Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease

Antiretroviral therapy (ART) is not a cure. Upon ART cessation, virus rapidly rebounds from latently-infected cells ("the HIV reservoir"). The reservoir is largely stabilized at the time of ART initiation and then decays slowly. Here, leveraging >500 longitudinal samples from 67 people with HIV (PWH) treated during acute infection, we developed a novel mathematical model to predict reservoir decay using the intact proviral DNA assay (IPDA) from peripheral CD4+ T cells. Nonlinear generalized additive models adjusted for initial CD4+ T count, pre-ART viral load, and timing of ART initiation demonstrated rapid biphasic decay of intact DNA (week 0-5: t1/2 ~0.71 months; week 5-24: t1/2 ~3.9 months) that extended out to 1 year of ART, with similar trends for defective DNA. Predicted reservoir decay were faster for participants individuals with earlier timing of ART initiation, higher initial CD4+ T cell count, and lower pre-ART viral load. These estimates are ~5-fold faster than prior reservoir decay estimates among chronic-treated PWH. Thus, these data add to our limited understanding of host viral control at the earliest stages of HIV reservoir stabilization, potentially informing future HIV cure efforts aimed at diverse, global population of PWH initiating ART at varying stages of disease.

A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size

The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). There have been few cohort-based studies evaluating host genomic or transcriptomic predictors of the HIV reservoir. We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 ART-suppressed people with HIV (PWH). After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, P3H3 and NBL1, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (KCNJ2, GJB2), inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q = 0.006), IL-1/NRLP3 inflammasome (q = 0.008), and IL-10 (q = 0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-α protein associations achieving statistical significance (p<0.05). Plasma IL-10 was also significantly inversely associated with HIV DNA (p = 0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. To our knowledge, this is the largest host transcriptomic study of the HIV reservoir. Our findings suggest that host gene expression may vary in response to the transcriptionally active reservoir and that changes in cellular proliferation genes may influence the size of the HIV reservoir. These findings add important data to the limited host genetic HIV reservoir studies to date.

Host variation in type I interferon signaling genes (MX1), C-C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size

OBJECTIVE

Prior genomewide association studies have identified variation in major histocompatibility complex (MHC) class I alleles and C-C chemokine receptor type 5 gene (CCR5Δ32) as genetic predictors of viral control, especially in 'elite' controllers, individuals who remain virally suppressed in the absence of therapy.

DESIGN

Cross-sectional genomewide association study.

METHODS

We analyzed custom whole exome sequencing and direct human leukocyte antigen (HLA) typing from 202 antiretroviral therapy (ART)-suppressed HIV+ noncontrollers in relation to four measures of the peripheral CD4+ T-cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T-cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression.

RESULTS

Previously reported 'protective' host genetic mutations related to viral setpoint (e.g. among elite controllers) were found to predict smaller HIV reservoir size. The HLA 'protective' B∗57:01 was associated with significantly lower HIV usRNA (q = 3.3 × 10-3), and among the largest subgroup, European ancestry individuals, the CCR5Δ32 deletion was associated with smaller HIV tDNA (P = 4.3 × 10-3) and usRNA (P = 8.7 × 10-3). In addition, genomewide analysis identified several single nucleotide polymorphisms in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q = 0.02), and the direction of these associations paralleled MX1 gene eQTL expression.

CONCLUSIONS

We observed a significant association between previously reported 'protective' MHC class I alleles and CCR5Δ32 with the HIV reservoir size in noncontrollers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.

Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection

The major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective antiretroviral therapy (ART). Most prior host genetic HIV studies have focused on identifying DNA polymorphisms (e.g., CCR5Δ32 , MHC class I alleles) associated with viral load among untreated "elite controllers" (~1% of HIV+ individuals who are able to control virus without ART). However, there have been few studies evaluating host genetic predictors of viral control for the majority of people living with HIV (PLWH) on ART. We performed host RNA sequencing and HIV reservoir quantification (total DNA, unspliced RNA, intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. Multivariate models included covariates for timing of ART initiation, nadir CD4+ count, age, sex, and ancestry. Lower HIV total DNA (an estimate of the total reservoir) was associated with upregulation of tumor suppressor genes NBL1 (q=0.012) and P3H3 (q=0.012). Higher HIV unspliced RNA (an estimate of residual HIV transcription) was associated with downregulation of several host genes involving inflammasome ( IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9 , CXCL3, CXCL10 ) and innate immune ( TLR7 ) signaling, as well as novel associations with potassium ( KCNJ2 ) and gap junction ( GJB2 ) channels, all q<0.05. Gene set enrichment analyses identified significant associations with TLR4/microbial translocation (q=0.006), IL-1β/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. HIV intact DNA (an estimate of the "replication-competent" reservoir) demonstrated trends with thrombin degradation ( PLGLB1 ) and glucose metabolism ( AGL ) genes, but data were (HIV intact DNA detected in only 42% of participants). Our findings demonstrate that among treated PLWH, that inflammation, innate immune responses, bacterial translocation, and tumor suppression/cell proliferation host signaling play a key role in the maintenance of the HIV reservoir during ART. Further data are needed to validate these findings, including functional genomic studies, and expanded epidemiologic studies in female, non-European cohorts.

Author Summary

Although lifelong HIV antiretroviral therapy (ART) suppresses virus, the major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective ART, "the HIV reservoir." HIV eradication strategies have focused on eliminating residual virus to allow for HIV remission, but HIV cure trials to date have thus far failed to show a clinically meaningful reduction in the HIV reservoir. There is an urgent need for a better understanding of the host-viral dynamics during ART suppression to identify potential novel therapeutic targets for HIV cure. This is the first epidemiologic host gene expression study to demonstrate a significant link between HIV reservoir size and several well-known immunologic pathways (e.g., IL-1β, TLR7, TNF-α signaling pathways), as well as novel associations with potassium and gap junction channels (Kir2.1, connexin 26). Further data are needed to validate these findings, including functional genomic studies and expanded epidemiologic studies in female, non-European cohorts.

HIV Disease Dynamics and Markers of Inflammation and CNS Injury During Primary HIV Infection and Their Relationship to Cognitive Performance

INTRODUCTION

Early systemic and central nervous system viral replication and inflammation may affect brain integrity in people with HIV, leading to chronic cognitive symptoms not fully reversed by antiretroviral therapy (ART). This study examined associations between cognitive performance and markers of CNS injury associated with acute HIV infection and ART.

METHODS

HIV-infected MSM and transgender women (average age: 27 years and education: 13 years) enrolled within 100 days from the estimated date of detectable infection (EDDI). A cognitive performance (NP) protocol was administered at enrollment (before ART initiation) and every 24 weeks until week 192. An overall index of cognitive performance (NPZ) was created using local normative data. Blood (n = 87) and cerebrospinal fluid (CSF; n = 29) biomarkers of inflammation and neuronal injury were examined before ART initiation. Regression analyses assessed relationships between time since EDDI, pre-ART biomarkers, and NPZ.

RESULTS

Adjusting for multiple comparisons, shorter time since EDDI was associated with higher pre-ART VL and multiple biomarkers in plasma and CSF. NPZ scores were within the normative range at baseline (NPZ = 0.52) and at each follow-up visit, with a modest increase through week 192. Plasma or CSF biomarkers were not correlated with NP scores at baseline or after ART.

CONCLUSIONS

Biomarkers of CNS inflammation, immune activation, and neuronal injury peak early and then decline during acute HIV infection, confirming and extending results of other studies. Neither plasma nor CSF biomarkers during acute infection corresponded to NP scores before or after sustained ART in this cohort with few psychosocial risk factors for cognitive impairment.

Microdrop Human Immunodeficiency Virus Sequencing for Incidence and Drug Resistance Surveillance

BACKGROUND

Precise and cost-efficient human immunodeficiency virus (HIV) incidence and drug resistance surveillances are in high demand for the advancement of the 90-90-90 "treatment for all" target.

METHODS

We developed microdrop HIV sequencing for the HIV incidence and drug resistance assay (HIDA), a single-blood-draw surveillance tool for incidence and drug resistance mutation (DRM) detection. We amplified full-length HIV envelope and pol gene sequences within microdroplets, and this compartmental amplification with long-read high-throughput sequencing enabled us to recover multiple unique sequences.

RESULTS

We achieved greater precision in determining the stage of infection than current incidence assays, with a 1.2% false recency rate (proportion of misclassified chronic infections) and a 262-day mean duration of recent infection (average time span of recent infection classification) from 83 recently infected and 81 chronically infected individuals. Microdrop HIV sequencing demonstrated an increased capacity to detect minority variants and linked DRMs. By screening all 93 World Health Organization surveillance DRMs, we detected 6 pretreatment drug resistance mutations with 2.6%-13.2% prevalence and cross-linked mutations.

CONCLUSIONS

HIDA with microdrop HIV sequencing may promote global HIV real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool that can be generalized for surveillance of other pathogens.

Comparison of cross-sectional HIV incidence assay results from dried blood spots and plasma

Background

Assays have been developed for cross-sectional HIV incidence estimation using plasma samples. Large scale surveillance programs are planned using dried blood spot (DBS) specimens for incidence assessment. However, limited information exists on the performance of HIV cross-sectional incidence assays using DBS.

Methods

The assays evaluated were: Maxim HIV-1 Limiting Antigen Avidity EIA (LAg-Avidity), Sedia HIV-1 BED-Capture EIA (BED-CEIA), and CDC modified BioRad HIV-1/2 Plus O Avidity-based Assay (CDC-BioRad Avidity) using pre-determined cutoff values. 100 matched HIV-1 positive plasma and DBS samples, with known duration of infection, from the Consortium for the Evaluation and Performance of HIV Incidence Assays repository were tested. All assays were run in duplicate. To examine the degree of variability within and between results for each sample type, both categorical and continuous results were analyzed. Associations were assessed with Bland Altman, R² values and Cohen’s kappa coefficient (ĸ).

Results

Intra-assay variability using the same sample type was similar for all assays (R² 0.96 to 1.00). The R² values comparing DBS and plasma results for LAg-Avidity, BED-CEIA, and CDC-BioRad Avidity were 0.96, 0.94, and 0.84, respectively. The concordance and ĸ values between DBS and plasma for all three assays were >87% and >0.64, respectively. The Bland-Altman analysis showed significant differences between plasma and DBS samples. For all three assays, a higher number of samples were classified as recent infections using DBS samples.

Conclusions

DBS and plasma sample results were highly correlated. However, when compared to plasma, each assay performed somewhat differently in DBS at the lower and higher ends of the dynamic range. DBS samples were more likely to be classified as recently infected by all three assays, which may lead to overestimation of incidence in surveys using performance criteria derived for plasma samples.

Longitudinal Genetic Characterization Reveals That Cell Proliferation Maintains a Persistent HIV Type 1 DNA Pool During Effective HIV Therapy

BACKGROUND

The stability of the human immunodeficiency virus type 1 (HIV-1) reservoir and the contribution of cellular proliferation to the maintenance of the reservoir during treatment are uncertain. Therefore, we conducted a longitudinal analysis of HIV-1 in T-cell subsets in different tissue compartments from subjects receiving effective antiretroviral therapy (ART).

METHODS

Using single-proviral sequencing, we isolated intracellular HIV-1 genomes derived from defined subsets of CD4(+) T cells from peripheral blood, gut-associated lymphoid tissue and lymph node tissue specimens from 8 subjects with virologic suppression during long-term ART at 2 time points (time points 1 and 2) separated by 7-9 months.

RESULTS

DNA integrant frequencies were stable over time (<4-fold difference) and highest in memory T cells. Phylogenetic analyses showed that subjects treated during chronic infection contained viral populations with up to 73% identical sequence expansions, only 3 of which were observed in specimens obtained before therapy. At time points 1 and 2, such clonally expanded populations were found predominantly in effector memory T cells from peripheral blood and lymph node tissue specimens.

CONCLUSIONS

Memory T cells maintained a relatively constant HIV-1 DNA integrant pool that was genetically stable during long-term effective ART. These integrants appear to be maintained by cellular proliferation and longevity of infected cells, rather than by ongoing viral replication.

Longitudinal characterization of depression and mood states beginning in primary HIV infection

Though depression is known to frequently afflict those with chronic HIV, mood during the early course of HIV is not well characterized. In a prospective study we assessed mood during primary HIV infection [primary HIV infection (PHI), <1 year duration], its association with neuropsychological performance and markers of neurological disease, and its longitudinal course including effects of antiretroviral therapy (ART). The Beck Depression Inventory (BDI) and Profile of Mood States (POMS) subscales were longitudinally administered prior to and after ART in PHI subjects. This evaluation of mood was done concurrently with blood, cerebrospinal fluid (CSF) and neuropsychological [total z and global deficit score (GDS)] evaluation at each visit. Analysis employed Spearman's rho, logistic regression, and linear mixed models. 47.7 % of the 65 men recruited at a median 3.5 months HIV duration met BDI criteria for clinical depression at baseline, classified as 'mild' (n = 11), 'moderate' (n = 11), or 'severe' (n = 9). Drug, alcohol, and depression history did not associate with BDI score. Proportional somatic-performance scores were worse than cognitive-affective scores (p = .0045). Vigor subscore of POMS was reduced compared to norms and correlated with total z (r = 0.33, p = 0.013) and GDS (r = -0.32, p = 0.016). BDI and POMS correlated with one another (r = 0.85, p < .0001), but not with CSF or plasma HIV RNA, WBC, albumin ratio or neopterin. Improvement was not observed in BDI and POMS over 330 total follow-up visits, even after initiation of ART. Depression was prevalent during PHI in our subjects, associated with abnormal somatic-performance and vigor scores. Neither neuropsychological performance nor disease biomarkers correlated with depressed mood. Mood indices did not improve over time in the presence of ART.

Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient

There is intense interest in developing curative interventions for HIV. How such a cure will be quantified and defined is not known. We applied a series of measurements of HIV persistence to the study of an HIV-infected adult who has exhibited evidence of cure after allogeneic hematopoietic stem cell transplant from a homozygous CCR5Δ32 donor. Samples from blood, spinal fluid, lymph node, and gut were analyzed in multiple laboratories using different approaches. No HIV DNA or RNA was detected in peripheral blood mononuclear cells (PBMC), spinal fluid, lymph node, or terminal ileum, and no replication-competent virus could be cultured from PBMCs. However, HIV RNA was detected in plasma (2 laboratories) and HIV DNA was detected in the rectum (1 laboratory) at levels considerably lower than those expected in ART-suppressed patients. It was not possible to obtain sequence data from plasma or gut, while an X4 sequence from PBMC did not match the pre-transplant sequence. HIV antibody levels were readily detectable but declined over time; T cell responses were largely absent. The occasional, low-level PCR signals raise the possibility that some HIV nucleic acid might persist, although they could also be false positives. Since HIV levels in well-treated individuals are near the limits of detection of current assays, more sensitive assays need to be developed and validated. The absence of recrudescent HIV replication and waning HIV-specific immune responses five years after withdrawal of treatment provide proof of a clinical cure.

There is intense interest in developing a cure for HIV. How such a cure will be quantified and defined is not known. We applied a series of measurements of HIV persistence to the study of an HIV+ adult who has exhibited evidence of cure after a stem cell transplant. Samples from blood, spinal fluid, lymph node, and gut were analyzed in multiple laboratories using different approaches. No HIV was detected in blood cells, spinal fluid, lymph node, or small intestine, and no infectious virus was recovered from blood. However, HIV was detected in plasma (2 laboratories) and HIV DNA was detected in the rectum (1 laboratory) at levels considerably lower than those expected in antiretroviral treated patients. The occasional, low-level HIV signals might be due to persistent HIV or might reflect false positives. The sensitivity of the current generation of assays to detect HIV RNA, HIV DNA, and infectious virus are close to the limits of detection. Improvements in these tests will be needed for future curative studies. The lack of rebounding virus after five years without therapy, the failure to isolate infectious virus, and the waning HIV-specific immune responses all indicate that the Berlin Patient has been effectively cured.

Host correlates distinguish low-risk and high-risk HIV-1 disease progression in HLA-B*5701 individuals (P6169)

HIV-1-infected individuals with HLA-B*57 alleles progress slowly to disease, in part due to restricted CD8+ T cell responses. However, some HLA-B*57 individuals progress faster to disease. We hypothesized that additional host correlates may explain the risk of disease progression. PBMC from six HLA-B*5701 patients were analyzed longitudinally and divided into high-risk and low-risk progressors based on CD4 counts at baseline. We developed a custom made Taqman array to measure mRNA expression of 34 anti-HIV-1 restriction factors. We named the overall gene expression as Cumulative Restriction or CuRe score. T cell activation, viral load, T cell counts and plasma sCD14 were also determined for all patients at all time-points. The CuRe score was significantly increased in high-risk progressors (p&lt;0.0001), with particular increases of APOBEC3F, APOBEC3G, tetherin, SAMHD1 and interferon-inducible genes. CuRe score correlated with viral load only in low-risk progressors (R&gt;0.60, P&lt;0.001). T cell activation was significantly elevated in high-risk progressors (p&lt;0.05), and correlated with a decline in CD4+ T cell counts (Spearman R=-0.92, P&lt;0.0001). Plasma sCD14 was significantly elevated in high-risk progressors, and correlated with CuRe score (R=0.79, P&lt;0.001). In our study, we show that combining a multiple gene expression array of anti-HIV-1 restriction factors and immunological parameters provide important measures of risk for disease progression in HLA-B*5701 individuals.

HIV-1 infection induces a novel B cell response against HERV-K (HML-2) TM protein (P6209)

The presence of HERV-K (HML-2) mRNA in plasma and a corresponding specific T cell response during HIV-1 infection is well-documented. We hypothesized that HIV-1 also induces a specific HERV-K (HML-2) EnvelopeBcell response due to the expression of envelope protein on the infected cell surface. This led to the concept that HERV-K (HML-2) Env could be used as an HIV-1 Associated Neo Antigen (HANA) to target infected cells. We showed that the humoral response against HERV-K (HML-2) Env is restricted to two sequences on each envelope sub-unit, the surface unit (SU) and transmembrane (TM) proteins. During HIV-1 infection, we observed an increase of the anti-TM antibody titer and a decrease of the anti-SU antibody titer. Interestingly, we found that HIV-1-infected elite controllers had high titers of anti-TM antibodies compared to HIV-1 infected patients on effective HAART or healthy uninfected donors. We showed that TM is preferentially transactivated and expressed on the cell surface in HIV-1 infected cells. Using HA-137, a human anti-TM antibody, we showed that TM protein is preferentially expressed in the myeloid cell subset as well as in a distinct T cell subset. These findings highlight the crucial role of the monocyte/macrophage lineage in the induction of the anti-HERV-K (HML-2) TM Bcell response.This study suggests that the anti-TM humoral response may play a role in HIV-1 pathogenesis and could provide a new tool for immunotherapeutic strategies.

Identification of human endogenous retrovirus (HERV-K(HML-2))-specific mucosal CD4+ T cell responses in HIV-1-exposed, seronegative individuals (P6195)

The transcriptional silence of human endogenous retroviruses (HERV) can be disrupted in HIV-1 infection. We have reported that the strength of the HERV-specific CD8+ T cell response predicts lower HIV-1 viral load in untreated adults. To determine whether HERV-K immunity plays a role in inhibiting HIV-1 replication at a major site of transmission and CD4+ T cell depletion, we assessed these responses in gut-associated lymphoid tissue (GALT) from rectosigmoid biopsies and blood of HIV-1 exposed, seronegative (HESN) individuals (n=6) by flow cytometry. CMV pp65- and HIV-1 Gag-specific T cells were also measured, and all responses were compared with peripheral antigen-specific responses in uninfected, low-risk controls (n=11). With the exception of stronger CMV-specific CD8+ T cell responses in the HESN group (p=0.024), there were no significant differences between the magnitudes of peripheral antigen-specific T cell responses in the HESN vs. controls. However, HESN subjects had remarkably robust mucosal HIV-1- (median %CD4+cytokine+cells=2.67) and HERV-specific (median %CD4+cytokine+cells=3.41) CD4+ responses, which were much stronger than the corresponding PBMC responses (p=0.0079 and p&lt;0.0001, respectively). These findings suggest that the GALT is an important site of HERV-K expression and immunity in individuals exposed to HIV-1, and should be further investigated in the context of novel vaccine strategies that target conserved antigens such as HERV.

[A 31-year-old pregnant woman with refractory hypercalcemia]

A 31-year-old pregnant woman presented with refractory severe hypercalcemia due to an advanced neuroendocrine tumor masquerading as hyperemesis gravidarum. Octreotide therapy and extensive tumor debulking surgery resulted in symptom control. After a prolonged stay in the intensive care unit due to parapneumonic acute respiratory distress syndrome, the patient delivered a healthy child. Neuroendocrine tumors are a rare complication of pregnancy and a seldom cause of refractory hypercalcemia.

Graph Drawing Aesthetics-Created by Users, Not Algorithms

Prior empirical work on layout aesthetics for graph drawing algorithms has concentrated on the interpretation of existing graph drawings. We report on experiments which focus on the creation and layout of graph drawings: participants were asked to draw graphs based on adjacency lists, and to lay them out "nicely." Two interaction methods were used for creating the drawings: a sketch interface which allows for easy, natural hand movements, and a formal point-and-click interface similar to a typical graph editing system. We find, in common with many other studies, that removing edge crossings is the most significant aesthetic, but also discover that aligning nodes and edges to an underlying grid is important. We observe that the aesthetics favored by participants during creation of a graph drawing are often not evident in the final product and that the participants did not make a clear distinction between the processes of creation and layout. Our results suggest that graph drawing systems should integrate automatic layout with the user's manual editing process, and provide facilities to support grid-based graph creation.

Oral cyclosporin A inhibits CD4 T cell P-glycoprotein activity in HIV-infected adults initiating treatment with nucleoside reverse transcriptase inhibitors

PURPOSE

P-glycoprotein limits the tissue penetration of many antiretroviral drugs. The aim of our study was to characterize the effects of the P-glycoprotein substrate cyclosporin A on T cell P-glycoprotein activity in human immunodeficiency virus-infected participants in the AIDS Clinical Trials Group study A5138.

METHODS

We studied P-glycoprotein activity on CD4 and CD8 T cells in 16 participants randomized to receive oral cyclosporin A (n=9) or not (n=7) during initiation antiretroviral therapy (ART) that did not include protease or non-nucleoside reverse transcriptase inhibitors.

RESULTS

CD4 T cell P-glycoprotein activity decreased by a median of 8 percentage points with cyclosporin A/ART (difference between cyclosporin A/ART vs. ART only, P= 0.001). Plasma trough cyclosporin A concentrations correlated with the change in P-glycoprotein activity in several T cell subsets.

CONCLUSIONS

Oral cyclosporin A can inhibit peripheral blood CD4 T cell P-glycoprotein activity. Targeted P-glycoprotein inhibition may enhance the delivery of ART to T cells.

Transmitted antiretroviral drug resistance among acute and recent HIV infections in North Carolina from 1998 to 2007

Background

Transmitted drug resistance (TDR) limits antiretroviral options and thus complicates the management of HIV-positive patients. HIV disproportionately affects the southern US, but available national estimates of TDR prevalence principally reflect large metropolitan centres outside this region.

Methods

The Duke/UNC Acute HIV Program has collected data on acute or recent HIV infections (ARHI) in North Carolina since 1998. Acute infections represent antibody-negative, RNA-positive patients. Recent infection was determined by history of HIV testing or concordance between detuned ELISA and antibody avidity assays. Genotypic sequence data from the earliest collected pretreatment plasma samples were analysed with the Stanford HIV Database and screened for surveillance drug resistance mutations (SDRMs).

Results

A total of 253 individuals with ARHI between May 1998 and May 2007 had complete genotypic sequence data for analysis; 39.5% were acute infections, 78.7% were male, 64.8% were non-White and 53.8% were men who have sex with men. The overall prevalence of TDR was 17.8%, with SDRMs for non-nucleoside/ nucleotide reverse transcriptase inhibitors (NNRTIs) in 9.5% of the cohort. Mutations for nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) were detected in 7.5% and for protease inhibitors (PIs) in 3.2%. K103N was the most common mutation (7.5%). Thymidine analogue mutations were found in 4.7% of samples; the most common PI SDRM was L90M (2.4%). Dual- or triple-class antiretroviral resistance was rare, encountered in only six (2.4%) samples.

Conclusions

The prevalence of TDR in North Carolina is similar to estimates from the US metropolitan areas. These findings have implications for initial regimen selection and secondary prevention efforts outside of large, metropolitan HIV epicentres.

Detection of HIV-1 in alternative specimen types using the APTIMA HIV-1 RNA Qualitative Assay

Peripheral blood mononuclear cells (PBMCs), saliva, seminal plasma, and dried blood spots were evaluated as specimen types for the APTIMA HIV-1 RNA Qualitative Assay (APTIMA HIV-1 Assay), which employs a target capture step to recover HIV-1-specific sequences from complex specimen types. Analytical sensitivity studies were carried out using samples that were either diluted or eluted with a buffered detergent and spiked with different concentrations of HIV-1 ranging from 1 to 10,000 copies/mL. PBMC samples spiked with HIV-1 had comparable analytical sensitivity to HIV-1 spiked plasma with a 95% limit of detection of 13.1 and 17.2 copies/mL, respectively. Analytical sensitivity in seminal plasma specimens diluted 1:5 and saliva diluted 1:2 was comparable to HIV-1 spiked dilution buffer alone. Whole blood and dried blood spot specimens spiked with HIV-1 had equivalent reactivity at 250 copies/spot (5000 copies/mL). However, the 95% limit of detection values were significantly different (293.7 copies/mL for whole blood and 2384 copies/mL for dried blood spot specimens). No significant effect on analytical sensitivity was observed when one HIV-1 positive dried blood spot punch was pooled with up to 9 HIV-1 negative dried blood spot punches. Together, these studies demonstrate that the APTIMA HIV-1 RNA Qualitative Assay can be used to process a diverse array of specimen types with minimal impact on analytical sensitivity for most specimen types.

Transmitted antiretroviral drug resistance among acute and recent HIV infections in North Carolina from 1998 to 2007

BACKGROUND

Transmitted drug resistance (TDR) limits antiretroviral options and thus complicates the management of HIV-positive patients. HIV disproportionately affects the southern US, but available national estimates of TDR prevalence principally reflect large metropolitan centres outside this region.

METHODS

The Duke/UNC Acute HIV Program has collected data on acute or recent HIV infections (ARHI) in North Carolina since 1998. Acute infections represent antibody-negative, RNA-positive patients. Recent infection was determined by history of HIV testing or concordance between detuned ELISA and antibody avidity assays. Genotypic sequence data from the earliest collected pretreatment plasma samples were analysed with the Stanford HIV Database and screened for surveillance drug resistance mutations (SDRMs).

RESULTS

A total of 253 individuals with ARHI between May 1998 and May 2007 had complete genotypic sequence data for analysis; 39.5% were acute infections, 78.7% were male, 64.8% were non-White and 53.8% were men who have sex with men. The overall prevalence of TDR was 17.8%, with SDRMs for non-nucleoside/nucleotide reverse transcriptase inhibitors (NNRTIs) in 9.5% of the cohort. Mutations for nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) were detected in 7.5% and for protease inhibitors (PIs) in 3.2%. K103N was the most common mutation (7.5%). Thymidine analogue mutations were found in 4.7% of samples; the most common PI SDRM was L90M (2.4%). Dual- or triple-class antiretroviral resistance was rare, encountered in only six (2.4%) samples.

CONCLUSIONS

The prevalence of TDR in North Carolina is similar to estimates from the US metropolitan areas. These findings have implications for initial regimen selection and secondary prevention efforts outside of large, metropolitan HIV epicentres.

Combined use of autoantibodies (IA-2 autoantibody, GAD autoantibody, insulin autoantibody, cytoplasmic islet cell antibodies) in type 1 diabetes: Combinatorial Islet Autoantibody Workshop

The aim of this workshop was to assess the ability of individual autoantibody (ab) assays and their use in combination to discriminate between type 1 diabetic and control sera. Coded aliquots of sera were measured in a total of 119 assays by 49 participating laboratories in 17 countries. The sera were from 51 patients with new onset type 1 diabetes and 101 healthy control subjects with no family history of diabetes. In the final analysis, data on diabetic sera were restricted to 43 subjects younger than age 30 years. The laboratories were asked to report results for these sera using their currently available anti-islet autoantibody assays. In addition, they were asked to combine information from their assays to classify sera as having high, moderate, or low probability of originating from a patient with type 1 diabetes. Actual strategies for combining assays were determined by each laboratory. There were no significant differences in sensitivity among 19 radioimmunoassays (RIAs) for IA-2 autoantibodies (cytoplasmic islet cell antibody [ICA] 512) using different constructs that included the intracellular portion of the molecule (mean sensitivity 73%). However, an enzyme-linked immunosorbent assay (ELISA) using the extracellular portion of the IA-2 molecule did not discriminate between diabetic and control sera. Among GAD autoantibody assays that achieved sensitivity >70%, 26 were RIAs and one was an ELISA. When the sera were ranked according to their autoantibody levels, the concordance for insulin autoantibodies (IAAs) in different laboratories was markedly less than for IA-2ab and GADab. Using a combination of autoantibody assays, several laboratories achieved excellent discrimination between diabetic and control sera (sensitivity up to 80% with false-positive rate of 0%). A variety of strategies for combining information from different assays were successful (e.g., those including and excluding ICA), and no one strategy emerged as clearly superior. In conclusion, IA-2/ICA512 autoantibodies are a marker of type 1 diabetes and can be measured consistently by most assays. Several different strategies for combining assays achieved high sensitivity with a low false-positive rate.

Geological evidence for solid-state convection in Europa's ice shell

The ice-rich surface of the jovian satellite Europa is sparsely cratered, suggesting that this moon might be geologically active today. Moreover, models of the satellite's interior indicate that tidal interactions with Jupiter might produce enough heat to maintain a subsurface liquid water layer. But the mechanisms of interior heat loss and resurfacing are currently unclear, as is the question of whether Europa has (or had at one time) a liquid water ocean. Here we report on the morphology and geological interpretation of distinct surface features-pits, domes and spots-discovered in high-resolution images of Europa obtained by the Galileo spacecraft. The features are interpreted as the surface manifestation of diapirs, relatively warm localized ice masses that have risen buoyantly through the subsurface. We find that the formation of the features can be explained by thermally induced solid-state convection within an ice shell, possibly overlying a liquid water layer. Our results are consistent with the possibility that Europa has a liquid water ocean beneath a surface layer of ice, but further tests and observations are needed to demonstrate this conclusively.

Galileo Encounter with 951 Gaspra: First Pictures of an Asteroid

Galileo images of Gaspra reveal it to be an irregularly shaped object (19 by 12 by 11 kilometers) that appears to have been created by a catastrophic collisional disruption of a precursor parent body. The cratering age of the surface is about 200 million years. Subtle albedo and color variations appear to correlate with morphological features: Brighter materials are associated with craters especially along the crests of ridges, have a stronger 1-micrometer absorption, and may represent freshly excavated mafic materials; darker materials exhibiting a significantly weaker 1-micrometer absorption appear concentrated in interridge areas. One explanation of these patterns is that Gaspra is covered with a thin regolith and that some of this material has migrated downslope in some areas.

Assessment of common idiotype PR4-Id in serial bleeds from lupus patients

Marked fluctuations in the levels of a common DNA-antibody idiotype, PR4-Id have been found on IgM and IgA antibodies in particular and to a lesser extent on IgG in serial bleeds of 14 lupus patients. Few clear cut examples were found of the PR4-Id levels reflecting disease activity. However, the idiotype expression was not simply related to total immunoglobulin levels and the controlling mechanisms of idiotype expression on different isotypes remain a matter of conjecture.

The Effects of Intramuscular and Intrathecal Administration of Streptomycin in Normal Dogs and in Dogs with Meningitis due to Escherichia Coli

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Angiomatous Malformations of the Brain : Successful Extirpation in Three Cases

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