Extended high viremics: a substantial fraction of individuals maintain high plasma viral RNA levels after acute HIV-1 subtype C infection

Acute HIV-1 infection viremia associate with rebound upon treatment interruption

BACKGROUND

Analytic treatment interruption (ATI) studies evaluate strategies to potentially induce remission in people living with HIV-1 but are often limited in sample size. We combined data from four studies that tested three interventions (vorinostat/hydroxychloroquine/maraviroc before ATI, Ad26/MVA vaccination before ATI, and VRC01 antibody infusion during ATI).

METHODS

The statistical validity of combining data from these participants was evaluated. Eleven variables, including HIV-1 viral load at diagnosis, Fiebig stage, and CD4+ T cell count were evaluated using pairwise correlations, statistical tests, and Cox survival models.

FINDINGS

Participants had homogeneous demographic and clinical characteristics. Because an antiviral effect was seen in participants who received VRC01 infusion post-ATI, these participants were excluded from the analysis, permitting a pooled analysis of 53 participants. Time to viral rebound was significantly associated with variables measured at the beginning of infection: pre-antiretroviral therapy (ART) viral load (HR = 1.34, p = 0.022), time to viral suppression post-ART initiation (HR = 1.07, p < 0.001), and area under the viral load curve (HR = 1.34, p = 0.026).

CONCLUSIONS

We show that higher viral loads in acute HIV-1 infection were associated with faster viral rebound, demonstrating that the initial stage of HIV-1 infection before ART initiation has a strong impact on viral rebound post-ATI years later.

FUNDING

This work was supported by a cooperative agreement between the Henry M. Jackson Foundation for the Advancement of Military Medicine and the US Department of the Army (W81XWH-18-2-0040). This research was funded, in part, by the US National Institute of Allergy and Infectious Diseases (AAI20052001) and the I4C Martin Delaney Collaboratory (5UM1AI126603-05).

Network methods and design of randomized trials: Application to investigation of COVID-19 vaccination boosters

Network science methods can be useful in design, monitoring, and analysis of randomized trials for control of spread of infections. Their usefulness arises from the role of statistical network models in molecular epidemiology and in study design. Computational models, such as agent-based models that propagate disease on simulated contact networks, can be used to investigate the properties of different study designs and analysis plans. Particularly valuable is the use of these methods to assess how magnitude and detectability of intervention effects depend on both individual-level and network-level characteristics of the enrolled populations. Such investigation also provides an important approach to assessing consequences of study data being incomplete or measured with error. To address these goals, we consider two statistical network models: exponential random graph models and the more flexible congruence class models. We focus first on an historical use of these methods in design and monitoring of a cluster randomized trial in Botswana to evaluate the effect of combination HIV prevention modalities compared to standard of care on HIV incidence. We then present a framework for the design of a study of booster vaccine effects on infection with, and forward transmission of, SARS-CoV-2 variants. Motivation for the study is driven in part by guidance from the United Kingdom to base approval of booster vaccines with "strain changes" that target variants on results of neutralizing antibody tests and information about safety, but without requiring evidence of clinical efficacy. Using designs informed by our agent-based network models, we show it may be feasible to conduct a trial of novel SARS-CoV-2 vaccines in a single large campus to obtain useful information regarding vaccine efficacy against susceptibility and infectiousness. If needed, the sample size could be increased by extending the study to a small number of campuses. Novel network methods may be useful in developing pragmatic SARS-CoV-2 vaccine trials that can leverage existing infrastructure to reduce costs and hasten the development of results.

Influence of Combination Antiretroviral Therapy on HIV-1 Serological Responses and Their Implications: A Systematic Review and Meta-Analysis

We aimed to analyze HIV-1 seroreversion caused by combination antiretroviral therapy (cART) and to explore antibody levels of anti-HIV-1 as an alternative biomarker of HIV-1 reservoir. We searched PubMed, Embase, the Cochrane Library, and Web of Science up to August 2021 for publications about the performance of HIV-1 serological assays or the association between antibody responses against HIV-1 and HIV-1 reservoirs. Potential sources of heterogeneity were explored by meta-regression analysis, including the year of publication, country, pretreatment viral load, sample size, the timing of treatment, time on cART, and principle or type of serological assay. Twenty-eight eligible studies with a total population of 1,883 were included in the meta-analysis. The pooled frequency of HIV-1 seronegativity is 38.0% (95% CI: 28.0%–49.0%) among children with vertical HIV-1 infection and cART initiation at the age of less than 6 months, while the percentage of HIV-1 seronegativity declined to 1.0% (95% CI: 0%–3.0%) when cART was initiated at the age of >6 months. For adult patients, 16.0% (95% CI: 9.0%–24.0%) of them were serologically negative when cART was initiated at acute/early infection of HIV-1, but the seronegative reaction was rarely detected when cART was started at chronic HIV-1 infection. Substantial heterogeneity was observed among the studies to estimate the frequency of HIV-1 seronegativity in the early-cART population (I² ≥ 70%, p < 0.05 and all), while mild heterogeneity existed for the deferred-cART subjects. Moreover, anti-HIV-1 antibody response positively correlates with HIV-1 reservoir size with a pooled rho of 0.43 (95% CI: 0.28–0.55), suggesting that anti-HIV antibody level may be a feasible biomarker of HIV-1 reservoir size.

Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population

Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States-African American or United States-European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.

The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020)

Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.

To achieve 95-95-95 targets we must reach men and youth: High level of knowledge of HIV status, ART coverage, and viral suppression in the Botswana Combination Prevention Project through universal test and treat approach

BACKGROUND

Increasing HIV treatment coverage is crucial to reducing population-level HIV incidence.

METHODS

The Botswana Combination Prevention Project (BCPP) was a community randomized trial examining the impact of multiple prevention interventions on population-level HIV incidence and was conducted from October 2013 through June 2017. Home and mobile campaigns offered HIV testing to all individuals ≥ age 16. All identified HIV-positive persons who were not on antiretroviral therapy (ART) were referred to treatment and tracked to determine linkage to care, ART status, retention in treatment, and viral suppression.

RESULTS

Of an estimated total of 14,270 people living with HIV (PLHIV) residing in the 15 intervention communities, BCPP identified 13,328 HIV-positive persons (93%). At study start, 10,703 (80%) of estimated PLHIV knew their status; 2,625 (20%) learned their status during BCPP, a 25% increase with the greatest increases occurring among men (37%) and youth (77%). At study start, 9,258 (65%) of estimated PLHIV were on ART. An additional 3,001 persons started ART through the study. By study end, 12,259 had initiated and were retained on ART, increasing coverage to 93%. A greater increase in ART coverage was achieved among men (40%) compared to women (29%). Of the 11,954 persons who had viral load (VL) test results, 11,687 (98%) were virally suppressed (HIV-1 RNA ≤400 copies/mL). Overall, 82% had documented VL suppression by study end.

CONCLUSIONS

Knowledge of HIV-positive status and ART coverage increased towards 95-95 targets with universal testing, linkage interventions, and ART. The increases in HIV testing and ART use among men and youth were essential to reaching these targets.

CLINICAL TRIAL NUMBER

NCT01965470.

Reaching 90-90-90 in Botswana

PURPOSE OF REVIEW

Botswana, a small country in southern Africa, has had a very high prevalence of HIV since about 1995. It seems important to analyze the response of this country to help us understand how it became one of the first nations to achieve the 90-90-90 targets.

RECENT FINDINGS

Botswana began a national program for treatment of HIV/AIDS with ARVs in 2002. Initially established in the four largest population centers, it expanded to more than 30 sites throughout the country by 2004. Also in 2004, an 'opt out' system for HIV testing was introduced. The government-sponsored ARV regimen for initiation was ZDV/3TC/EFV until 2008, then TDF/FTC/EFV until 2016, when it became TDF/FTC/DTG along with the introduction of treatment for all. Levels of both acquired and transmitted drug resistance have been low. In late 2013, we began the Ya Tsie or Botswana Combination Prevention Project (BCCP), a cluster randomized trial for 100 000 exurban and rural adults in 30 villages that included enhanced testing, linkage to care, and ARV treatment for 15 intervention villages, one in each pair. A 20% baseline survey in 2013-2015 revealed 29% prevalence and values that were already close to 90-90-90. With 83.3% of HIV-positive adults knowing they were infected, 87.4% of those knowing they were infected already on ARV, and 96.5% of those on ARV in complete viral suppression, this represented a combined value of 70.2% toward the target of 73%. By best estimates, incidence fell by about 30% over the 29-month period of the trial, which is compatible with Botswana reaching a 90% reduction in incidence in 10 years as proposed by the UNAIDS model. On the basis of an end-of-study survey in three intervention villages, we estimate that Botswana could reach 95-95-95 by 2019.

SUMMARY

These results illustrate that it is possible to reach 90-90-90 in countries with very high HIV prevalence.

Joint penalized spline modeling of multivariate longitudinal data, with application to HIV-1 RNA load levels and CD4 cell counts

Motivated by the need to jointly model the longitudinal trajectories of HIV viral load levels and CD4 counts during the primary infection stage, we propose a joint penalized spline modeling approach that can be used to model the repeated measurements from multiple biomarkers of various types (eg, continuous, binary) simultaneously. This approach allows for flexible trajectories for each marker, accounts for potentially time-varying correlation between markers, and is robust to misspecification of knots. Despite its advantages, the application of multivariate penalized spline models, especially when biomarkers may be of different data types, has been limited in part due to its seemingly complexity in implementation. To overcome this, we describe a procedure that transforms the multivariate setting to the univariate one, and then makes use of the generalized linear mixed effect model representation of a penalized spline model to facilitate its implementation with standard statistical software. We performed simulation studies to evaluate the validity and efficiency through joint modeling of correlated biomarkers measured longitudinally compared to the univariate modeling approach. We applied this modeling approach to longitudinal HIV-1 RNA load and CD4 count data from Southern African cohorts to estimate features of the joint distributions such as the correlation and the proportion of subjects with high viral load levels and high CD4 cell counts over time.

High discordance in blood and genital tract HIV-1 drug resistance in Indian women failing first-line therapy

Objectives

Examine HIV-1 plasma viral load (PVL) and genital tract (GT) viral load (GVL) and drug resistance in India.

Methods

At the YRG Centre for AIDS Research and Education, Chennai, we tested: PVL in women on first-line ART for ≥6 months; GVL when PVL >2000 copies/mL; and plasma, genital and proviral reverse transcriptase drug resistance when GVL >2000 copies/mL. Wilcoxon rank-sum and Fisher's exact tests were used to identify failure and resistance associations. Pearson correlations were calculated to evaluate PVL-GVL associations. Inter-compartmental resistance discordance was evaluated using generalized estimating equations.

Results

Of 200 women, 37% had detectable (>400 copies/mL) PVL and 31% had PVL >1000 copies/mL. Of women with detectable PVL, 74% had PVL >2000 copies/mL, of which 74% had detectable GVL. Higher PVL was associated with higher GVL. Paired plasma and genital sequences were available for 21 women; mean age of 34 years, median ART duration of 33 months, median CD4 count of 217 cells/mm3, median PVL of 5.4 log10 copies/mL and median GVL of 4.6 log10 copies/mL. Drug resistance was detected in 81%-91% of samples and 67%-76% of samples had dual-class resistance. Complete three-compartment concordance was seen in only 10% of women. GT-proviral discordance was significantly larger than plasma-proviral discordance. GT or proviral mutations discordant from plasma led to clinically relevant resistance in 24% and 30%, respectively.

Conclusions

We identified high resistance and high inter-compartmental resistance discordance in Indian women, which might lead to unrecognized resistance transmission and re-emergence compromising treatment outcomes, particularly relevant to countries like India, where sexual HIV transmission is predominant.

A signature for biological heterogeneity in susceptibility to HIV infection?

Data on female sex workers and sero-discordant couples indicate a pattern of waning of the risk of HIV infection with longer duration of exposure to infected partners. Understanding risk of HIV acquisition and transmission is critical to understanding HIV epidemiology and informing prevention interventions. Informed by empirical data, we aimed to develop a statistical model to explain these observations. In our proposed model, the time to infection for each individual is exponentially distributed, but the marginal (population averaged) distribution of time to infection follows a Weibull distribution with shape parameter of about 0.5, and with the Lévy distribution being the mixing distribution. Simulations based on this model demonstrated how HIV epidemics are destined to emerge rapidly, because of the rapid sero-conversion upon exposure, but also simultaneously destined to saturate and decline rapidly after emergence, just as observed for the HIV epidemics in sub-Saharan Africa. These results imply considerable individual variability in infection risk, probably because of biological heterogeneity in the susceptibility to HIV infection. Factoring this variability in mathematical models, through the methodology provided here, could be critical for valid estimations of impact of HIV interventions and assessments of cost-effectiveness.

Prediction of extended high viremia among newly HIV-1-infected persons in sub-Saharan Africa

Objective

Prompt identification of newly HIV-infected persons, particularly those who are most at risk of extended high viremia (EHV), allows important clinical and transmission prevention benefits. We sought to determine whether EHV could be predicted during early HIV infection (EHI) from clinical, demographic, and laboratory indicators in a large HIV-1 incidence study in Africa.

Design

Adults acquiring HIV-1 infection were enrolled in an EHI study assessing acute retroviral syndrome (ARS) symptoms and viral dynamics.

Methods

Estimated date of infection (EDI) was based on a positive plasma viral load or p24 antigen test prior to seroconversion, or the mid-point between negative and positive serological tests. EHV was defined as mean untreated viral load ≥5 log₁₀ copies/ml 130–330 days post-EDI. We used logistic regression to develop risk score algorithms for predicting EHV based on sex, age, number of ARS symptoms, and CD4 and viral load at diagnosis.

Results

Models based on the full set of five predictors had excellent performance both in the full population (c-statistic = 0.80) and when confined to persons with each of three HIV-1 subtypes (c-statistic = 0.80–0.83 within subtypes A, C, and D). Reduced models containing only 2–4 predictors performed similarly. In a risk score algorithm based on the final full-population model, predictor scores were one for male sex and enrollment CD4<350 cells/mm³, and two for having enrollment viral load >4.9 log₁₀ copies/ml. With a risk score cut-point of two, this algorithm was 85% sensitive (95% CI: 76%-91%) and 61% specific (55%-68%) in predicting EHV.

Conclusions

Simple risk score algorithms can reliably identify persons with EHI in sub-Saharan Africa who are likely to sustain high viral loads if treatment is delayed. These algorithms may be useful for prioritizing intensified efforts around care linkage and retention, treatment initiation, adherence support, and partner services to optimize clinical and prevention outcomes.

High HIV-1 RNA Among Newly Diagnosed People in Botswana

HIV-1 RNA level is strongly associated with HIV transmission risk. We sought to determine whether HIV-1 RNA level was associated with prior knowledge of HIV status among treatment-naive HIV-infected individuals in Botswana, a country with high rates of antiretroviral treatment (ART) coverage. This information may be helpful in targeting HIV diagnosis and treatment efforts in similar high HIV prevalence settings in a population-based survey. HIV-infected individuals were identified during a household survey performed in 30 communities across Botswana. ART-naive persons with detectable HIV-1 RNA (>400 copies/mL) were divided into two groups, newly diagnosed and individuals tested in the past who knew about their HIV infection at the time of household visit, but had not taken ART. Levels of HIV-1 RNA were compared between groups, overall and by age and gender. Among 815 HIV-infected ART-naive persons with detectable virus, newly diagnosed individuals had higher levels of HIV-1 RNA (n = 490, median HIV-1 RNA 4.35, interquartile range (IQR) 3.79-4.91 log₁₀ copies/mL) than those who knew about their HIV-positive status (n = 325, median HIV-1 RNA 4.10, IQR 3.55-4.68 log₁₀ copies/mL; p values <.001, but p value = .011 after adjusting for age and gender). A nonsignificant trend for higher HIV-1 RNA was found among newly diagnosed men 30 years of age or older (median HIV-1 RNA 4.58, IQR 4.07-5.02 log₁₀ copies/mL vs. 4.17, 3.61-4.71 log₁₀ copies/mL). Newly diagnosed individuals have elevated levels of HIV-1 RNA. This study highlights the need for early diagnosis and treatment of HIV infection for purposes of HIV epidemic control, even in a setting with high ART coverage.

Estimating the annual risk of HIV transmission within HIV sero-discordant couples in sub-Saharan Africa

OBJECTIVE

To estimate the annual risk of HIV transmission (ϕ) within HIV sero-discordant couples in 23 countries in sub-Saharan Africa (SSA), by utilizing newly available national population-based data and accounting for factors known to potentially affect this estimation.

METHODS

We used a recently developed pair-based mathematical model that accommodates for HIV-dynamics temporal variation, sexual risk-behavior heterogeneity, and antiretroviral therapy (ART) scale-up.

RESULTS

Estimated country-specific ϕ (in absence of ART) ranged between 4.2% (95% uncertainty interval (UI): 1.9%-6.3%) and 47.4% (95% UI: 37.2%-69.0%) per person-year (ppy), with a median of 12.4%. ϕ was strongly associated with HIV prevalence, with a Pearson correlation coefficient of 0.92, and was larger in high- versus low-HIV-prevalence countries. ϕ increased by 1.31% (95% confidence interval: 1.00%-1.55%) ppy for every 1% increase in HIV prevalence.

CONCLUSIONS

ϕ estimates were similar to earlier estimates, and suggested considerable heterogeneity in HIV infectiousness across SSA. This heterogeneity may explain, partly, the differences in epidemic scales.

HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach

BACKGROUND

Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection.

METHODS

Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering.

RESULTS

Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]).

CONCLUSIONS

A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.

Viral Decay Dynamics and Mathematical Modeling of Treatment Response: Evidence of Lower in vivo Fitness of HIV-1 Subtype C

BACKGROUND

Despite the high prevalence of HIV-1 subtype C (HIV-1C) worldwide, information on HIV-1C viral dynamics and response to antiretroviral therapy (ART) is limited. We sought to measure viral load decay dynamics during treatment and estimate the within-host basic reproductive ratio, R0, and the critical efficacy, εc, for successful treatment of HIV-1C infection.

METHODS

Individuals initiated on first-line ART in India and monitored for 6 months of treatment were considered. Viral load, CD4 count, and adherence data were collected at baseline, 4, 12, 16 and 24 weeks after ART initiation. Drug resistance genotyping was performed at baseline. R0 and εc were estimated using a mathematical model.

RESULTS

Among 257 patients with complete data, mean baseline viral load was 5.7 log10 copies per milliliter and median CD4 count was 165 cells per cubic millimeter. Primary drug resistance was present in 3.1% at baseline. At 6 months, 87.5% had undetectable viral load, indicating excellent response to ART despite high baseline viremia. After excluding those with transmitted resistance, suboptimal adherence and viral rebound, data from 112 patients were analyzed using a mathematical model. We estimated the median R0 to be 5.3. The corresponding εc was ∼0.8.

CONCLUSIONS

These estimates of R0 and εc are smaller than current estimates for HIV-1B, suggesting that HIV-1C exhibits lower in vivo fitness compared with HIV-1B, which allows successful treatment despite high baseline viral loads. The lower fitness, and potentially lower virulence, together with high viral loads may underlie the heightened transmission potential of HIV-1C and its growing global spread.

Update on current management of chronic kidney disease in patients with HIV infection

The prevalence of HIV-associated chronic kidney disease (CKD) varies geographically and depends on the definition of CKD used, ranging from 4.7% to 38% globally. The incidence, however, has decreased with the use of effective combined antiretroviral therapy (cART). A wide variety of histological patterns are seen in HIV-associated kidney diseases that include glomerular and tubulointerstitial pathology. In resource-rich settings, there has been a plateau in the incidence of end-stage renal disease secondary to HIV-associated nephropathy (HIVAN). However, the prevalence of end-stage renal disease in HIV-positive individuals has risen, mainly due to increased longevity on cART. There is a disparity in the occurrence of HIVAN among HIV-positive individuals such that there is an 18- to 50-fold increased risk of developing kidney disease among HIV-positive individuals of African descent aged between 20 and 64 years and who have a poorer prognosis compared with their European descent counterparts, suggesting that genetic factors play a vital role. Other risk factors include male sex, low CD4 counts, and high viral load. Improvement in renal function has been observed after initiation of cART in patients with HIV-associated CKD. Treatment with an angiotensin-converting enzyme inhibitor/angiotensin receptor blocker is recommended, when clinically indicated in patients with confirmed or suspected HIVAN or clinically significant albuminuria. Other standard management approaches for patients with CKD are recommended. These include addressing other cardiovascular risk factors (appropriate use of statins and aspirin, weight loss, cessation of smoking), avoidance of nephrotoxins, and management of serum bicarbonate and uric acid, anemia, calcium, and phosphate abnormalities. Early diagnosis of kidney disease by screening of HIV-positive individuals for the presence of kidney disease is critical for the optimal management of these patients. Screening for the presence of kidney disease upon detection of HIV infection and annually thereafter in high-risk populations is recommended.

APOL1 Risk Variants Are Strongly Associated with HIV-Associated Nephropathy in Black South Africans

APOL1 variants are associated with HIV-associated nephropathy and FSGS in African Americans. The prevalence of these variants in African populations with CKD in HIV-1 infection has not been investigated. We determined the role of APOL1 variants in 120 patients with HIV-associated nephropathy and CKD and 108 controls from a South-African black population. Patients with CKD were selected on the basis of histology. Genotypes were successfully determined for APOL1 G1 and G2 variants and 42 single nucleotide polymorphisms, including 18 ancestry informative markers, for 116 patients with CKD (96.7%; 38 patients with HIV-associated nephropathy, 39 patients with HIV-positive CKD, and 39 patients with HIV-negative CKD), and 108 controls (100%). Overall, 79% of patients with HIV-associated nephropathy and 2% of population controls carried two risk alleles. In a recessive model, individuals carrying any combination of two APOL1 risk alleles had 89-fold higher odds (95% confidence interval, 18 to 912; P<0.001) of developing HIV-associated nephropathy compared with HIV-positive controls. Population allele frequencies were 7.3% for G1 and 11.1% for G2. APOL1 risk alleles were not significantly associated with other forms of CKD. These results indicate HIV-positive, antiretroviral therapy-naïve South-African blacks with two APOL1 risk alleles are at very high risk for developing HIV-associated nephropathy. Further studies are required to determine the effect of APOL1 risk variants on kidney diseases in other regions of sub-Saharan Africa.

Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries

OBJECTIVES

The use of the NNRTI rilpivirine in low- and middle-income countries (LMICs) is under debate. The main objective of this study was to provide further clinical insights and biochemical evidence on the usefulness of rilpivirine in LMICs.

PATIENTS AND METHODS

Rilpivirine resistance was assessed in 5340 therapy-naive and 13,750 first-generation NNRTI-failed patients from Europe and therapy-naive HIV-1 subtype C (HIV-1C)-infected individuals from India (n = 617) and Ethiopia (n = 127). Rilpivirine inhibition and binding affinity assays were performed using patient-derived HIV-1C reverse transcriptases (RTs).

RESULTS

Primary rilpivirine resistance was rare, but the proportion of patients with >100,000 HIV-1 RNA copies/mL pre-ART was high in patients from India and Ethiopia, limiting the usefulness of rilpivirine as a first-line drug in LMICs. In patients failing first-line NNRTI treatments, cross-resistance patterns suggested that 73% of the patients could benefit from switching to rilpivirine-based therapy. In vitro inhibition assays showed ∼ 2-fold higher rilpivirine IC50 for HIV-1C RT than HIV-1B RT. Pre-steady-state determination of rilpivirine-binding affinities revealed 3.7-fold lower rilpivirine binding to HIV-1C than HIV-1B RT. Structural analysis indicated that naturally occurring polymorphisms close to the NNRTI-binding pocket may reduce rilpivirine binding, leading to lower susceptibility of HIV-1C to rilpivirine.

CONCLUSIONS

Our clinical and biochemical findings indicate that the usefulness of rilpivirine has limitations in HIV-1C-dominated epidemics in LMICs, but the drug could still be beneficial in patients failing first-line therapy if genotypic resistance testing is performed.

Southern Africa: the Highest Priority Region for HIV Prevention and Care Interventions

The global HIV pandemic began to expand rapidly in southern Africa a decade later than was noted in central Africa, Europe, the Caribbean, and North America. Multiple factors played a role in this rapid expansion which led Southern Africa to become the most heavily afflicted region for HIV/AIDS globally. In this issue of Current HIV/AIDS Reports, investigators with active research interests in the region have reviewed key elements of the causes of and responses to the epidemic. Putative causes of the high HIV prevalence in the region are discussed, including host and viral biology, human behavior, politics and policy, structural factors, health services, health workforce, migration, traditional healers' role, and other issues. Regional epidemiological trends are described and forecasted. Issues related to the continuum of HIV care and treatment are highlighted. We hope that the reviews will prove useful to those policymakers, health care workers, and scientists who are striving to reduce the burden of HIV in the southern African region, as well as prove insightful for key issues of broader global relevance.

African origins and chronic kidney disease susceptibility in the human immunodeficiency virus era

Chronic kidney disease (CKD) is a major public health problem worldwide with the estimated incidence growing by approximately 6% annually. There are striking ethnic differences in the prevalence of CKD such that, in the United States, African Americans have the highest prevalence of CKD, four times the incidence of end stage renal disease when compared to Americans of European ancestry suggestive of genetic predisposition. Diabetes mellitus, hypertension and human immunodeficiency virus (HIV) infection are the major causes of CKD. HIV-associated nephropathy (HIVAN) is an irreversible form of CKD with considerable morbidity and mortality and is present predominantly in people of African ancestry. The APOL1 G1 and G2 alleles were more strongly associated with the risk for CKD than the previously examined MYH9 E1 risk haplotype in individuals of African ancestry. A strong association was reported in HIVAN, suggesting that 50% of African Americans with two APOL1 risk alleles, if untreated, would develop HIVAN. However these two variants are not enough to cause disease. The prevailing belief is that modifying factors or second hits (including genetic hits) underlie the pathogenesis of kidney disease. This work reviews the history of genetic susceptibility of CKD and outlines current theories regarding the role for APOL1 in CKD in the HIV era.

High frequency of transmitted HIV-1 Gag HLA class I-driven immune escape variants but minimal immune selection over the first year of clade C infection

In chronic HIV infection, CD8+ T cell responses to Gag are associated with lower viral loads, but longitudinal studies of HLA-restricted CD8+ T cell-driven selection pressure in Gag from the time of acute infection are limited. In this study we examined Gag sequence evolution over the first year of infection in 22 patients identified prior to seroconversion. A total of 310 and 337 full-length Gag sequences from the earliest available samples (median = 14 days after infection [Fiebig stage I/II]) and at one-year post infection respectively were generated. Six of 22 (27%) individuals were infected with multiple variants. There was a trend towards early intra-patient viral sequence diversity correlating with viral load set point (p = 0.07, r = 0.39). At 14 days post infection, 59.7% of Gag CTL epitopes contained non-consensus polymorphisms and over half of these (35.3%) comprised of previously described CTL escape variants. Consensus and variant CTL epitope proportions were equally distributed irrespective of the selecting host HLA allele and most epitopes remained unchanged over 12 months post infection. These data suggest that intrapatient diversity during acute infection is an indicator of disease outcome. In this setting, there is a high rate of transmitted CTL escape variants and limited immune selection in Gag during the first year of infection. These data have relevance for vaccine strategies designed to elicit effective CD8+ T cell immune responses.

The HIV epidemic in Southern Africa - Is an AIDS-free generation possible?

Southern Africa, home to about 20 % of the global burden of infection continues to experience high rates of new HIV infection despite substantial programmatic scale-up of treatment and prevention interventions. While several countries in the region have had substantial reductions in HIV infection, almost half a million new infections occurred in this region in 2012. Sexual transmission remains the dominant mode of transmission. A recent national household survey in Swaziland revealed an HIV prevalence of 14.3 % among 18-19 year old girls, compared to 0.8 % among their male peers. Expanded ART programmes in Southern Africa have resulted in dramatically decreased HIV incidence and HIV mortality rates. In South Africa alone, it is estimated that more than 2.1 million of the 6.1 million HIV-positive people were receiving ART by the end of 2012, and that this resulted in more than 2.7 million life-years saved, and hundreds of thousands of HIV infections averted. Biological, behavioural and structural factors all contribute to the ongoing high rates of new HIV infection; however, as the epidemic matures and mortality is reduced from increased ART coverage, epidemiological trends become hard to quantify. What is clear is that a key driver of the Southern African epidemic is the high incidence rate of infection in young women, a vulnerable population with limited prevention options. Moreover, whilst ongoing trials of combination prevention, microbicides and behavioural economics hold promise for further epidemic control, an AIDS-free generation will not be realised unless incident infections in key populations are reduced.

Predicting time to threshold for initiating antiretroviral treatment to evaluate cost of treatment as prevention of human immunodeficiency virus

The goal of this paper is to predict the additional amount of antiretroviral treatment that would be required to implement a policy of treating all HIV-infected people at time of detection of infection rather than at the time that their CD4 T-lymphocyte counts are observed to be below a threshold-the current standard of care. We describe a sampling-based inverse prediction method for predicting time from HIV infection to attainment of the CD4 threshold and apply it to a set of treatment-naive HIV-infected subjects in a village in Botswana who participated in a household survey that collected cross-sectional CD4 counts. The inferential target of interest is the population-level mean time to reaching CD4-based treatment threshold in this group of subjects. To address the challenges arising from the fact that these subject's dates of HIV infection are unknown, we make use of data from an auxiliary cohort study of subjects enrolled shortly after HIV infection in which CD4 counts were measured over time. We use a multiple imputation framework to combine across the different sources of data, and discuss how the methods compensate for the length-biased sampling inherent in cross-sectional screening procedures, such as household surveys. We comment on how the results bear upon analyses of costs of implementation of treatment-for-prevention use of antiretroviral drugs in HIV prevention interventions.

Sample size considerations in the design of cluster randomized trials of combination HIV prevention

Background Cluster randomized trials have been utilized to evaluate the effectiveness of HIV prevention strategies on reducing incidence. Design of such studies must take into account possible correlation of outcomes within randomized units. Purpose To discuss power and sample size considerations for cluster randomized trials of combination HIV prevention, using an HIV prevention study in Botswana as an illustration. Methods We introduce a new agent-based model to simulate the community-level impact of a combination prevention strategy and investigate how correlation structure within a community affects the coefficient of variation - an essential parameter in designing a cluster randomized trial. Results We construct collections of sexual networks and then propagate HIV on them to simulate the disease epidemic. Increasing level of sexual mixing between intervention and standard-of-care (SOC) communities reduces the difference in cumulative incidence in the two sets of communities. Fifteen clusters per arm and 500 incidence cohort members per community provide 95% power to detect the projected difference in cumulative HIV incidence between SOC and intervention communities (3.93% and 2.34%) at the end of the third study year, using a coefficient of variation 0.25. Although available formulas for calculating sample size for cluster randomized trials can be derived by assuming an exchangeable correlation structure within clusters, we show that deviations from this assumption do not generally affect the validity of such formulas. Limitations We construct sexual networks based on data from Likoma Island, Malawi, and base disease progression on longitudinal estimates from an incidence cohort in Botswana and in Durban as well as a household survey in Mochudi, Botswana. Network data from Botswana and larger sample sizes to estimate rates of disease progression would be useful in assessing the robustness of our model results. Conclusion Epidemic modeling plays a critical role in planning and evaluating interventions for prevention. Simulation studies allow us to take into consideration available information on sexual network characteristics, such as mixing within and between communities as well as coverage levels for different prevention modalities in the combination prevention package.

Sources of HIV incidence among stable couples in sub-Saharan Africa

Introduction

The recent availability of efficacious prevention interventions among stable couples offers new opportunities for reducing HIV incidence in sub-Saharan Africa. Understanding the dynamics of HIV incidence among stable couples is critical to inform HIV prevention strategy across sub-Saharan Africa.

Methods

We quantified the sources of HIV incidence arising among stable couples in sub-Saharan Africa using a cohort-type mathematical model parameterized by nationally representative data. Uncertainty and sensitivity analyses were incorporated.

Results

HIV incidence arising among stable concordant HIV-negative couples contribute each year, on average, 29.4% of total HIV incidence; of those, 22.5% (range: 11.1%–39.8%) are infections acquired by one of the partners from sources external to the couple, less than 1% are infections acquired by both partners from external sources within a year and 6.8% (range: 3.6%–11.6%) are transmissions to the uninfected partner in the couple in less than a year after the other partner acquired the infection from an external source. The mean contribution of stable HIV sero-discordant couples to total HIV incidence is 30.4%, with most of those, 29.7% (range: 9.1%–47.9%), being due to HIV transmissions from the infected to the uninfected partner within the couple. The remaining incidence, 40.2% (range: 23.7%–64.6%), occurs among persons not in stable couples.

Conclusions

Close to two-thirds of total HIV incidence in sub-Saharan Africa occur among stable couples; however, only half of this incidence is attributed to HIV transmissions from the infected to the uninfected partner in the couple. The remaining incidence is acquired through extra-partner sex. Substantial reductions in HIV incidence can be achieved only through a prevention approach that targets all modes of HIV exposure among stable couples and among individuals not in stable couples.

HIV-1 subtype C is not associated with higher risk of heterosexual HIV-1 transmission: a multinational study among HIV-1 serodiscordant couples

BACKGROUND

HIV-1 subtype C has emerged as the most prevalent strain of HIV-1 worldwide, leading to speculation that subtype C may be more transmissible than other subtypes. We compared the risk of HIV-1 transmission for subtype C versus non-C subtypes (A, D, G and recombinant forms) among heterosexual African HIV-1 serodiscordant couples.

METHODS

We conducted a nested case-control analysis using data from two prospective cohort studies of heterosexual HIV-1 serodiscordant couples from six countries in eastern and southern Africa. Cases (N = 121) included incident HIV-1 transmissions that were established as linked within the serodiscordant partnership by viral sequencing; controls (N = 501) were nontransmitting HIV-1-infected partners. Subtype was determined for partial env and gag genes. Multiple logistic regression controlled for age and gender of the HIV-1-nfected partner and self-reported unprotected sex. Plasma and genital HIV-1 RNA concentrations were compared between subtype C and non-C subtypes using generalized estimating equations.

RESULTS

HIV-1 subtype C was not associated with increased risk of HIV-1 transmission compared with non-C subtypes: env adjusted odds ratio (adjOR) 1.14 [95% confidence interval (CI) 0.74-1.75, P = 0.6] and gag adjOR 0.98 (95% CI 0.63-1.52, P = 0.9). Plasma and genital HIV-1 RNA levels did not differ significantly for subtype C versus non-C.

CONCLUSION

In a geographically diverse population of heterosexual African HIV-1 serodiscordant couples, subtype C was not associated with greater risk of HIV-1 transmission compared with non-C subtypes, arguing against the hypothesis that subtype C is more transmissible compared with other common subtypes.

Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana

BACKGROUND

Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities.

METHODS

To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits.

RESULTS

The overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters.

CONCLUSIONS

The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.

The risk of HIV transmission within HIV-1 sero-discordant couples appears to vary across sub-Saharan Africa

BACKGROUND

Representative and precise estimates for the annual risk of HIV transmission (ϕ) from the infected to the uninfected partner in a stable HIV-1 sero-discordant couple (SDC) are not available. Nevertheless, quantifying HIV infectiousness is critical to understanding HIV epidemiology and implementing prevention programs.

MATERIALS AND METHODS

We estimated ϕ and examined its variation across 23 countries in sub-Saharan Africa (SSA) by constructing and analyzing a mathematical model that describes HIV dynamics among SDCs. The model was parameterized using empirical measures such as those of the nationally representative Demographic and Health Surveys. Uncertainty and sensitivity analyses were conducted to assess the robustness of the findings.

RESULTS

We estimated a median ϕ of 11.1 per 100 person-years across SSA. A clustering based on HIV population prevalence was observed with a median ϕ of 7.5 per 100 person-years in low HIV prevalence countries (<5%) compared to 19.5 per 100 person-years in high prevalence countries (>5%). The association with HIV prevalence explained 67% of the variation in ϕ, and suggested an increase of 0.95 per 100 person-years in ϕ for every 1% increase in HIV prevalence.

CONCLUSIONS

Empirical measures from cohort studies appear to underestimate HIV infectiousness in SSA. The risk of HIV transmission among SDCs appears also to vary across SSA, and this may have contributed to the contrasting HIV epidemic trajectories in this continent.

Intra-host evolutionary rates in HIV-1C env and gag during primary infection

BACKGROUND

HIV-1 nucleotide substitution rates are central for understanding the evolution of HIV-1. Their accurate estimation is critical for analysis of viral dynamics, identification of divergence time of HIV variants, inference of HIV transmission clusters, and modeling of viral evolution.

METHODS

Intra-patient nucleotide substitution rates in HIV-1C gag and env gp120 V1C5 were analyzed in a longitudinal cohort of 32 individuals infected with a single viral variant. Viral quasispecies were derived by single genome amplification/sequencing from serially sampled blood specimens collected at median (IQR) of 5 (4-6) times per subject from enrollment (during Fiebig stages II to V) over a median (IQR) of 417 (351-471) days post-seroconversion (p/s). HIV-1C evolutionary rates were estimated by BEAST v.1.7 using a relaxed lognormal molecular clock model. The effect of antiretroviral therapy (ART) on substitution rates in gag and env was assessed in a subset of six individuals who started ARV therapy during the follow-up period.

RESULTS

During primary HIV-1C infection, the intra-patient substitution rates were estimated at a median (IQR) of 5.22E-03 (3.28E-03-7.55E-03) substitutions per site per year of infection within gag, and 1.58E-02 (9.99E-03-2.04E-02) substitutions per site per year within env gp120 V1C5. The substitution rates in env gp120 V1C5 were higher than in gag (p<0.001, Wilcoxon signed rank test). The median (IQR) relative rates of evolution at codon positions 1, 2, and 3 were 0.73 (0.48-0.84), 0.67 (0.52-0.86), and 1.54 (1.21-1.71) in gag, and 1.01 (0.86-1.15), 1.05 (0.99-1.21), and 0.86 (0.67-0.94) in env gp120 V1C5, respectively. A first to the third position codon rate ratio >1.0 within env was found in 25 (78.1%) cases, but only in 4 (12.5%) cases in gag, while a second to the third position codon rate ratio >1.0 in env was observed in 26 (81.3%) cases, but in gag only in 2 (6.3%) cases (p<0.001 for both comparisons, Fisher's exact test). No ART effect on substitution rates in gag and env was found, at least within the first 3-4 months after ART initiation. Individuals with early viral set point ⩾4.0 log10 copies/ml had higher substitution rates in env gp120 V1C5 (median (IQR) 1.88E-02 (1.54E-02-2.46E-02) vs. 1.04E (7.24E-03-1.55E-02) substitutions per site per year; p=0.017, Mann-Whitney sum rank test), while individuals with early viral set point ⩾3.0 log10 copies/ml had higher substitution rates in gag (median (IQR) 5.66E-03 (3.45E-03-7.94E-03) vs. 1.78E-03 (4.57E-04-5.15E-03); p=0.028; Mann-Whitney sum rank test).

CONCLUSIONS

The results suggest that in primary HIV-1C infection, (1) intra-host evolutionary rates in env gp120 V1C5 are about 3-fold higher than in gag; (2) selection pressure in env is more frequent than in gag; (3) initiation of ART does not change substitution rates in HIV-1C env or gag, at least within the first 3-4 months after starting ART; and (4) intra-host evolutionary rates in gag and env gp120 V1C5 are higher in individuals with elevated levels of early viral set point.

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

Background

The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef’s most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D.

Results

Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function.

Conclusions

Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

BACKGROUND

The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef's most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D.

RESULTS

Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function.

CONCLUSIONS

Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.

Future of phylogeny in HIV prevention

The success of the HIV Prevention Trials Network 052 trial has led to revisions in HIV-1 treatment guidelines. Antiretroviral therapy may reduce the risk of HIV-1 transmissions at the population level. The design of successful treatment as prevention interventions will be predicated on a comprehensive understanding of the spatial, temporal, and biological dynamics of heterosexual men who have sex with men and intravenous drug user epidemics. Viral phylogenetics can capture the underlying structure of transmission networks based on the genetic interrelatedness of viral sequences and cluster networks that could not be otherwise identified. This article describes the phylogenetic expansion of the Montreal men who have sex with men epidemic over the last decade. High rates of coclustering of primary infections are associated with 1 infection leading to 13 onward transmissions. Phylogeny substantiates the role of primary and recent stage infection in transmission dynamics, underlying the importance of timely diagnosis and immediate antiretroviral therapy initiation to avert transmission cascades.

Changes in HIV-1 subtypes B and C genital tract RNA in women and men after initiation of antiretroviral therapy

BACKGROUND

Combination antiretroviral therapy (cART) reduces genital tract human immunodeficiency virus type 1 (HIV-1) load and reduces the risk of sexual transmission, but little is known about the efficacy of cART for decreasing genital tract viral load (GTVL) and differences in sex or HIV-1 subtype.

METHODS

HIV-1 RNA from blood plasma, seminal plasma, or cervical wicks was quantified at baseline and at weeks 48 and 96 after entry in a randomized clinical trial of 3 cART regimens.

RESULTS

One hundred fifty-eight men and 170 women from 7 countries were studied (men: 55% subtype B and 45% subtype C; women: 24% subtype B and 76% subtype C). Despite similar baseline CD4(+) cell counts and blood plasma viral loads, women with subtype C had the highest GTVL (median, 5.1 log10 copies/mL) compared to women with subtype B and men with subtype C or B (4.0, 4.0, and 3.8 log10 copies/mL, respectively; P < .001). The proportion of participants with a GTVL below the lower limit of quantification (LLQ) at week 48 (90%) and week 96 (90%) was increased compared to baseline (16%; P < .001 at both times). Women were significantly less likely to have GTVL below the LLQ compared to men (84% vs 94% at week 48, P = .006; 84% vs 97% at week 96, P = .002), despite a more sensitive assay for seminal plasma than for cervical wicks. No difference in GTVL response across the 3 cART regimens was detected.

CONCLUSIONS

The female genital tract may serve as a reservoir of persistent HIV-1 replication during cART and affect the use of cART to prevent sexual and perinatal transmission of HIV-1.

The importance of extended high viremics in models of HIV spread in South Africa

Recent studies found a substantial fraction of 'extended high viremics' among HIV-1 subtype C, the most common subtype in southern Africa. Extended high viremics are HIV infected individuals who maintain a high viral load for a longer time period than usual after the initial infection. They are more infectious during this period, and their infection progresses to full-blown AIDS and death much faster than usual. This study investigates the impact of extended high viremics on the spread of the HIV epidemic in South Africa. We develop a simple deterministic compartmental model for HIV infection that includes extended high viremics. As the available data on extended high viremics are limited, we parameterize this model using only the fraction of extended high viremics among new infections and the reduced life-span of extended high viremics. We find that without extended high viremics, the HIV prevalence in South Africa would have remained close to its 1990 level, instead of increasing to the current epidemic levels. We also find that the greater the fraction of extended high viremics among susceptibles, the greater the steady-state HIV prevalence and the more sensitive the steady-state prevalence is to the HIV transmission probability. These results suggest that extended high viremics have an impact on the HIV epidemic in South Africa; justify the need for comprehensive epidemiological studies since the current data is limited; and suggest that future models of HIV for southern Africa should explicitly model extended high viremics.

Have the explosive HIV epidemics in sub-Saharan Africa been driven by higher community viral load?

OBJECTIVE

The HIV epidemic has carved contrasting trajectories around the world with sub-Saharan Africa (SSA) being most affected. We hypothesized that mean HIV-1 plasma RNA viral loads are higher in SSA than other areas, and that these elevated levels may contribute to the scale of epidemics in this region.

DESIGN AND METHODS

To evaluate this hypothesis, we constructed a database of means of 71,668 viral load measurements from 44 cohorts in seven regions of the world. We used linear regression statistical models to estimate differences in viral load between regions. We also constructed and analyzed a mathematical model to describe the impact of the regional viral load differences on HIV epidemic trajectory.

RESULTS

We found substantial regional viral load heterogeneity. The mean viral load in SSA was 0.58 log(10) copies/ml higher than in North America (95% confidence interval 0.45-0.71); this represents about a four-fold increase. The highest mean viral loads were found in Southern and East Africa, whereas in Asia, Europe, North America, and South America, mean viral loads were comparable. Mathematical modeling indicated that conservatively 14% of HIV infections in a representative population in Kenya could be attributed to the enhanced infectiousness of patients with heightened viral load.

CONCLUSION

We conclude that community viral load appears to be higher in SSA than in other regions and this may be a central driver of the massive HIV epidemics in this region. The elevated viral loads in SSA may reflect, among other factors, the high burden of co-infections or the preponderance of HIV-1 subtype C infection.

tat Exon 1 exhibits functional diversity during HIV-1 subtype C primary infection

Human immunodeficiency virus type 1 (HIV-1) Tat is a mediator of viral transcription and is involved in the control of virus replication. However, associations between HIV-1 Tat diversity and functional effects during primary HIV-1 infection are still unclear. We estimated selection pressures in tat exon 1 using the mixed-effects model of evolution with 672 viral sequences generated from 20 patients infected with HIV-1 subtype C (HIV-1C) over 500 days postseroconversion. tat exon 1 residues 3, 4, 21, 24, 29, 39, and 68 were under positive selection, and we established that specific amino acid signature patterns were apparent in primary HIV-1C infection compared with chronic infection. We assessed the impact of these mutations on long terminal repeat (LTR) activity and found that Tat activity was negatively affected by the Ala(21) substitution identified in 13/20 (65%) of patients, which reduced LTR activity by 88% (± 1%) (P < 0.001). The greatest increase in Tat activity was seen with the Gln(35)/Lys(39) double mutant that resulted in an additional 49% (± 14%) production of LTR-driven luciferase (P = 0.012). There was a moderate positive correlation between Tat-mediated LTR activity and HIV-1 RNA in plasma (P = 0.026; r = 0.400) after 180 days postseroconversion that was reduced by 500 days postseroconversion (P = 0.043; r = 0.266). Although Tat activation of the LTR is not a strong predictor of these clinical variables, there are significant linear relationships between Tat transactivation and patients' plasma viral loads and CD4 counts, highlighting the complex interplay between Tat mutations in early HIV-1C infection.

Impact of HIV-1 subtype on CD4 count at HIV seroconversion, rate of decline, and viral load set point in European seroconverter cohorts

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1) subtype may influence disease progression. We compared CD4 lymphocyte cell count levels at seroconversion, decline rates and viral load set point in individuals infected with different HIV-1 subtypes.

METHODS

We used data from the Concerted Action on SeroConversion to AIDS and Death in Europe (CASCADE) collaboration, restricted to those infected since 1996, aged ≥15 years, and applied mixed effects models for CD4 cell count decline and median regression for viral load set point (mean level 6-24 months from seroconversion).

RESULTS

The analysis included 3364 seroconverters with known HIV-1 subtypes. Compared with subtype B, CD4 at seroconversion was significantly higher for subtype CRF01 and lower for subtype C. Subsequent CD4 decline was significantly slower for subtypes A and CRF02 and marginally slower for subtype C compared with B. Mean CD4 loss at 2 years of seroconversion for white men exposed through sex between men, aged 30-39 years, having seroconverted since 2006, enrolled within 6 months of seroconversion, and without acute infection was 88, 142, 100, 130, 103, and 167 cells/µL for subtypes A, B, C, CRF01_AE, CRF02_AG, and G, respectively. In adjusted analysis, median viral load set point and time to clinical AIDS/death did not differ significantly by subtype, although all subtypes, except C, tended to have lower levels compared with B.

CONCLUSIONS

HIV-1 subtype significantly influences seroconversion CD4 cell levels and decline rates but not viral load set point. These findings may be helpful to HIV-positive individuals and their attending physicians in understanding disease progression.

Only a fraction of new HIV infections occur within identifiable stable discordant couples in sub-Saharan Africa

OBJECTIVE

To estimate the contribution of HIV-1 sero-conversions among stable HIV sero-discordant couples (SDCs) to total HIV population-level incidence in sub-Saharan Africa.

DESIGN AND METHODS

We constructed a mathematical model, grounded in nationally representative demographic and epidemiological data, that estimates the annual number of HIV-1 transmissions from the infected partners to the uninfected partners among established SDCs, and compares its value to an estimate for the overall HIV population-level incidence in 20 countries in sub-Saharan Africa. We defined identifiable HIV-1 transmissions among SDCs as those that a hypothetical screening and intervention program would have the potential to avert. Uncertainty and sensitivity analyses were incorporated to assess the robustness of the findings.

RESULTS

Across the 20 countries, an average of 29% (range: 10-52%) of new HIV-1 infections occurred in which one partner in an identifiable SDC infected the other. The percentage of total HIV new infections in a country that occurred within such identifiable SDCs tended to be lower in countries with larger general population HIV epidemics. For most countries, HIV-1 incidence among SDCs is unlikely to exceed 50% of new HIV infections in the whole population.

CONCLUSION

Only a fraction of HIV-1 heterosexual transmissions occur within identifiable SDCs. Prevention within SDCs at scale requires a series of potentially challenging programmatic requirements to be met. Despite the importance of prevention programs aiming at protecting the sero-negative partner in an SDC, a wider strategy utilizing the full range of prevention modalities, which would limit the original generation of SDCs, is also needed.

Plasma viral loads during early HIV-1 infection are similar in subtype C- and non-subtype C-infected African seroconverters

Recent data suggest that infection with human immunodeficiency virus type 1 (HIV-1) subtype C results in prolonged high-level viremia (>5 log10 copies/mL) during early infection. We examined the relationship between HIV-1 subtype and plasma viremia among 153 African seroconverters. Mean setpoint viral loads were similar for C and non-C subtypes: 4.36 vs 4.42 log10 copies/mL (P = .61). The proportion of subtype C-infected participants with viral loads >5 log10 copies/mL was not greater than the proportion for those with non-C infection. Our data do not support the hypothesis that higher early viral load accounts for the rapid spread of HIV-1 subtype C in southern Africa.

Developing concurrency messages for the black community in Seattle, Washington

In the United States, Blacks are disproportionately impacted by HIV/AIDS. Sexual networks and concurrent relationships have emerged as important contributors to the heterosexual transmission of HIV. To date, Africa is the only continent where an understanding of the impact of sexual concurrency has been conveyed in HIV prevention messaging. This project was developed by researchers and members of the Seattle, Washington, African American and African-Born communities, using the principles of community-based participatory research (CBPR). Interest in developing concurrency messaging came from the community and resulted in the successful submission of a community-academic partnership proposal to develop and disseminate HIV prevention messaging around concurrency. The authors describe (a) the development of concurrency messaging through the integration of collected formative data and findings from the scientific literature; (b) the process of disseminating the message in the local Black community; and (c) important factors to consider in the development of similar campaigns.

High viremia and low level of transmitted drug resistance in anti-retroviral therapy-naïve perinatally-infected children and adolescents with HIV-1 subtype C infection

Background

High plasma viremia in HIV-1 infection is associated with rapid CD4 cell decline and faster disease progression. Children with HIV infection have high viral loads, particularly in early childhood. In this study we sought to understand the relationship between duration of HIV-1 infection and viral dynamics among perinatally-infected children and adolescents in India along with transmitted drug resistance in this population.

Methods

During 2007–2011, cross-sectional samples were collected from ART-naïve children (n = 105) with perinatally-acquired HIV infection, aged 2–16 years from Bangalore, India. CD4 counts, viral load and in-house genotyping were performed and transmitted drug resistance mutations were identified using the World Health Organization recommendations for Surveillance of Drug Resistance Mutations (SDRM_2009) list.

Results

Among 105 children studied, 73.3% (77/105) were asymptomatic, but had a median viral load of 5.24 log copies/mL (IQR 4.62-5.66). In the adolescent age group, 54% (21/39) had high levels of viremia (median 5.14 log copies/mL) but were asymptomatic. HIV-1 subtyping identified 98% strains (103/105) as subtype C; one A1 and one unique recombinant form (URF). Transmitted NRTI resistance was 1.9% (2/105); NNRTI resistance was 4.8% (5/105) and overall prevalence of transmitted drug resistance was 5.7% (6/105).

Conclusions

The high burden of plasma viremia found among untreated asymptomatic adolescents needs to be addressed both from an individual angle to halt disease progression, and from a public health perspective to arrest horizontal transmission. The low level of transmitted drug resistance among perinatally-infected children is reassuring; however with improving ART access globally, regular genotyping surveillance is indicated.

The future of HIV prevention

In the decades since the emergence of HIV, numerous approaches to prevent transmission have been tested with varying degrees of success. Because a highly effective vaccine will not be available within the next decade, it is increasingly clear that preventing new HIV infections will require successful implementation of promising behavioral and biomedical interventions in combination. These prevention packages must be sufficiently flexible to include a variety of evidence-based interventions that serve each dynamic population they target, particularly those who are most vulnerable. To optimize the impact of combination intervention packages, well-designed implementation science studies are vital. Efficacy in a clinical trial does not necessarily translate to effectiveness at the population-level, and prioritized research studies should investigate programmatic implementation and operations scale-up and new methods to monitor and evaluate these processes both for organization and cost-effectiveness. With an estimated 2.7 million people becoming newly infected with HIV in 2010, the prevention of HIV remains an urgent global health priority. Since the emergence of HIV/AIDS more than 30 years ago, the evidence base for HIV prevention has expanded and evolved. Here we explore the status of evidence-based HIV prevention, describing both the continuing challenges and the emerging opportunities to reduce HIV incidence.

HIV treatment as prevention: optimising the impact of expanded HIV treatment programmes

Until now, decisions about how to allocate ART have largely been based on maximising the therapeutic benefit of ART for patients. Since the results of the HPTN 052 study showed efficacy of antiretroviral therapy (ART) in preventing HIV transmission, there has been increased interest in the benefits of ART not only as treatment, but also in prevention. Resources for expanding ART in the short term may be limited, so the question is how to generate the most prevention benefit from realistic potential increases in the availability of ART. Although not a formal systematic review, here we review different ways in which access to ART could be expanded by prioritising access to particular groups based on clinical or behavioural factors. For each group we consider (i) the clinical and epidemiological benefits, (ii) the potential feasibility, acceptability, and equity, and (iii) the affordability and cost-effectiveness of prioritising ART access for that group. In re-evaluating the allocation of ART in light of the new data about ART preventing transmission, the goal should be to create policies that maximise epidemiological and clinical benefit while still being feasible, affordable, acceptable, and equitable.

Using HIV viral load to guide treatment-for-prevention interventions

PURPOSE OF REVIEW

To provide evidence that HIV-1 RNA load can guide treatment-for-prevention interventions to mitigate the HIV epidemic.

RECENT FINDINGS

Some HIV-infected individuals maintain increased levels of HIV-1 RNA load after acute infection for an extended period of time, and can disproportionately contribute to the spread of HIV in the community. The recent HIV Prevention Trials Network 052 study has demonstrated 96% efficacy for initiation of early antiretroviral treatment (ART) in HIV-1 serodiscordant couples.

SUMMARY

The level of HIV-1 RNA load in plasma is the major biological predictor of virus transmission. HIV-infected individuals who maintain increased levels of HIV-1 RNA load, extended high viremics, can transmit virus at higher rates. Combinatorial ART decreases HIV replication, thus reducing rates of virus transmission. Identifying high viremics and placing them on ART seems an attractive strategy that has the potential to achieve both individual benefits by lowering risk for early onset of clinical AIDS and public health benefits by reducing HIV transmission. A key logistical challenge is to screen for high viremics among HIV-positive individuals. Efficacy of the modified treatment-for-prevention approach focused on high viremics is being evaluated in ongoing and upcoming clinical trials. If efficacious, such an approach could be used widely to mitigate and control the HIV epidemic.

Viral diversity and diversification of major non-structural genes vif, vpr, vpu, tat exon 1 and rev exon 1 during primary HIV-1 subtype C infection

To assess the level of intra-patient diversity and evolution of HIV-1C non-structural genes in primary infection, viral quasispecies obtained by single genome amplification (SGA) at multiple sampling timepoints up to 500 days post-seroconversion (p/s) were analyzed. The mean intra-patient diversity was 0.11% (95% CI; 0.02 to 0.20) for vif, 0.23% (95% CI; 0.08 to 0.38) for vpr, 0.35% (95% CI; −0.05 to 0.75) for vpu, 0.18% (95% CI; 0.01 to 0.35) for tat exon 1 and 0.30% (95% CI; 0.02 to 0.58) for rev exon 1 during the time period 0 to 90 days p/s. The intra-patient diversity increased gradually in all non-structural genes over the first year of HIV-1 infection, which was evident from the vif mean intra-patient diversity of 0.46% (95% CI; 0.28 to 0.64), vpr 0.44% (95% CI; 0.24 to 0.64), vpu 0.84% (95% CI; 0.55 to 1.13), tat exon 1 0.35% (95% CI; 0.14 to 0.56 ) and rev exon 1 0.42% (95% CI; 0.18 to 0.66) during the time period of 181 to 500 days p/s. There was a statistically significant increase in viral diversity for vif (p = 0.013) and vpu (p = 0.002). No associations between levels of viral diversity within the non-structural genes and HIV-1 RNA load during primary infection were found. The study details the dynamics of the non-structural viral genes during the early stages of HIV-1C infection.