesus Macaques.","volume":"12","author":"AM Cadena","year":"2021","journal-title":"Nat Commun"},{"issue":"4","key":"ppat.1011676.ref077","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41591-020-0782-y","article-title":"CTLA-4 and PD-1 dual blockade induces SIV reactivation without control of rebound after antiretroviral therapy interruption","volume":"26","author":"J Harper","year":"2020","journal-title":"Nat Med"},{"issue":"19","key":"ppat.1011676.ref078","doi-asserted-by":"crossref","first-page":"9748","DOI":"10.1128\/JVI.00993-15","article-title":"Expansion of Simian Immunodeficiency Virus (SIV)-Specific CD8 T Cell Lines from SIV-Naive Mauritian Cynomolgus Macaques for Adoptive Transfer.","volume":"89","author":"MS Mohns","year":"2015","journal-title":"J Virol"},{"issue":"30","key":"ppat.1011676.ref079","doi-asserted-by":"crossref","first-page":"4465","DOI":"10.1016\/j.vaccine.2012.04.082","article-title":"A trivalent recombinant Ad5 gag\/pol\/nef vaccine fails to protect rhesus macaques from infection or control virus replication after a limiting-dose heterologous SIV challenge","volume":"30","author":"MR Reynolds","year":"2012","journal-title":"Vaccine"},{"issue":"8","key":"ppat.1011676.ref080","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1089\/aid.2017.0046","article-title":"Rare Control of SIVmac239 Infection in a Vaccinated Rhesus Macaque","volume":"33","author":"MA Martins","year":"2017","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"6","key":"ppat.1011676.ref081","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1016\/S0002-9440(10)65450-8","article-title":"A nonhuman primate model for the selective elimination of CD8+ lymphocytes using a mouse-human chimeric monoclonal antibody","volume":"154","author":"JE Schmitz","year":"1999","journal-title":"Am J Pathol"},{"issue":"22","key":"ppat.1011676.ref082","doi-asserted-by":"crossref","first-page":"11876","DOI":"10.1128\/JVI.01153-09","article-title":"Defective Human Immunodeficiency Virus-Specific CD8 + T-Cell Polyfunctionality, Proliferation, and Cytotoxicity Are Not Restored by Antiretroviral Therapy","volume":"83","author":"SA Migueles","year":"2009","journal-title":"J Virol"},{"issue":"4","key":"ppat.1011676.ref083","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"P Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"issue":"3","key":"ppat.1011676.ref084","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"PA Ewels","year":"2020","journal-title":"Nat Biotechnol"},{"key":"ppat.1011676.ref085","author":"H Patel","year":"2022","journal-title":"Plastered Magnesium Mongoose"},{"issue":"8","key":"ppat.1011676.ref086","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1093\/bioinformatics\/btt087","article-title":"EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments","volume":"29","author":"N Leng","year":"2013","journal-title":"Bioinformatics"},{"issue":"4","key":"ppat.1011676.ref087","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/bioinformatics\/btp692","article-title":"RNA-Seq gene expression estimation with read mapping uncertainty","volume":"26","author":"B Li","year":"2009","journal-title":"Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1011676","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T00:00:00Z","timestamp":1696464000000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011676","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T18:08:30Z","timestamp":1696529310000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011676"}},"subtitle":[],"editor":[{"given":"Guido","family":"Silvestri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,9,25]]},"references-count":87,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2023,9,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1011676","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1011676","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9,25]]}}}