HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study

Background: It is unknown if extremely early initiation of antiretroviral therapy (ART) may lead to long-term ART-free HIV remission or cure. As a result, we studied 2 individuals recruited from a pre-exposure prophylaxis (PrEP) program who started prophylactic ART an estimated 10 days (Participant A; 54-year-old male) and 12 days (Participant B; 31-year-old male) after infection with peak plasma HIV RNA of 220 copies/mL and 3,343 copies/mL, respectively. Extensive testing of blood and tissue for HIV persistence was performed, and PrEP Participant A underwent analytical treatment interruption (ATI) following 32 weeks of continuous ART. Methods and findings Colorectal and lymph node tissues, bone marrow, cerebral spinal fluid (CSF), plasma, and very large numbers of peripheral blood mononuclear cells (PBMCs) were obtained longitudinally from both participants and were studied for HIV persistence in several laboratories using molecular and culture-based detection methods, including a murine viral outgrowth assay (mVOA). Both participants initiated PrEP with tenofovir/emtricitabine during very early Fiebig stage I (detectable plasma HIV-1 RNA, antibody negative) followed by 4-drug ART intensification. Following peak viral loads, both participants experienced full suppression of HIV-1 plasma viremia. Over the following 2 years, no further HIV could be detected in blood or tissue from PrEP Participant A despite extensive sampling from ileum, rectum, lymph nodes, bone marrow, CSF, circulating CD4+ T cell subsets, and plasma. No HIV was detected from tissues obtained from PrEP Participant B, but low-level HIV RNA or DNA was intermittently detected from various CD4+ T cell subsets. Over 500 million CD4+ T cells were assayed from both participants in a humanized mouse outgrowth assay. Three of 8 mice infused with CD4+ T cells from PrEP Participant B developed viremia (50 million input cells/surviving mouse), but only 1 of 10 mice infused with CD4+ T cells from PrEP Participant A (53 million input cells/mouse) experienced very low level viremia (201 copies/mL); sequence confirmation was unsuccessful. PrEP Participant A stopped ART and remained aviremic for 7.4 months, rebounding with HIV RNA of 36 copies/mL that rose to 59,805 copies/mL 6 days later. ART was restarted promptly. Rebound plasma HIV sequences were identical to those obtained during acute infection by single-genome sequencing. Mathematical modeling predicted that the latent reservoir size was approximately 200 cells prior to ATI and that only around 1% of individuals with a similar HIV burden may achieve lifelong ART-free remission. Furthermore, we observed that lymphocytes expressing the tumor marker CD30 increased in frequency weeks to months prior to detectable HIV-1 RNA in plasma. This study was limited by the small sample size, which was a result of the rarity of individuals presenting during hyperacute infection. Conclusions: We report HIV relapse despite initiation of ART at one of the earliest stages of acute HIV infection possible. Near complete or complete loss of detectable HIV in blood and tissues did not lead to indefinite ART-free HIV remission. However, the small numbers of latently infected cells in individuals treated during hyperacute infection may be associated with prolonged ART-free remission

Memory CD4 + T-Cells Expressing HLA-DR Contribute to HIV Persistence During Prolonged Antiretroviral Therapy.

To date, most assays for measuring the human immunodeficiency virus (HIV-1) reservoir do not include memory CD4+ T-cells expressing the activation marker, human leukocyte antigen-antigen D related (HLA-DR). However, little is known concerning the role these cells play in maintaining persistent HIV-1 during effective antiretroviral therapy (ART). To address this issue, we examined, cellular activation/exhaustion markers (Ki67, CCR5, PD-1, Lag-3 and Tim-3) and viral gag-pol DNA sequences within HLA-DR- and HLA-DR+ memory CD4+ T-cell subsets longitudinally from the peripheral blood of six participants over 3 to ≥15 years of effective therapy. HLA-DR expression was readily detected during the study period in all participants. The average expression levels of CCR5, PD-1 and Tim-3 were higher on the HLA-DR+ T-cell subset whereas the average of LAG-3 expression was higher on their HLA-DR- counterpart. The proportion of HIV-infected cells increased within the HLA-DR+ subset by an average of 18% per year of ART whereas the frequency of infected HLA-DR- T-cells slightly decreased over time (5% per year). We observed that 20-33% of HIV-DNA sequences from the early time points were genetically identical to viral sequences from the last time point within the same cell subset during ART. This indicates that a fraction of proviruses persists within HLA-DR+ and HLA-DR- T-cell subsets during prolonged ART. Our HIV-DNA sequence analyses also revealed that cells transitioned between the HLA-DR+ and HLA-DR- phenotypes. The Ki67 expression, a marker for cellular proliferation, and the combined markers of Ki67/PD-1 averaged 19-fold and 22-fold higher on the HLA-DR+ T-cell subset compared to their HLA-DR- counterpart. Moreover, cellular proliferation, as reflected by the proportion of genetically identical HIV-DNA sequences, increased within both T-cell subsets over the study period; however, this increase was greater within the HLA-DR+ T-cells. Our research revealed that cellular transition and proliferation contribute to the persistence of HIV in HLA-DR+ and HLA-DR- T-cell subsets during prolonged therapy. As such, the HIV reservoir expands during effective ART when both the HLA-DR+ and HLA-DR- cell subsets are included, and therapeutic interventions aimed at reducing the HIV-1 reservoir should target HLA-DR+ and HLA-DR- T-cells

Observer les circulations et analyser les POsitions SOciales Multilocatisées

This project is thought of as an empirical and conceptual brick to better understand the infra-national spatialization of the social structure. Our team made up of sociologists, geographers, demographers and economists, using statistical and ethnographic methods, proposes to study the multilocalization of social positions. This must be understood both synchronically, for all people whose movements in the domestic, family, professional or even leisure contexts, are part of various spatial contexts; but also diachronically, through biographies and social experiences sedimented over time, producing multi-sited socializations. In particular, we discuss the trend, still dominant today, to locate individuals or social groups through the prism of a single place at a given time – the address of the main residence on the survey’s date. Our project thus seeks to assess the role played by the multiple and differentiated spatial inclusion of individuals and social groups. This program offers a more dynamic, biographical vision of the effects of place and social stratification, since, if followed, the same person aggregates various spatial and social experiences that can coexist, in the same place, or in different places. We set ourselves four objectives. The first will be to propose a new social geography of France not based on the rural-urban gradient but on the social morphology of space, distinguishing territories according to their socio-professional composition in particular. We hope to identify sociologically close territories beyond their classification according to the rural-urban gradient. The second will be to specify the circulations of different social groups. We expect to identify circuits in space linking socially homologous rural and urban points. We will also be interested in individual circulations which, by their heterogeneity, stand out from these collective circuits. The third objective will lead us to grasp the effects on the socialization and social positioning of these individual movements on the members of the different social groups involved. To do this, we will introduce the notion of space of circulation accumulating in a way all the social positions held in different places of a person. It is assumed that these experiences generally combine homologous social positions but that they can all add up to be diversified. Finally, the last objective, we will try to grasp the effects of these mobilities on localized relations in the places where social groups with diverse social experiences meet, describing social conflicts but also social relations in terms of class alliance.Ce projet se pense comme une brique empirique et conceptuelle pour mieux appréhender la spatialisation infra-nationale de la structure sociale. Notre équipe composée de sociologues, de géographes, de démographes et d’économistes, mobilisant des méthodes statistiques et ethnographiques, se propose d’étudier la multilocalisation des positions sociales. Celle-ci doit s’entendre à la fois synchroniquement, pour toutes les personnes dont les circulations dans le cadre domestique, familial, professionnel, voire du loisir, s’inscrivent dans divers contextes spatiaux ; mais également diachroniquement, à travers des biographies et des expériences sociales sédimentées dans le temps, produisant des socialisations multisituées. Nous questionnons en particulier la tendance, encore dominante aujourd’hui, à localiser les individus ou les groupes au prisme d’un lieu unique à un moment donné – l’adresse de la résidence principale à la date de l’enquête. Notre projet cherche ainsi à évaluer le rôle que joue l’inscription spatiale multiple et différenciée des individus et des groupes sociaux. Ce programme propose une vision plus dynamique, biographique, des effets de lieu et de la stratification sociale, puisque, si on le suit, une même personne agrège des expériences spatiales et sociales variées et peuvent coexister, en un même lieu, des groupes sociaux variés par leurs trajectoires sociales et par les autres lieux qu’ils investissent. On se fixe quatre objectifs. Le premier sera de proposer une nouvelle géographe sociale de la France non fondée sur le gradient rural-urbain mais sur la morphologie sociale de l’espace, distinguant des territoires selon leur composition socio-professionnelle notamment. Nous espérons identifier des territoires sociologiquement proches par-delà leur classification selon le gradient rural urbain. Le second sera de préciser les circulations propres aux différents groupes sociaux. Nous nous attendons à identifier dans l’espace des circuits reliant des points ruraux et urbains socialement homologues, identifiants des circuits de classes supérieurs, et des circuits de classes populaires par exemple, étendant les processus de ségrégation spatiale bien au-delà de la grande ville, vers les lieux de destination, mais aussi dans la circulation. Nous nous intéresserons également aux circulations individuelles qui par leur hétérogénéité se démarquent de ces circuits collectifs. Le troisième objectif nous portera à saisir les effets sur la socialisation et le positionnement social de ces circulations individuelles sur les membres des différents groupes sociaux impliqués. Pour ce faire, nous introduirons la notion d’espace de circulation cumulant en quelque sorte l’ensemble des positions sociales tenues dans différents lieux d’une personne. On suppose que ces expériences cumulent généralement des positions sociales homologues mais qu’elles peuvent tout ajutant se révéler diversifiées. Enfin, dernier objectif, nous tenterons de saisir les effets de ces mobilités sur les rapports localisés dans les lieux où se retrouvent des groupes sociaux aux expériences sociales diverses, décrivant les conflits sociaux mais aussi les rapports sociaux en termes d’alliance de classe

Anti-HIV Antibody Responses and the HIV Reservoir Size during Antiretroviral Therapy

<div><p>Background</p><p>A major challenge to HIV eradication strategies is the lack of an accurate measurement of the total burden of replication-competent HIV (the “reservoir”). We assessed the association of anti-HIV antibody responses and the estimated size of the reservoir during antiretroviral therapy (ART).</p><p>Methods</p><p>We evaluated anti-HIV antibody profiles using luciferase immunoprecipitation systems (LIPS) assay in relation to several blood-based HIV reservoir measures: total and 2-LTR DNA (rtPCR or droplet digital PCR); integrated DNA (<i>Alu</i> PCR); unspliced RNA (rtPCR), multiply-spliced RNA (TILDA), residual plasma HIV RNA (single copy PCR), and replication-competent virus (outgrowth assay). We also assessed total HIV DNA and RNA in gut-associated lymphoid tissue (rtPCR). Spearman correlations and linear regressions were performed using log-transformed blood- or tissue-based reservoir measurements as predictors and log-transformed antibody levels as outcome variables.</p><p>Results</p><p>Among 51 chronically HIV-infected ART-suppressed participants (median age = 57, nadir CD4+ count = 196 cells/mm3, ART duration = 9 years), the most statistically significant associations were between antibody responses to integrase and HIV RNA in gut-associated lymphoid tissue (1.17 fold-increase per two-fold RNA increase, P = 0.004) and between antibody responses to matrix and integrated HIV DNA in resting CD4+ T cells (0.35 fold-decrease per two-fold DNA increase, P = 0.003). However, these associations were not statistically significant after a stringent Bonferroni-adjustment of P<0.00045. Multivariate models including age and duration of ART did not markedly alter results.</p><p>Conclusions</p><p>Our findings suggest that anti-HIV antibody responses may reflect the size of the HIV reservoir during chronic treated HIV disease, possibly via antigen recognition in reservoir sites. Larger, prospective studies are needed to validate the utility of antibody levels as a measure of the total body burden of HIV during treatment.</p></div

High levels of genetically intact HIV in HLA-DR+ memory T cells indicates their value for reservoir studies.

ObjectiveThe contribution of HLA-DR+ memory CD4 T cells to the HIV reservoir during prolonged antiretroviral therapy is unclear as these cells are commonly excluded when assessing for replication-competent HIV. To address this issue, we examined the distribution of genetically intact HIV DNA within HLA-DR- and HLA-DR+ memory CD4 T cells and the RNA transcriptional profile of these cells during antiretroviral therapy.Design/methodsFull-length DNA sequencing was used to examine the HIV DNA landscape within HLA-DR+ and HLA-DR- memory CD4 T cells. RNA quantification and sequencing was used to interrogate the relationship between HLA-DR status and HIV RNA transcription.ResultsHLA-DR+ CD4 T cells contained a high frequency of genetically intact HIV genomes, contributing over half of the genetically intact viral sequences to the reservoir. Expansions of genetically identical sequences were identified in all T-cell subsets, indicating that cellular proliferation maintains genetically intact and defective viral DNA during therapy. Intracellular HIV RNA levels in HLA-DR+ and HLA-DR- T cells were not statistically different by either long terminal repeat quantitative PCR quantification or single-genome RNA sequencing of the p6-RT region.ConclusionThe high proportion of intact viral DNA sequences in the proliferative HLA-DR+ subset suggests they are critical in maintaining HIV infection during effective therapy. As such, these cells should be included in any immune intervention targeting HIV during effective therapy

Impact of Antiretroviral Therapy Duration on HIV-1 Infection of T Cells within Anatomic Sites.

Understanding the impact of antiretroviral therapy (ART) duration on HIV-infected cells is critical for developing successful curative strategies. To address this issue, we conducted a cross-sectional/inter-participant genetic characterization of HIV-1 RNA from pre- and on-therapy plasmas and HIV-1 DNA from CD4+ T cell subsets derived from peripheral blood (PB), lymph node (LN), and gut tissues of 26 participants after 3 to 17.8 years of ART. Our studies revealed in four acute/early participants who had paired PB and LN samples a substantial reduction in the proportion of HIV-infected cells per year on therapy within the LN. Extrapolation to all 12 acute/early participants estimated a much smaller reduction in the proportion of HIV-1-infected cells within LNs per year on therapy that was similar to that in the participants treated during chronic infection. LN-derived effector memory T (TEM) cells contained HIV-1 DNA that was genetically identical to viral sequences derived from pre- and on-therapy plasma samples. The proportion of identical HIV-1 DNA sequences increased within PB-derived TEM cells. However, the infection frequency of TEM cells in PB was stable, indicating that cellular proliferation that compensates for T cell loss over time contributes to HIV-1 persistence. This study suggests that ART reduces HIV-infected T cells and that clonal expansion of HIV-infected cells maintains viral persistence. Importantly, LN-derived TEM cells are a probable source of HIV-1 genomes capable of producing infectious HIV-1 and should be targeted by future curative strategies.IMPORTANCE HIV-1 persists as an integrated genome in CD4+ memory T cells during effective therapy, and cessation of current treatments results in resumption of viral replication. To date, the impact of antiretroviral therapy duration on HIV-infected CD4+ T cells and the mechanisms of viral persistence in different anatomic sites is not clearly elucidated. In the current study, we found that treatment duration was associated with a reduction in HIV-infected T cells. Our genetic analyses revealed that CD4+ effector memory T (TEM) cells derived from the lymph node appeared to contain provirus that was genetically identical to plasma-derived virions. Moreover, we found that cellular proliferation counterbalanced the decay of HIV-infected cells throughout therapy. The contribution of cellular proliferation to viral persistence is particularly significant in TEM cells. Our study emphasizes the importance of HIV-1 intervention and provides new insights into the location of memory T cells infected with HIV-1 DNA, which is capable of contributing to viremia

Impact of Antiretroviral Therapy Duration on HIV-1 Infection of T Cells within Anatomic Sites.

Understanding the impact of antiretroviral therapy (ART) duration on HIV-infected cells is critical for developing successful curative strategies. To address this issue, we conducted a cross-sectional/inter-participant genetic characterization of HIV-1 RNA from pre- and on-therapy plasmas and HIV-1 DNA from CD4+ T cell subsets derived from peripheral blood (PB), lymph node (LN), and gut tissues of 26 participants after 3 to 17.8 years of ART. Our studies revealed in four acute/early participants who had paired PB and LN samples a substantial reduction in the proportion of HIV-infected cells per year on therapy within the LN. Extrapolation to all 12 acute/early participants estimated a much smaller reduction in the proportion of HIV-1-infected cells within LNs per year on therapy that was similar to that in the participants treated during chronic infection. LN-derived effector memory T (TEM) cells contained HIV-1 DNA that was genetically identical to viral sequences derived from pre- and on-therapy plasma samples. The proportion of identical HIV-1 DNA sequences increased within PB-derived TEM cells. However, the infection frequency of TEM cells in PB was stable, indicating that cellular proliferation that compensates for T cell loss over time contributes to HIV-1 persistence. This study suggests that ART reduces HIV-infected T cells and that clonal expansion of HIV-infected cells maintains viral persistence. Importantly, LN-derived TEM cells are a probable source of HIV-1 genomes capable of producing infectious HIV-1 and should be targeted by future curative strategies.IMPORTANCE HIV-1 persists as an integrated genome in CD4+ memory T cells during effective therapy, and cessation of current treatments results in resumption of viral replication. To date, the impact of antiretroviral therapy duration on HIV-infected CD4+ T cells and the mechanisms of viral persistence in different anatomic sites is not clearly elucidated. In the current study, we found that treatment duration was associated with a reduction in HIV-infected T cells. Our genetic analyses revealed that CD4+ effector memory T (TEM) cells derived from the lymph node appeared to contain provirus that was genetically identical to plasma-derived virions. Moreover, we found that cellular proliferation counterbalanced the decay of HIV-infected cells throughout therapy. The contribution of cellular proliferation to viral persistence is particularly significant in TEM cells. Our study emphasizes the importance of HIV-1 intervention and provides new insights into the location of memory T cells infected with HIV-1 DNA, which is capable of contributing to viremia

Estimated effects of measures of peripheral blood total or integrated HIV-1 DNA on anti-HIV antibody responses^a.

<p>Estimated effects of measures of peripheral blood total or integrated HIV-1 DNA on anti-HIV antibody responses<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160192#t002fn002" target="_blank">^a</a>.</p

Antibody profiles against seven different HIV-1 antigens in the HIV cohort used for reservoir measurements.

<p>The antibody levels against each of the seven HIV proteins were determined in HIV-uninfected (N = 8) and HIV-infected ART-suppressed (N = 51) participants. The antibody levels are plotted on the Y-axis using a log₁₀scale, and the geometric mean with 95% CI are shown. Comparison between the two groups for all the antigens revealed highly statistically significant higher antibody responses in HIV-infected participants (p<0.0001), as expected. Abbreviations: GP120 = envelope glycoprotein 120; GP41 = envelope glycoprotein 41; RT = reverse transcriptase; INT = integrase; PR = protease; MA = matrix; CA = capsid; NV = HIV-uninfected; HIV = HIV-infected.</p

Association between measures of cell-associated HIV-1 DNA and RNA from gut-associated lymphoid tissue (GALT) and anti-HIV antibody responses^a.

<p>Association between measures of cell-associated HIV-1 DNA and RNA from gut-associated lymphoid tissue (GALT) and anti-HIV antibody responses<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160192#t003fn002" target="_blank">^a</a>.</p