Comparison of serum and plasma viral RNA measurements in primary and chronic human immunodeficiency virus type 1 infection

Overview of the Analytes Applied in Genotypic HIV Drug Resistance Testing

The close monitoring of HIV drug resistance using genotypic HIV drug resistance testing (HIVDRT) has become essential for effective HIV/AIDS management at both individual and population levels. Over the years, a broad spectrum of analytes or specimens have been applied or attempted in HIVDRT; however, the suitability and performance of these analytes in HIVDRT and the clinical relevance of the results from them may vary significantly. This article provides a focused overview of the performance, strengths, and weaknesses of various analytes while used in HIVDRT, which may inform the optimal analytes selection in different application contexts.

Higher parental occupational social contact is associated with a reduced risk of incident pediatric type 1 diabetes: Mediation through molecular enteroviral indices

We aimed to examine the association between parental occupational social contact and hygiene factors on type 1 diabetes (T1D) risk and possible mediation of these effects through child enteroviral infection. We interviewed 333 incident T1D cases and 660 controls from 2008–2011 in Melbourne, Australia. Enteroviral indices (ribonucleic acid by reverse transcription polymerase chain reaction and Coxsackie B virus antibody levels) in peripheral blood were measured in nested case control samples. Parent occupational social contact was assessed by the number of well or sick children, adults or animals contacted daily through work. Higher parental occupational social contact was strongly associated with reduced T1D risk with evidence of dose response (contact with the well or sick score, Adjusted odds ratio (AOR) per category: 0.73 (95% Confidence Interval (CI): 0.66, 0.81); P<0.001 or AOR 0.63 (95% CI: 0.53, 0.75); P<0.001) respectively). Nine of the ten parental social contact indices, were significant mediated through one or more enteroviral indices. The strength of association between enterovirus presence and T1D onset increased with child age (1.2 fold increase per year; P = 0.05). Lower child hand hygiene enhanced the adverse effect of low parental occupational contact with the sick; Synergy Index 5.16 (95% CI: 3.61, 7.36). The interaction between hand washing and parental occupational contact is more consistent with protection against parental enteroviral shedding than the sharing of a protective infectious agent or microbiome.

Understanding the effects of different HIV transmission models in individual-based microsimulation of HIV epidemic dynamics in people who inject drugs

We investigated how different models of HIV transmission, and assumptions regarding the distribution of unprotected sex and syringe-sharing events ('risk acts'), affect quantitative understanding of HIV transmission process in people who inject drugs (PWID). The individual-based model simulated HIV transmission in a dynamic sexual and injecting network representing New York City. We constructed four HIV transmission models: model 1, constant probabilities; model 2, random number of sexual and parenteral acts; model 3, viral load individual assigned; and model 4, two groups of partnerships (low and high risk). Overall, models with less heterogeneity were more sensitive to changes in numbers risk acts, producing HIV incidence up to four times higher than that empirically observed. Although all models overestimated HIV incidence, micro-simulations with greater heterogeneity in the HIV transmission modelling process produced more robust results and better reproduced empirical epidemic dynamics.

Associations of common variants in the BST2 region with HIV-1 acquisition in African American and European American people who inject drugs

OBJECTIVE

The bone marrow stromal cell antigen 2 (BST2) gene encodes a host restriction factor that acts as an innate immune sensor of HIV-1 exposure and suppresses release of HIV-1 particles. We aimed to identify associations of variants in the BST2 gene region with HIV-1 acquisition and disease progression.

DESIGN/METHODS

Using HIV+ cases and HIV- controls from the Urban Health Study (n=3136 African Americans and European Americans who inject drugs), we tested 470 variants in BST2 and its flanking regions for association with HIV-1 acquisition and log-transformed viral load.

RESULTS

We found that the single nucleotide polymorphism (SNP) rs113189798 surpassed the P value threshold corrected for multiple testing. The rs113189798-G allele (frequency=16% in African Americans, 4% in European Americans) was associated with increased HIV-1 acquisition risk (meta-analysis P=1.43 × 10): odds ratio (95% confidence interval) of 1.22 (1.01-1.49) in African Americans and 2.17 (1.43-3.33) in European Americans. We also found that the previously reported rs12609479-A allele (frequency=35% in African Americans, 81% in European Americans) was nominally associated with decreased risk of acquiring HIV-1 in our study (meta-analysis P=0.036). Rs12609479-A is predicted to increase BST2 expression and thereby decrease risk of acquiring HIV-1. Rs113189798 and rs12609479 were only weakly correlated [square of the correlation coefficient (r)=0.2-0.4] and represented distinct association signals. None of our tested variants were significantly associated with log-transformed viral load among the HIV-infected cases.

CONCLUSION

Our findings support BST2 as a genetic susceptibility factor for HIV-1 acquisition: identifying a novel SNP association for rs13189798 and linking the previously reported regulatory SNP rs12609479 to HIV-1 acquisition.

Efficient Quantification of HIV-1 in Heparin Plasma Spiked with Cultured HIV-1 by the Roche Cobas TaqMan and Abbott RealTime HIV-1 Tests

The current automated real-time HIV-1 viral load assays, the Roche Cobas AmpliPrep/Cobas TaqMan test and the Abbott RealTime test, are FDA cleared for use with EDTA plasma. We show that both real-time reverse transcription-PCR (RT-PCR) tests reliably quantify HIV-1 RNA in heparin plasma specimens spiked with HIV-1 isolate MN.

Immunologic and virologic events in early HIV infection predict subsequent rate of progression

BACKGROUND

Variability in human immunodeficiency virus (HIV) disease progression cannot be fully predicted by CD4(+) T cell counts or viral load (VL). Because central memory T (T(CM)) cells play a critical role in the pathogenesis of simian immunodeficiency virus disease, we hypothesized that quantifying these cells in early HIV infection could provide prognostic information.

METHODS

We measured expression of CD45RO, chemokine (C-C motif) receptor (CCR) 5, CCR7, CD27, and CD28 to enumerate naive and memory subsets in samples from recently infected individuals. We also quantified proliferation, CD127 expression, and cell-associated VL. Disease progression was compared across subgroups defined by these measurements, using Kaplan-Meier survival curves and multivariate Cox proportional hazards regression.

RESULTS

Four hundred sixty-six subjects contributed 101 events. The proportion or absolute count of T(CM) cells did not correlate with disease progression, defined as the time to AIDS or death. However, significant associations were observed for proliferation within CD4(+) or CD8(+) T cells, loss of naive or CD127(+) memory CD8(+) T cells, and CD4(+) T cell-associated VL.

CONCLUSIONS

Our results demonstrate that the extent of the immunopathogenesis established early in HIV infection predicts the course of future disease. Because antiretroviral drug treatment reverses such defects in part, our study provides mechanistic clues to why early use of antiretrovirals may prove beneficial.

Importance of promoting HIV testing for preventing secondary transmissions: modelling the Australian HIV epidemic among men who have sex with men

BACKGROUND

We address the research questions: (i) what proportion of new HIV infections is transmitted from people who are (a) undiagnosed, (b) in primary HIV infection (PHI), (c) on antiretroviral therapy?; and (ii) what is the expected epidemiological impact of (a) increasing the proportion of newly acquired HIV infections receiving early treatment, and (b) increasing HIV testing rates?

METHODS

We used a mathematical model to simulate HIV transmission in the population of men who have sex with men (MSM) in Australia. We calibrated the model using established biological and clinical data and a wide range of Australian MSM epidemiological and behavioural data sources.

RESULTS

We estimate that ~19% of all new HIV infections are transmitted from the ~3% of Australian HIV-infected MSM who are in PHI; ~31% of new HIV infections are estimated to be transmitted from the ~9% of MSM with undiagnosed HIV. We estimate that the average number of infections caused per HIV-infected MSM through the duration of PHI is ~0.14-0.28.

CONCLUSIONS

The epidemiological impact of increasing treatment in PHI would be modest due to insufficient detection of newly-infected individuals. In contrast, increases in HIV testing rates could have substantial epidemiological consequences. The benefit of testing will also increase over time. Promoting increases in the coverage and frequency of testing for HIV could be a highly-effective public health intervention, but the population-level impact of interventions based on promoting early treatment of patients diagnosed in PHI is likely to be small. Treating PHI requires further evaluation of its long-term effects on HIV-infected individuals.

Clinical prognostic value of RNA viral load and CD4 cell counts during untreated HIV-1 infection--a quantitative review

Background

The prognostic value of CD4 counts and RNA viral load for identifying treatment need in HIV-infected individuals depends on (a) variation within and among individuals, and (b) relative risks of clinical progression per unit CD4 or RNA difference.

Methodology/Principal Findings

We reviewed these measurements across (a) 30 studies, and (b) 16 cohorts of untreated seropositive adults. Median within-population interquartile ranges were 74,000 copies/mL for RNA with no significant change during the course of infection; and 330 cells/µL for CD4, with a slight proportional increase over infection. Applying measurement and physiological fluctuations observed on chronically infected patients, we estimate that 45% of population-level variation in RNA, and 25% of variation in CD4, were due to within-patient fluctuations. Comparing a patient with RNA at upper 75^th centile with a patient at median RNA, 5-year relative risks were 1.4 (95% CI 1.2–1.7) for AIDS and 1.5 (1.3–1.9) for death, without change over the course of infection. In contrast, for a patient with CD4 count at the lower 75^th centile, relative risks increased from 1.0 at seroconversion to maxima of 6.3 (4.4–8.9) for AIDS and 5.5 (2.7–10.1) for death by year 6, when the population median had fallen to 300 cells/µL. Below 300 cells/µL, prognostic power did not increase, due to a narrower CD4 range.

Conclusions

Findings support the current WHO recommendation (used with clinical criteria) to start antiretroviral treatment in low-income settings at CD4 thresholds of 200–350 cells/µL, without pre-treatment RNA monitoring – while not precluding earlier treatment based on clinical, socio-demographic or public health criteria.

Relation between HIV viral load and infectiousness: a model-based analysis

BACKGROUND

A consensus statement released on behalf of the Swiss Federal Commission for HIV/AIDS suggests that people receiving effective antiretroviral therapy-ie, those with undetectable plasma HIV RNA (<40 copies per mL)-are sexually non-infectious. We analysed the implications of this statement at a population level.

METHODS

We used a simple mathematical model to estimate the cumulative risk of HIV transmission from effectively treated HIV-infected patients (HIV RNA <10 copies per mL) over a prolonged period. We investigated the risk of unprotected sexual transmission per act and cumulatively over many exposures, within couples initially discordant for HIV status.

FINDINGS

Assuming that each couple had 100 sexual encounters per year, the cumulative probability of transmission to the serodiscordant partner each year is 0.0022 (uncertainty bounds 0.0008-0.0058) for female-to-male transmission, 0.0043 (0.0016-0.0115) for male-to-female transmission, and 0.043 (0.0159-0.1097) for male-to-male transmission. In a population of 10 000 serodiscordant partnerships, over 10 years the expected number of seroconversions would be 215 (80-564) for female-to-male transmission, 425 (159-1096) for male-to-female transmission, and 3524 (1477-6871) for male-to-male transmission, corresponding to an increase in incidence of four times compared with incidence under current rates of condom use.

INTERPRETATION

Our analyses suggest that the risk of HIV transmission in heterosexual partnerships in the presence of effective treatment is low but non-zero and that the transmission risk in male homosexual partnerships is high over repeated exposures. If the claim of non-infectiousness in effectively treated patients was widely accepted, and condom use subsequently declined, then there is the potential for substantial increases in HIV incidence.

FUNDING

Australian Research Council.

Pre-HAART HIV burden approximates post-HAART viral levels following interruption of therapy in patients with sustained viral suppression

OBJECTIVE

To evaluate the relationship between the HIV viral burden in individuals prior to receiving highly-active antiretroviral therapy (HAART) and the viral burden after withdrawal of HAART.

DESIGN AND SETTING

Retrospective cohort study at the National Institutes of Health, Bethesda, Maryland, USA.

PATIENTS

Fourteen HIV-infected patients who achieved and maintained viral control on HAART who subsequently discontinued HAART.

MAIN OUTCOME MEASURES

Pre- and post-HAART viral loads measured from plasma or serum.

RESULTS

Patients achieved viral control (< 500 copies/ml) on HAART in a median 28 days (range, 15-490 days; mean, 72 days), maintained viral control for a median 661 days (range, 53-1067 days; mean, 611 days), and subsequently discontinued HAART for a median 49 days (range, 14-196 days; mean, 73 days). The median difference between the pre- and post-HAART viral loads was 0.16 log10 (range, -0.72 to 1.05 log10; mean, 0.19 log10). The median absolute difference between the pre- and post-HAART viral loads was 0.43 log10 (range, 0.06-1.05 log10; mean, 0.46 log10). Nine individuals had post-HAART values higher than pre-HAART values, five had lower values. Median duration between pre- and post-HAART viral load measurements was 1757 days (range, 117-3177 days; mean, 1756 days), or 4.8 years.

CONCLUSIONS

After discontinuing HAART, individuals had rebounds in their viral burdens approximating pre-HAART levels, even after a significant lapse of time approaching 5 years. Our data suggest that an intrinsic viral load set-point may exist, and that a single interruption of an effective regimen with viral suppression for almost 2 years does not significantly alter this set-point.

HIV-1 RNA levels in an African population-based cohort and their relation to CD4 lymphocyte counts and World Health Organization clinical staging

Apart from a small number of reports from people who are based in hospitals, data on viral load in HIV-infected people in sub-Saharan Africa, where most infections occur, are lacking. We report serum HIV-1 RNA levels in a population-based cohort in rural Uganda using the nucleic acid sequence-based amplification procedure (NASBA) test kit and describe their relation to CD4 counts and World Health Organization (WHO) clinical staging. The median (interquartile range [IQR]) viral loads were 87,000 copies/ml (37,500-295,000 copies/ml) in 40 prevalent cases infected for >6 years, and 31,000 copies/ml (7800-174,000 copies/ml) in 65 incident cases with seroconversion dates within the previous 6 years. Although we found a correlation between viral load and absolute CD4 count (p < .0001), there was no evidence for an association with CD4 decline (p = .1). Overall, there was a significant trend of increasing viral load with worsening clinical stage from a median viral load of 15,000 for those in WHO stage 1 (asymptomatic) to 150,600 copies/ml for those in stage 4 (AIDS; p < .001). However, the association was seen only in incident cases. Thus, we found that the NASBA test on serum was a useful indicator of disease stage especially in persons known to be infected for <6 years. Such baseline data are important for vaccine research, and if antiretroviral drugs become available to more than a few people in Africa, it will be important that accurate viral load estimations are available at least in a proportion of people to monitor the effectiveness of treatment, and measure the compliance and emerging resistance to these drugs.

Reduction of the viral load of HIV-1 after the intraperitoneal administration of dextrin 2-sulphate in patients with AIDS

OBJECTIVE

To determine the safety and efficacy of the sulphated polysaccharide, dextrin 2-sulphate, when delivered to the lymphatic circulation by the peritoneal route.

DESIGN

An open Phase I/II dose-escalation clinical study in which six patients with AIDS were treated with seven courses of dextrin 2-sulphate each lasting 1 month.

METHODS

During each course of treatment, the drug was administered daily for 28 days using an intraperitoneal catheter. Viral load was measured at frequent intervals using a plasma tissue culture infectious dose (TCID) assay, a cellular TCID assay, p24 antigenaemia, HIV-1 RNA and HIV-1 DNA. Plasma beta-chemokine levels were also measured.

RESULTS

Dose escalation was completed without toxicity. A total of 7 patient-months of treatment were completed. With increasing doses of dextrin 2-sulphate, the infectious plasma viraemia, cellular viraemia and p24 antigenaemia all fell during the period of drug administration, but with no significant change in HIV-1 RNA. This was associated with increased plasma levels of macrophage inflammatory protein (MIP)-1alpha and MIP-1beta. Dextrin 2-sulphate accumulated in peritoneal macrophages and induced the release of MIP-1alpha and MIP-1beta from these cells in vitro. These beta-chemokines could have augmented the cell surface-mediated anti-HIV-1 effect of dextrin 2-sulphate in vivo by binding to and blocking the CC-chemokine receptor-5. A second fall in infectious plasma viraemia, cellular viraemia, p24 antigenaemia and HIV-1 RNA was seen at day 100 which was then sustained for several months. A clinical improvement in Kaposi's sarcoma was also seen.

CONCLUSIONS

Our results suggest that the intraperitoneal administration of dextrin 2-sulphate can reduce the replication of HIV-1 in patients with AIDS. With increasing doses of dextrin 2-sulphate, the fall in viral load was seen during the period of drug administration and again 2 months after completing treatment.