HIV subtype diversity worldwide.

PURPOSE OF REVIEW: To provide a summary of the current data on the global HIV subtype diversity and distribution by region. HIV is one of the most genetically diverse pathogens due to its high-mutation and recombination rates, large population size and rapid replication rate. This rapid evolutionary process has resulted in several HIV subtypes that are heterogeneously globally distributed. RECENT FINDINGS: Subtype A remains the most prevalent strain in parts of East Africa, Russia and former Soviet Union countries; subtype B in Europe, Americas and Oceania; subtype C in Southern Africa and India; CRF01_AE in Asia and CRF02_AG in Western Africa. Recent studies based on near full-length genome sequencing highlighted the growing importance of recombinant variants and subtype C viruses. SUMMARY: The dynamic change in HIV subtype distribution presents future challenges for diagnosis, treatment and vaccine design and development. An increase in recombinant viruses suggests that coinfection and superinfection by divergent HIV strains has become more common necessitating continuous surveillance to keep track of the viral diversity. Cheaper near full-length genome sequencing approaches are critical in improving HIV subtype estimations. However, missing subtype data and low sequence sampling levels are still a challenge in some geographical regions. VIDEO ABSTRACT: http://links.lww.com/COHA/A14

Prevention of the sexual transmission of HIV-1: preparing for success

There are four opportunities for HIV prevention: before exposure, at the moment of exposure, immediately after exposure, and as secondary prevention focused on infected subjects. Until recently, most resources have been directed toward behavioral strategies aimed at preventing exposure entirely. Recognizing that these strategies are not enough to contain the epidemic, investigators are turning their attention to post-exposure prevention opportunities. There is increasing focus on the use of ART–either systemic or topical (microbicides)–to prevent infection at the moment of exposure. Likewise, there is growing evidence that ART treatment of infected people could serve as prevention as well. A number of ongoing clinical trials will shed some light on the potential of these approaches. Above all, prevention of HIV requires decision-makers to focus resources on strategies that are most effective. Finally, treatment of HIV and prevention of HIV must be considered and deployed together

Short Communication: Choosing the Right Program for the Identification of HIV-1 Transmission Networks from Nucleotide Sequences Sampled from Different Populations.

HIV-TRAnsmission Cluster Engine (HIV-TRACE) and Cluster Picker are some of the most widely used programs for identifying HIV-1 transmission networks from nucleotide sequences. However, choosing between these tools is subjective and often a matter of personal preference. Because these software use different algorithms to detect HIV-1 transmission networks, their optimal use is better suited with different sequence data sets and under different scenarios. The performance of these tools has previously been evaluated across a range of genetic distance thresholds without an assessment of the differences in the structure of networks identified. In this study, we tested both programs on the same HIV-1 pol sequence data set (n?=?2,017) from three Ugandan populations to examine their performance across different risk groups and evaluate the structure of networks identified. HIV-TRACE that uses a single-linkage algorithm identified more nodes in the same networks that were connected by sparse links than Cluster Picker. This suggests that the choice of the program used for identifying networks should depend on the study aims, the characteristics of the population being investigated, dynamics of the epidemic, sampling design, and the nature of research questions being addressed for optimum results. HIV-TRACE could be more applicable with larger data sets where the aim is to identify larger clusters that represent distinct transmission chains and in more diverse populations where infection has occurred over a period of time. In contrast, Cluster Picker is applicable in situations where more closely connected clusters are expected in the studied populations

A prospective study of trends in consumption of cigarettes and alcohol among adults in a rural Ugandan population cohort, 1994-2011

OBJECTIVES: To characterise trends over time in smoking and alcohol consumption in a rural Ugandan population between 1994 and 2011. METHODS: We used self-reported data from a long-standing population cohort - the General Population Cohort. From 1989-1999, the study population comprised about 10,000 residents of 15 adjacent villages. From 1999, 10 more villages were added, doubling the population. Among adults (≥13 years, who comprise about half of the total study population) data on smoking were collected in 1994/95, 2008/9 and in 2010/11. Data on alcohol were collected in 1996/1997, 2000/2001, 2009/2010 and 2010/2011. RESULTS: The reported prevalence of smoking among men was 17% in 1994/1995, 14% in 2008/2009 and 16% in 2010/2011; equivalent figures for women were 1.5%, 1% and 2%. In the most recent time period, for both sexes combined, prevalence of smoking increased from 1.5% in those aged <29 years, to 18% in those 50+ years (P<0.001); prevalence was 14.8% in the lowest tertile of socio-economic status, decreasing to 3.7% in the highest (P<0.001). For alcohol consumption, current drinking was reported by 39% in 1996/1997, 35% in 2000/2001 and 28% in 2010/2011; men were more likely to drink than women (32.9% vs. 23.5% in 2010/2011) and consumption increased with age (P<0.001); was associated with low socio-economic status, riskier sexual behaviour and being HIV positive (P<0.001). CONCLUSION: In this rural Ugandan population, consumption of cigarettes and alcohol is higher among men than women, increases with age and is more frequent among those with low socio-economic status. We find no evidence of increases in either exposure over time. This article is protected by copyright. All rights reserved

'Test and Treat' Among Women at High Risk for HIV-infection in Kampala, Uganda: Antiretroviral Therapy Initiation and Associated Factors.

Data on implementation of 'Test and Treat' among key populations in sub-Saharan Africa are still limited. We examined factors associated with prompt antiretroviral therapy/ART (within 1 month of HIV-positive diagnosis or 1 week if pregnant) among 343 women at high risk for HIV infection in Kampala-Uganda, of whom 28% initiated prompt ART. Most (95%) reported paid sex within 3 months prior to enrolment. Multivariable logistic regression was used to determine baseline characteristics associated with prompt ART. Sex work as main job, younger age and being widowed/separated were associated with lower odds of prompt ART; being enrolled after 12 months of implementing the intervention was associated with higher odds of prompt ART. Younger women, widowed/separated and those reporting sex work as their main job need targeted interventions to start ART promptly after testing. Staff supervision and mentoring may need strengthening during the first year of implementing 'test and treat' interventions

Pregnancy, parturition and preeclampsia in women of African ancestry.

Maternal and associated neonatal mortality rates in sub-Saharan Africa remain unacceptably high. In Mulago Hospital (Kampala, Uganda), 2 major causes of maternal death are preeclampsia and obstructed labor and their complications, conditions occurring at the extremes of the birthweight spectrum, a situation encapsulated as the obstetric dilemma. We have questioned whether the prevalence of these disorders occurs more frequently in indigenous African women and those with African ancestry elsewhere in the world by reviewing available literature. We conclude that these women are at greater risk of preeclampsia than other racial groups. At least part of this susceptibility seems independent of socioeconomic status and likely is due to biological or genetic factors. Evidence for a genetic contribution to preeclampsia is discussed. We go on to propose that the obstetric dilemma in humans is responsible for this situation and discuss how parturition and birthweight are subject to stabilizing selection. Other data we present also suggest that there are particularly strong evolutionary selective pressures operating during pregnancy and delivery in Africans. There is much greater genetic diversity and less linkage disequilibrium in Africa, and the genes responsible for regulating birthweight and placentation may therefore be easier to define than in non-African cohorts. Inclusion of African women into research on preeclampsia is an essential component in tackling this major disparity of maternal health

Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort.

BACKGROUND: Identifying immunogens that induce HIV-1-specific immune responses is a lengthy process that can benefit from computational methods, which predict T-cell epitopes for various HLA types. METHODS: We tested the performance of the NetMHCpan4.0 computational neural network in re-identifying 93 T-cell epitopes that had been previously independently mapped using the whole proteome IFN-γ ELISPOT assays in 6 HLA class I typed Ugandan individuals infected with HIV-1 subtypes A1 and D. To provide a benchmark we compared the predictions for NetMHCpan4.0 to MHCflurry1.2.0 and NetCTL1.2. RESULTS: NetMHCpan4.0 performed best correctly predicting 88 of the 93 experimentally mapped epitopes for a set length of 9-mer and matched HLA class I alleles. Receiver Operator Characteristic (ROC) analysis gave an area under the curve (AUC) of 0.928. Setting NetMHCpan4.0 to predict 11-14mer length did not improve the prediction (37-79 of 93 peptides) with an inverse correlation between the number of predictions and length set. Late time point peptides were significantly stronger binders than early peptides (Wilcoxon signed rank test: p = 0.0000005). MHCflurry1.2.0 similarly predicted all but 2 of the peptides that NetMHCpan4.0 predicted and NetCTL1.2 predicted only 14 of the 93 experimental peptides. CONCLUSION: NetMHCpan4.0 class I epitope predictions covered 95% of the epitope responses identified in six HIV-1 infected individuals, and would have reduced the number of experimental confirmatory tests by > 80%. Algorithmic epitope prediction in conjunction with HLA allele frequency information can cost-effectively assist immunogen design through minimizing the experimental effort

The effect of anthelmintic treatment during pregnancy on HIV plasma viral load: results from a randomized, double-blind, placebo-controlled trial in Uganda.

BACKGROUND: To investigate the effect of helminth infections and their treatment during pregnancy on HIV load, we conducted a 2 × 2 factorial randomized controlled trial of albendazole versus placebo and praziquantel versus placebo in pregnant women in Entebbe, Uganda. METHODS: Two hundred sixty-four HIV-infected pregnant women from the Entebbe Mother and Baby Study (ISRCTN 32849447) were included in this analysis. Women were tested for helminth infections at enrollment, and mean HIV load was compared between infected and uninfected groups. The effect of anthelmintic treatment on HIV load was evaluated at 6 weeks after treatment and at delivery using linear regression and adjusting for enrollment viral load. RESULTS: Hookworm and Trichuris infections were associated with higher mean viral load at enrollment [adjusted mean difference 0.24 log10 copies/mL, 95% confidence interval (CI): 0.01 to 0.47, P = 0.03, and 0.37 log(10) copies/mL, 95% CI: 0.00 to 0.74, P = 0.05, respectively]. There were no associations between viral load and other helminth species. There was some evidence that albendazole reduced viral load at 6 weeks after treatment (adjusted mean difference -0.17, 95% CI: -0.36 to 0.01, P = 0.07); however, this effect did not differ according to mother's hookworm infection status and had diminished at delivery (adjusted mean difference -0.11, 95% CI: -0.28 to 0.07, P = 0.23). There was no effect of praziquantel treatment on HIV load at any time point. CONCLUSIONS: Infection with some soil-transmitted helminth species is associated with increased HIV load in pregnancy. Treatment with albendazole causes a small decrease in HIV load; however, this may not represent a direct effect of worm removal

Comparison of HIV Risk Behaviors Between Clinical Trials and Observational Cohorts in Uganda.

Many key populations have high-risk behaviors for HIV infection making them suitable for HIV vaccine efficacy trials. However, these behaviors may change when participants enroll into a trial. We used HIV simulated vaccine efficacy trials (SiVETs) nested within observational cohorts of fisherfolks and female sex workers in Uganda to evaluate this difference. We screened observational cohort participants for enrolment into SiVETs, until 572 were enrolled. Those not enrolled (n = 953) continued participation in the observational cohorts. We determined risk behaviors at baseline and at 1 year, assigned a numeric score to each behavior and defined composite score as the sum of reported behaviors. We compared changes in scores over 12 months. Both observational cohorts and SiVETs saw a significant decrease in score but greatest in the SiVETs. Investigators recruiting for trials from these populations should consider the likely effect of reduction in risk behaviors on incident HIV infection and trial statistical power

Comparison of retention in observational cohorts and nested simulated HIV vaccine efficacy trials in the key populations in Uganda.

BACKGROUND: Outcomes in observational studies may not best estimate those expected in the HIV vaccine efficacy trials. We compared retention in Simulated HIV Vaccine Efficacy Trials (SiVETs) and observational cohorts drawn from two key populations in Uganda. METHODS: Two SiVETs were nested within two observational cohorts, one in Fisherfolk (FF) and another one in Female Sex Workers (FSW). Adult participants in each observational cohort were screened for enrolment into SiVETs. Those screened-out or not screened continued participation in the observational (non-SiVET) cohorts. SiVET participants were administered a licensed hepatitis B vaccine in a schedule that mimicked an actual HIV vaccine efficacy trial. Both cohorts were followed for 12 months and retention was assessed through dropout, defined as lost to follow up, being uncontactable, refusal to continue or missing the last study clinic visit. Dropout rates were compared using Poisson models giving rate ratios and 95% confidence intervals (95%CI). RESULTS: Out of 1525 participants (565 FF and 960 FSW), 572 (38%) were enrolled into SiVETs (282-FF and 290-FSW), and 953 (62%) remained in the non-SiVET cohorts. Overall, 326 (101 SiVET, 225 non-SiVET) dropped out in 1260 Person Years of Observation (PYO), a dropout rate of 25.9 /100 PYO (95%CI: 23.2-28.8); fewer dropped out in the SiVET cohorts (18.4, 95% CI: 15.1-22.4) than in the non-SiVET cohorts (31.6, 95% CI: 27.8-36.1), rate ratio (RR) =0.58, 95% CI: 0.46-0.73. In all cohorts, the dropout was more marked in FSW than in FF population. Duration lived in community was associated with dropout in both SiVETs and religion in both non-SiVET cohorts. CONCLUSION: The rate of dropout was lower in SiVET compared to non-SiVET cohort. Though the difference in dropout between SiVET and non-SiVET was generally similar, the actual dropout rates were higher in the FSW population. Conduct of SiVETs in these key populations could mean that designing HIV Vaccine Efficacy Trials will benefit from lower dropout rate shown in SiVET than non-SiVET observational cohort