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1.  Nondisclosure of HIV Status in a Clinical Trial Setting: Antiretroviral Drug Screening Can Help Distinguish Between Newly Diagnosed and Previously Diagnosed HIV Infection 
In The HIV Prevention Trials Network 061 study, 155 human immunodeficiency virus (HIV)–infected men reported no prior HIV diagnosis; 83 of those men had HIV RNA levels of <1000 copies/mL at enrollment. Antiretroviral drug testing revealed that 65 of the 83 (78.3%) men were on antiretroviral treatment. Antiretroviral drug testing can help distinguish between newly diagnosed and previously diagnosed HIV infection.
doi:10.1093/cid/cit672
PMCID: PMC3864502  PMID: 24092804
HIV; antiretroviral; self-report; MSM; new diagnosis
2.  Age, Race/Ethnicity, and Behavioral Risk Factors Associated with Per-Contact Risk of HIV Infection Among Men Who Have Sex with Men in the United States 
Objective
Young men who have sex with men (MSM) and MSM of color have the highest HIV incidence in the US. To explore possible explanations for these disparities and known individual risk factors we analyzed the per-contact risk (PCR) of HIV seroconversion in the early highly active antiretroviral therapy era.
Methods
Data from three longitudinal studies of MSM, HIVNET Vaccine Preparedness Study, EXPLORE behavioral efficacy trial, and VAX004 vaccine efficacy trial were pooled. The analysis included visits where participants reported unprotected receptive anal intercourse (URA), protected receptive anal intercourse (PRA), or unprotective insertive anal intercourse (UIA) with an HIV seropositive, unknown HIV serostatus, or an HIV seronegative partner. We used regression standardization to estimate average PCRs for each type of contact, with bootstrap confidence intervals.
Results
The estimated PCR was highest for URA with an HIV seropositive partner (0.73%; 95%BCI 0.45%-0.98%) followed by URA with a partner of unknown HIV serostatus (0.49%; 95%BCI 0.32%-0.62%). The estimated PCR for PRA and UIA with an HIV seropositive partner was 0.08% (95%BCI 0.0%-0.19%) and 0.22% (95%BCI 0.05%-0.39%) respectively. Average PCRs for URA and UIA with HIV seropositive partners were higher by 0.14-0.34% among younger participants and higher by 0.08% for UIA among Latino participants compared to White participants. Estimated PCRs increased with increasing number of sexual partners, use of methamphetamines or poppers, and history of sexually transmitted infection.
Conclusions
Susceptibility or partner factors may explain the higher HIV conversion risk for younger MSM, some MSM of color, and those reporting individual risk factors.
doi:10.1097/QAI.0b013e3182a98bae
PMCID: PMC3894586  PMID: 24419067
HIV; MSM; USA; per contact risk
3.  In Pursuit of an HIV Vaccine: Designing Efficacy Trials in the Context of Partially Effective Nonvaccine Prevention Modalities 
AIDS Research and Human Retroviruses  2013;29(11):1513-1523.
Abstract
The HIV prevention landscape is evolving rapidly, and future efficacy trials of candidate vaccines, which remain the best long-term option for stemming the HIV epidemic, will be conducted in the context of partially effective nonvaccine prevention modalities. It is essential that these trials provide for valid and efficient evaluation of vaccine efficacy and immune correlates. The availability of partially effective prevention modalities presents opportunities to study their interactions with vaccines to maximally reduce HIV incidence. This article proposes an approach for conducting future vaccine efficacy trials in the context of background use of partially effective nonvaccine prevention modalities, and for conducting future vaccine efficacy trials that provide nonvaccine prevention modalities in one or more of the randomized study groups. Strategies are discussed for responding to emerging evidence on nonvaccine prevention modalities during ongoing vaccine trials. Next-generation HIV vaccine efficacy trials will almost certainly be more complex in their design and implementation but may become more relevant to at-risk populations and better suited to the ultimate goal of reducing HIV incidence at the population level.
doi:10.1089/aid.2012.0385
PMCID: PMC3809388  PMID: 23597282
4.  Participant Experiences and Facilitators and Barriers to Pill Use Among Men Who Have Sex with Men in the iPrEx Pre-Exposure Prophylaxis Trial in San Francisco 
AIDS Patient Care and STDs  2013;27(10):560-566.
Abstract
In 2010, the iPrEx study demonstrated efficacy of daily emtricitabine/tenofovir disoproxil fumarate (FTC/TDF) pre-exposure prophylaxis (PrEP) in reducing HIV acquisition among men who have sex with men. Adherence to study product was critical for PrEP efficacy, and varied considerably, with FTC/TDF detection rates highest in the United States. We conducted a qualitative study to gain insights into the experiences of iPrEx participants in San Francisco (SF) where there was high confirmed adherence, to understand individual and contextual factors influencing study product use in this community. In 2009 and 2011, we conducted focus groups and in-depth interviews in 36 and 16 SF iPrEx participants, respectively. Qualitative analyses indicate that participants joined the study out of altruism. They had a clear understanding of study product use, and pill taking was facilitated by establishing or building on an existing routine. Participants valued healthcare provided by the study and relationships with staff, whom they perceived as nonjudgmental, and found client-centered counseling to be an important part of the PrEP package. This facilitated pill taking and accurate reporting of missed doses. Adherence barriers included changes in routine, side effects/intercurrent illnesses, and stress. Future PrEP adherence interventions should leverage existing routines and establish client-centered relationships/ environments to support pill taking and promote accurate reporting.
doi:10.1089/apc.2013.0116
PMCID: PMC3791030  PMID: 24093809
5.  Sources of Racial/Ethnic Differences in Awareness of HIV Vaccine Trials 
American journal of public health  2014;104(8):e112-e118.
Objectives
We explored the relative effects of 2 awareness components—exposure and attention—on racial/ethnic differences in HIV vaccine trial awareness among men who have sex with men (MSM).
Methods
Surveys assessing awareness of and attitudes toward HIV vaccine trials were administered to 1723 MSM in 6 US cities. Proxy measures of exposure included use of HIV resources and other health care services, community involvement, income, and residence. Attention proxy measures included research attitudes, HIV susceptibility, and HIV message fatigue. Using logistic regression models, we assessed the extent to which these proxies accounted for racial/ethnic differences in vaccine trial awareness.
Results
White MSM reported significantly (P < .01) higher rates of HIV vaccine trial awareness (22%) compared with Latino (17%), Black (13%) and “other” (13%) MSM. Venue-based exposure proxies and research-directed attitudinal attention proxies were significantly associated with awareness, but only accounted for the White-Latino disparity in awareness. No proxies accounted for the White-Black or White- “other” differentials in awareness.
Conclusions
Sources of disparities in awareness of HIV vaccine trials remain to be explained. Future trials seeking to promote diverse participation should explore additional exposure and attention mediators.
doi:10.2105/AJPH.2014.301893
PMCID: PMC4103242  PMID: 24922153
6.  Anal Sex Role Segregation and Versatility among Men Who Have Sex with Men: EXPLORE Study 
Anal sex role patterns and correlates during unprotected anal sex were examined longitudinally among HIV-negative men who have sex with men (MSM). 9.6% were exclusively receptive, 16.7% exclusively insertive, and 63.0% versatile. Versatility was more likely with primary and HIV-negative/unknown status partners and among younger men and substance users, but less likely among Blacks and with higher number of partners. Exclusively receptive role was more likely with HIV-negative/unknown status partners and among younger men and substance users, but less likely with higher number of partners. Examining anal sex role patterns helps understand the factors that drive the epidemic among MSM.
doi:10.1097/QAI.0b013e318299cede
PMCID: PMC3804162  PMID: 23945255
Role Segregation; Versatility; Anal Sex Role; men who have sex with men; HIV
7.  Sexual risk behavior among HIV-uninfected men who have sex with men (MSM) participating in a tenofovir pre-exposure prophylaxis (PrEP) randomized trial in the United States 
Objective
To evaluate for changes in sexual behaviors associated with daily pill-use among MSM participating in a PrEP trial.
Design
Randomized, double-blind, placebo-controlled trial. Participants were randomized 1:1:1:1 to receive tenofovir disoproxil fumarate or placebo at enrollment or after a 9-month delay and followed for 24 months.
Methods
400 HIV-negative MSM reporting anal sex with a man in the past 12 months and meeting other eligibility criteria enrolled in San Francisco, Atlanta, and Boston. Sexual risk was assessed at baseline and quarterly visits using Audio Computer-Assisted Self-Interview. The association of pill-taking with sexual behavior was evaluated using logistic and negative-binomial regression for repeated measures.
Results
Overall indices of behavioral risk declined or remained stable during follow-up. Mean numbers of partners and proportion reporting unprotected anal sex (UAS) declined during follow-up (p<0.05), and mean UAS episodes remained stable. During the initial 9 months, changes in risk practices were similar in the group that began pills immediately vs. those in the delayed arm. These indices of risk did not differ significantly after initiation of pill-use in the delayed arm or continuation of study medication in the immediate arm. Use of poppers, amphetamines, and sexual performance-enhancing drugs were independently associated with one or more indices of sexual risk.
Conclusions
There was no evidence of risk compensation among HIV-uninfected MSM in this clinical trial. Monitoring for risk compensation should continue now that PrEP has been shown to be efficacious in MSM and other populations and will be provided in open-label trials and other contexts.
doi:10.1097/QAI.0b013e31828f097a
PMCID: PMC3904758  PMID: 23481668
risk compensation; behavioral disinhibition; sexual risk behavior; PrEP; MSM
8.  Acceptability of self-conducted home-based HIV testing among men who have sex with men in Brazil: data from an on-line survey 
Cadernos de saude publica  2014;30(4):724-734.
The Brazilian HIV/AIDS epidemic is concentrated among men who have sex with men (MSM), however HIV testing rates among MSM are not commensurate with their risk. Strategies to expand early diagnosis may include use of self-conducted home-based testing kits, which are now available for purchase in the US. In April 2011 we conducted a survey with Brazilian MSM using Facebook to assess HIV testing preferences and acceptability of home-based testing. Among 356 previously tested, HIV-negative MSM, 47% reported a preference for home-based testing, 27% preferred clinic-based testing, and 26% had no preference. Less frequent testers and those who had considered testing but failed to test were more likely to prefer home-based testing. Close to 90% reported that they would use self-test kits; 62% and 54% said they would use home-based testing to make choices about unprotected sex with regular and new partners, respectively. Concerns included difficulty to understand the tests (32%) and receiving results alone (23%). Overall, home-based testing may appeal to MSM and result in increased testing frequency. Research on feasibility and utilization of self-tests in practice is needed.
PMCID: PMC4138047  PMID: 24896048
Male Homosexuality; HIV; Serologic Tests
9.  Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1 
Nature genetics  2007;39(6):733-740.
Allotypes of the natural killer (NK) cell receptor KIR3DL1 vary in both NK cell expression patterns and inhibitory capacity upon binding to their ligands, HLA-B Bw4 molecules, present on target cells. Using a sample size of over 1,500 human immunodeficiency virus (HIV)+ individuals, we show that various distinct allelic combinations of the KIR3DL1 and HLA-B loci significantly and strongly influence both AIDS progression and plasma HIV RNA abundance in a consistent manner. These genetic data correlate very well with previously defined functional differences that distinguish KIR3DL1 allotypes. The various epistatic effects observed here for common, distinct KIR3DL1 and HLA-B Bw4 combinations are unprecedented with regard to any pair of genetic loci in human disease, and indicate that NK cells may have a critical role in the natural history of HIV infection.
doi:10.1038/ng2035
PMCID: PMC4135476  PMID: 17496894
10.  Can Male Circumcision Have an Impact on the HIV Epidemic in Men Who Have Sex with Men? 
PLoS ONE  2014;9(7):e102960.
Background
Three trials have demonstrated the prophylactic effect of male circumcision (MC) for HIV acquisition among heterosexuals, and MC interventions are underway throughout sub-Saharan Africa. Similar efforts for men who have sex with men (MSM) are stymied by the potential for circumcised MSM to acquire HIV easily through receptive sex and transmit easily through insertive sex. Existing work suggests that MC for MSM should reach its maximum potential in settings where sexual role segregation is historically high and relatively stable across the lifecourse; HIV incidence among MSM is high; reported willingness for prophylactic circumcision is high; and pre-existing circumcision rates are low. We aim to identify the likely public health impact that MC interventions among MSM would have in one setting that fulfills these conditions—Peru—as a theoretical upper bound for their effectiveness among MSM generally.
Methods and Findings
We use a dynamic, stochastic sexual network model based in exponential-family random graph modeling and parameterized from multiple behavioral surveys of Peruvian MSM. We consider three enrollment criteria (insertive during 100%, >80% or >60% of UAI) and two levels of uptake (25% and 50% of eligible men); we explore sexual role proportions from two studies and different frequencies of switching among role categories. Each scenario is simulated 10 times. We estimate that efficiency could reach one case averted per 6 circumcisions. However, the population-level impact of an optimistic MSM-MC intervention in this setting would likely be at most ∼5–10% incidence and prevalence reductions over 25 years.
Conclusions
Roll-out of MC for MSM in Peru would not result in a substantial reduction in new HIV infections, despite characteristics in this population that could maximize such effects. Additional studies are needed to confirm these results for other MSM populations, and providers may consider the individual health benefits of offering MC to their MSM patients.
doi:10.1371/journal.pone.0102960
PMCID: PMC4116164  PMID: 25076493
11.  Risk Behavior among Women enrolled in a Randomized Controlled Efficacy Trial of an Adenoviral Vector Vaccine to Prevent HIV Acquisition: the Step Study 
AIDS (London, England)  2013;27(11):1763-1770.
Objectives
Report of risk behavior, HIV incidence, and pregnancy rates among women participating in the Step Study, a phase IIB trial of MRKAd5 HIV-1 gag/pol/nef vaccine in HIV-negative individuals who were at high risk of HIV-1.
Design
Prospective multicenter, double-blinded, placebo-controlled trial
Methods
Women were from North American (NA) and Caribbean and South America (CSA) sites. Risk behavior was collected at screening and 6-month intervals. Differences in characteristics between groups were tested with Chi-square, two-sided Fisher’s exact tests, and Wilcoxon rank sum tests. Generalized estimating equation models were used to assess behavioral change.
Results
Among 1134 enrolled women, the median number of male partners was 18; 73.8% reported unprotected vaginal sex, 15.9% unprotected anal sex and 10.8% evidence of a sexually transmitted infection in the 6 months prior to baseline. With 3344 person-years (p–y) of follow up, there were 15 incident HIV infections: incidence rate was 0.45 per 100/p-y (95% CI 0.25, 0.74). Crack cocaine use in both regions (relative risk [RR]=2.4 [1.7,3.3]) and in CSA, unprotected anal sex (RR=6.4 [3.8. 10.7]) and drug use (RR=4.1 [2.1, 8.0]) were baseline risk behaviors associated with HIV acquisition. There was a marked reduction in risk behaviors after study enrollment with some recurrence in unprotected vaginal sex. Of 963 non-sterilized women, 304 (31.6%) became pregnant.
Conclusions
Crack cocaine use and unprotected anal sex are important risk criteria to identify high-risk women for HIV efficacy trials. Pregnancy during the trial was a common occurrence and needs to be considered in trial planning for prevention trials in women.
doi:10.1097/QAD.0b013e328360c83e
PMCID: PMC3918499  PMID: 23807272
12.  Integrated Strategies for Combination HIV Prevention: Principles and examples for men who have sex with men in the Americas and heterosexual African populations 
Combination HIV prevention is a high priority for increasing the impact of partially efficacious HIV prevention interventions for specific populations and settings. Developing the package requires critical review of local epidemiology of HIV infection regarding populations most impacted and most at risk, drivers of HIV infection, and available interventions to address these risk factors. Interventions should be considered in terms of the evidence basis for efficacy, potential synergies, feasibility of delivery at scale, which is important in order to achieve high coverage and impact, coupled with high acceptability to populations, which will impact uptake, adherence, and retention. Evaluation requires process measures of uptake, adherence, retention, and outcome measures of reduction in HIV infectiousness and acquisition. Three examples of combination prevention concepts are summarized for men who have sex with men (MSM) in the Americas, young women in sub-Saharan Africa, and HIV-1 serodiscordant couples.
doi:10.1097/QAI.0b013e3182986f3a
PMCID: PMC3708491  PMID: 23764638
Combination HIV prevention; integrated prevention; men who have sex with men; young women in Africa; HIV-1 serodiscordant couples
13.  HIV Diversity as a Biomarker for HIV Incidence Estimation: Including a High-Resolution Melting Diversity Assay in a Multiassay Algorithm 
Journal of Clinical Microbiology  2014;52(1):115-121.
Multiassay algorithms (MAAs) can be used to estimate cross-sectional HIV incidence. We previously identified a robust MAA that includes the BED capture enzyme immunoassay (BED-CEIA), the Bio-Rad Avidity assay, viral load, and CD4 cell count. In this report, we evaluated MAAs that include a high-resolution melting (HRM) diversity assay that does not require sequencing. HRM scores were determined for eight regions of the HIV genome (2 in gag, 1 in pol, and 5 in env). The MAAs that were evaluated included the BED-CEIA, the Bio-Rad Avidity assay, viral load, and the HRM diversity assay, using HRM scores from different regions and a range of region-specific HRM diversity assay cutoffs. The performance characteristics based on the proportion of samples that were classified as MAA positive by duration of infection were determined for each MAA, including the mean window period. The cross-sectional incidence estimates obtained using optimized MAAs were compared to longitudinal incidence estimates for three cohorts in the United States. The performance of the HRM-based MAA was nearly identical to that of the MAA that included CD4 cell count. The HRM-based MAA had a mean window period of 154 days and provided cross-sectional incidence estimates that were similar to those based on cohort follow-up. HIV diversity is a useful biomarker for estimating HIV incidence. MAAs that include the HRM diversity assay can provide accurate HIV incidence estimates using stored blood plasma or serum samples without a requirement for CD4 cell count data.
doi:10.1128/JCM.02040-13
PMCID: PMC3911463  PMID: 24153134
14.  A Comparison of Two Measures of HIV Diversity in Multi-Assay Algorithms for HIV Incidence Estimation 
PLoS ONE  2014;9(6):e101043.
Background
Multi-assay algorithms (MAAs) can be used to estimate HIV incidence in cross-sectional surveys. We compared the performance of two MAAs that use HIV diversity as one of four biomarkers for analysis of HIV incidence.
Methods
Both MAAs included two serologic assays (LAg-Avidity assay and BioRad-Avidity assay), HIV viral load, and an HIV diversity assay. HIV diversity was quantified using either a high resolution melting (HRM) diversity assay that does not require HIV sequencing (HRM score for a 239 base pair env region) or sequence ambiguity (the percentage of ambiguous bases in a 1,302 base pair pol region). Samples were classified as MAA positive (likely from individuals with recent HIV infection) if they met the criteria for all of the assays in the MAA. The following performance characteristics were assessed: (1) the proportion of samples classified as MAA positive as a function of duration of infection, (2) the mean window period, (3) the shadow (the time period before sample collection that is being assessed by the MAA), and (4) the accuracy of cross-sectional incidence estimates for three cohort studies.
Results
The proportion of samples classified as MAA positive as a function of duration of infection was nearly identical for the two MAAs. The mean window period was 141 days for the HRM-based MAA and 131 days for the sequence ambiguity-based MAA. The shadows for both MAAs were <1 year. Both MAAs provided cross-sectional HIV incidence estimates that were very similar to longitudinal incidence estimates based on HIV seroconversion.
Conclusions
MAAs that include the LAg-Avidity assay, the BioRad-Avidity assay, HIV viral load, and HIV diversity can provide accurate HIV incidence estimates. Sequence ambiguity measures obtained using a commercially-available HIV genotyping system can be used as an alternative to HRM scores in MAAs for cross-sectional HIV incidence estimation.
doi:10.1371/journal.pone.0101043
PMCID: PMC4072769  PMID: 24968135
15.  Syphilis Predicts HIV Incidence Among Men and Transgender Women Who Have Sex With Men in a Preexposure Prophylaxis Trial 
Syphilis infection was associated with HIV incidence in an HIV-prevention trial that randomized participants to once-daily emtricitabine/tenofovir (FTC/TDF) vs placebo. FTC/TDF had no effect on the association between incident syphilis and HIV acquisition; syphilis infection did not decrease FTC/TDF efficacy.
Background. Syphilis infection may potentiate transmission of human immunodeficiency virus (HIV). We sought to determine the extent to which HIV acquisition was associated with syphilis infection within an HIV preexposure prophylaxis (PrEP) trial and whether emtricitabine/tenofovir (FTC/TDF) modified that association.
Methods. The Preexposure Prophylaxis Initiative (iPrEx) study randomly assigned 2499 HIV-seronegative men and transgender women who have sex with men (MSM) to receive oral daily FTC/TDF or placebo. Syphilis prevalence at screening and incidence during follow-up were measured. Hazard ratios for the effect of incident syphilis on HIV acquisition were calculated. The effect of FTC/TDF on incident syphilis and HIV acquisition was assessed.
Results. Of 2499 individuals, 360 (14.4%) had a positive rapid plasma reagin test at screening; 333 (92.5%) had a positive confirmatory test, which did not differ between the arms (FTC/TDF vs placebo, P = .81). The overall syphilis incidence during the trial was 7.3 cases per 100 person-years. There was no difference in syphilis incidence between the study arms (7.8 cases per 100 person-years for FTC/TDF vs 6.8 cases per 100 person-years for placebo, P = .304). HIV incidence varied by incident syphilis (2.8 cases per 100 person-years for no syphilis vs 8.0 cases per 100 person-years for incident syphilis), reflecting a hazard ratio of 2.6 (95% confidence interval, 1.6–4.4; P < .001). There was no evidence for interaction between randomization to the FTC/TDF arm and incident syphilis on HIV incidence.
Conclusions. In HIV-seronegative MSM, syphilis infection was associated with HIV acquisition in this PrEP trial; a syphilis diagnosis should prompt providers to offer PrEP unless otherwise contraindicated.
doi:10.1093/cid/ciu450
PMCID: PMC4166980  PMID: 24928295
chemoprophylaxis; HIV prevention; MSM; preexposure prophylaxis; syphilis
16.  Efficacy Trial of a DNA/rAd5 HIV-1 Preventive Vaccine 
The New England journal of medicine  2013;369(22):2083-2092.
Background
A safe and effective vaccine for the prevention of human immunodeficiency virus type 1 (HIV-1) infection is a global priority. We tested the efficacy of a DNA prime–recombinant adenovirus type 5 boost (DNA/rAd5) vaccine regimen in persons at increased risk for HIV-1 infection in the United States.
Methods
At 21 sites, we randomly assigned 2504 men or transgender women who have sex with men to receive the DNA/rAd5 vaccine (1253 participants) or placebo (1251 participants). We assessed HIV-1 acquisition from week 28 through month 24 (termed week 28+ infection), viral-load set point (mean plasma HIV-1 RNA level 10 to 20 weeks after diagnosis), and safety. The 6-plasmid DNA vaccine (expressing clade B Gag, Pol, and Nef and Env proteins from clades A, B, and C) was administered at weeks 0, 4, and 8. The rAd5 vector boost (expressing clade B Gag-Pol fusion protein and Env glycoproteins from clades A, B, and C) was administered at week 24.
Results
In April 2013, the data and safety monitoring board recommended halting vaccinations for lack of efficacy. The primary analysis showed that week 28+ infection had been diagnosed in 27 participants in the vaccine group and 21 in the placebo group (vaccine efficacy, −25.0%; 95% confidence interval, −121.2 to 29.3; P = 0.44), with mean viral-load set points of 4.46 and 4.47 HIV-1 RNA log10 copies per milliliter, respectively. Analysis of all infections during the study period (41 in the vaccine group and 31 in the placebo group) also showed lack of vaccine efficacy (P = 0.28). The vaccine regimen had an acceptable side-effect profile.
Conclusions
The DNA/rAd5 vaccine regimen did not reduce either the rate of HIV-1 acquisition or the viral-load set point in the population studied. (Funded by the National Institute of Allergy and Infectious Diseases; ClinicalTrials.gov number, NCT00865566.)
doi:10.1056/NEJMoa1310566
PMCID: PMC4030634  PMID: 24099601
17.  Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic 
PLoS Genetics  2014;10(4):e1004295.
HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the extent and phenotypic impact of this phenomenon in an immunogenetically diverse population, we genotypically and functionally compared linked HLA and HIV (Gag/Nef) sequences from 358 historic (1979–1989) and 382 modern (2000–2011) specimens from four key cities in the North American epidemic (New York, Boston, San Francisco, Vancouver). Inferred HIV phylogenies were star-like, with approximately two-fold greater mean pairwise distances in modern versus historic sequences. The reconstructed epidemic ancestral (founder) HIV sequence was essentially identical to the North American subtype B consensus. Consistent with gradual diversification of a “consensus-like” founder virus, the median “background” frequencies of individual HLA-associated polymorphisms in HIV (in individuals lacking the restricting HLA[s]) were ∼2-fold higher in modern versus historic HIV sequences, though these remained notably low overall (e.g. in Gag, medians were 3.7% in the 2000s versus 2.0% in the 1980s). HIV polymorphisms exhibiting the greatest relative spread were those restricted by protective HLAs. Despite these increases, when HIV sequences were analyzed as a whole, their total average burden of polymorphisms that were “pre-adapted” to the average host HLA profile was only ∼2% greater in modern versus historic eras. Furthermore, HLA-associated polymorphisms identified in historic HIV sequences were consistent with those detectable today, with none identified that could explain the few HIV codons where the inferred epidemic ancestor differed from the modern consensus. Results are therefore consistent with slow HIV adaptation to HLA, but at a rate unlikely to yield imminent negative implications for cellular immunity, at least in North America. Intriguingly, temporal changes in protein activity of patient-derived Nef (though not Gag) sequences were observed, suggesting functional implications of population-level HIV evolution on certain viral proteins.
Author Summary
Upon HIV transmission, many – though not all – immune escape mutations selected in the previous host will revert to the consensus residue. The persistence of certain escape mutations following transmission has led to concerns that these could gradually accumulate in circulating HIV sequences over time, thereby undermining host antiviral immune potential as the epidemic progresses. As certain immune-driven mutations reduce viral fitness, their spread through the population could also have consequences for the average replication capacity and/or protein function of circulating HIV sequences. Here, we characterized HIV sequences, linked to host immunogenetic information, from patients enrolled in historic (1979–1989) and modern (2000–2011) HIV cohorts from four key cities in the North American epidemic. We reconstructed the epidemic's ancestral (founder) HIV sequence and assessed the subsequent extent to which known HIV immune escape mutations have spread in the population. Our data support the gradual spread of many - though not all - immune escape mutations in HIV sequences over time, but to an extent that is unlikely to have major immediate immunologic consequences for the North American epidemic. Notably, in vitro assessments of ancestral and patient-derived HIV sequences suggested functional implications of ongoing HIV evolution for certain viral proteins.
doi:10.1371/journal.pgen.1004295
PMCID: PMC3998893  PMID: 24762668
18.  HIV-1 Drug Resistance in the iPrEx Preexposure Prophylaxis Trial 
The Journal of Infectious Diseases  2014;210(8):1217-1227.
Background. The iPrEx study demonstrated that combination oral emtricitabine and tenofovir disoproxil fumarate (FTC/TDF) as preexposure prophylaxis (PrEP) protects against HIV acquisition in men who have sex with men and transgender women. Selection for drug resistance could offset PrEP benefits.
Methods. Phenotypic and genotypic clinical resistance assays characterized major drug resistant mutations. Minor variants with FTC/TDF mutations K65R, K70E, M184V/I were measured using 454 deep sequencing and a novel allele-specific polymerase chain reaction (AS-PCR) diagnostic tolerant to sequence heterogeneity.
Results. Control of primer-binding site heterogeneity resulted in improved accuracy of minor variant measurements by AS-PCR. Of the 48 on-study infections randomized to FTC/TDF, none showed FTC/TDF mutations by clinical assays despite detectable drug levels in 8 participants. Two randomized to FTC/TDF had minor variant M184I detected at 0.53% by AS-PCR or 0.75% by deep sequencing, only 1 of which had low but detectable drug levels. Among those with acute infection at randomization to FTC/TDF, M184V or I mutations that were predominant at seroconversion waned to background levels within 24 weeks after discontinuing drug.
Conclusions. Drug resistance was rare in iPrEx on-study FTC/TDF-randomized seroconverters, and only as low-frequency minor variants. FTC resistance among those initiating PrEP with acute infection waned rapidly after drug discontinuation.
Clinical Trials Registration. NCT00458393.
doi:10.1093/infdis/jiu233
PMCID: PMC4176446  PMID: 24740633
454 deep sequencing; AS-PCR; drug resistance; HIV-1; minor variant; preexposure prophylaxis; PrEP; FTC/TDF
19.  The HVTN503/Phambili HIV vaccine trial: a comparison of younger and older participants 
By comparing younger to older participants enrolled in a HIV vaccine efficacy trial, we aimed to gain insights into the inclusion of adolescents in future trials. This was a sub-analysis of a multisite HIV vaccine randomized clinical trial in South Africa, conducted January-September, 2007. Motivations for trial enrollment, social harms, adverse events, and loss to follow-up were compared between younger (18-20 years old) and older participants (21-35 years old). Both younger (n=238) and older participants (n=563) were equally likely to report enrolling for altruistic reasons. Younger females were less likely than older participants to join for trial reimbursement (p=0.005), while younger males were more likely to enroll because the vaccine may provide protection from HIV-acquisition (p<0.001). There were no significant differences in the number of social harms reported. Compared to males over 20 years-old, 18-20-year-old females were less likely to experience adverse events (OR=0.1, CI 0.01-0.80) and no more likely to be lost to follow up (OR=0.7, CI 0.39-1.25), while 18-20-year-old males were no more likely to experience adverse events (OR=1.3, CI 0.58-2.83) or loss to follow-up (OR=0.8, CI 0.51-1.41). Our data support the inclusion of younger participants who are at risk for HIV in future HIV vaccine efficacy trials.
doi:10.1177/0956462413506892
PMCID: PMC3968181  PMID: 24104693
HIV; vaccine trials; clinical trials; youth; South Africa
20.  LILRB2 Interaction with HLA Class I Correlates with Control of HIV-1 Infection 
PLoS Genetics  2014;10(3):e1004196.
Natural progression of HIV-1 infection depends on genetic variation in the human major histocompatibility complex (MHC) class I locus, and the CD8+ T cell response is thought to be a primary mechanism of this effect. However, polymorphism within the MHC may also alter innate immune activity against human immunodeficiency virus type 1 (HIV-1) by changing interactions of human leukocyte antigen (HLA) class I molecules with leukocyte immunoglobulin-like receptors (LILR), a group of immunoregulatory receptors mainly expressed on myelomonocytic cells including dendritic cells (DCs). We used previously characterized HLA allotype-specific binding capacities of LILRB1 and LILRB2 as well as data from a large cohort of HIV-1-infected individuals (N = 5126) to test whether LILR-HLA class I interactions influence viral load in HIV-1 infection. Our analyses in persons of European descent, the largest ethnic group examined, show that the effect of HLA-B alleles on HIV-1 control correlates with the binding strength between corresponding HLA-B allotypes and LILRB2 (p = 10−2). Moreover, overall binding strength of LILRB2 to classical HLA class I allotypes, defined by the HLA-A/B/C genotypes in each patient, positively associates with viral replication in the absence of therapy in patients of both European (p = 10−11–10−9) and African (p = 10−5–10−3) descent. This effect appears to be driven by variations in LILRB2 binding affinities to HLA-B and is independent of individual class I allelic effects that are not related to the LILRB2 function. Correspondingly, in vitro experiments suggest that strong LILRB2-HLA binding negatively affects antigen-presenting properties of DCs. Thus, we propose an impact of LILRB2 on HIV-1 disease outcomes through altered regulation of DCs by LILRB2-HLA engagement.
Author Summary
Leukocyte immunoglobulin-like receptors B1 and B2 (LILRB1 and LILRB2) bind HLA class I allotypes with variable affinities. Here, we show that the binding strength of LILRB2 to HLA class I positively associates with level of viremia in a large cohort of untreated HIV-1-infected patients. This effect appears to be driven by HLA-B polymorphism and demonstrates independence from class I allelic effects on viral load. Our in vitro experiments suggest that strong LILRB2-HLA binding negatively affects antigen-presenting properties of dendritic cells (DCs). Thus, we propose an impact of LILRB2 on HIV-1 immune control through altered regulation of DCs by LILRB2-HLA engagement.
doi:10.1371/journal.pgen.1004196
PMCID: PMC3945438  PMID: 24603468
21.  Early Experiences Implementing Pre-exposure Prophylaxis (PrEP) for HIV Prevention in San Francisco 
PLoS Medicine  2014;11(3):e1001613.
Albert Liu and colleagues report early experiences with uptake and delivery of pre-exposure prophylaxis(PrEP)for HIV prevention in three different settings in San Francisco. PrEP can be an important component of a comprehensive HIV prevention program and can complement efforts to increase HIV testing, linkage to care, and early initiation of antiretroviral therapy.
Please see later in the article for the Editors' Summary
doi:10.1371/journal.pmed.1001613
PMCID: PMC3942317  PMID: 24595035
23.  Concomitant Socioeconomic, Behavioral, and Biological Factors Associated with the Disproportionate HIV Infection Burden among Black Men Who Have Sex with Men in 6 U.S. Cities 
PLoS ONE  2014;9(1):e87298.
Background
American Black men who have sex with men (MSM) are disproportionately affected by HIV, but the factors associated with this concentrated epidemic are not fully understood.
Methods
Black MSM were enrolled in 6 US cities to evaluate a multi-component prevention intervention, with the current analysis focusing on the correlates of being newly diagnosed with HIV compared to being HIV-uninfected or previously diagnosed with HIV.
Results
HPTN 061 enrolled 1553 Black MSM whose median age was 40; 30% self-identified exclusively as gay or homosexual, 29% exclusively as bisexual, and 3% as transgender. About 1/6th (16.2%) were previously diagnosed with HIV (PD); of 1263 participants without a prior HIV diagnosis 7.6% were newly diagnosed (ND). Compared to PD, ND Black MSM were younger (p<0.001); less likely to be living with a primary partner (p<0.001); more likely to be diagnosed with syphilis (p<0.001), rectal gonorrhea (p = 0.011) or chlamydia (p = 0.020). Compared to HIV-uninfected Black MSM, ND were more likely to report unprotected receptive anal intercourse (URAI) with a male partner in the last 6 months (p<0.001); and to be diagnosed with syphilis (p<0.001), rectal gonorrhea (p = 0.004), and urethral (p = 0.025) or rectal chlamydia (p<0.001). They were less likely to report female (p = 0.002) or transgender partners (p = 0.018). Multivariate logistic regression analyses found that ND Black MSM were significantly more likely than HIV-uninfected peers to be unemployed; have STIs, and engage in URAI. Almost half the men in each group were poor, had depressive symptoms, and expressed internalized homophobia.
Conclusions
ND HIV-infected Black MSM were more likely to be unemployed, have bacterial STIs and engage in URAI than other Black MSM. Culturally-tailored programs that address economic disenfranchisement, increase engagement in care, screen for STIs, in conjunction with safer sex prevention interventions, may help to decrease further transmission in this heavily affected community.
doi:10.1371/journal.pone.0087298
PMCID: PMC3909083  PMID: 24498067
24.  HIV Incidence Determination in the United States: A Multiassay Approach 
The Journal of Infectious Diseases  2012;207(2):232-239.
Background. Accurate testing algorithms are needed for estimating human immunodeficiency virus (HIV) incidence from cross-sectional surveys.
Methods. We developed a multiassay algorithm (MAA) for HIV incidence that includes the BED capture enzyme immunoassay (BED-CEIA), an antibody avidity assay, HIV load, and CD4+ T-cell count. We analyzed 1782 samples from 709 individuals in the United States who had a known duration of HIV infection (range, 0 to >8 years). Logistic regression with cubic splines was used to compare the performance of the MAA to the BED-CEIA and to determine the window period of the MAA. We compared the annual incidence estimated with the MAA to the annual incidence based on HIV seroconversion in a longitudinal cohort.
Results. The MAA had a window period of 141 days (95% confidence interval [CI], 94–150) and a very low false-recent misclassification rate (only 0.4% of 1474 samples from subjects infected for >1 year were misclassified as indicative of recent infection). In a cohort study, annual incidence based on HIV seroconversion was 1.04% (95% CI, .70%–1.55%). The incidence estimate obtained using the MAA was essentially identical: 0.97% (95% CI, .51%–1.71%).
Conclusions. The MAA is as sensitive for detecting recent HIV infection as the BED-CEIA and has a very low rate of false-recent misclassification. It provides a powerful tool for cross-sectional HIV incidence determination.
doi:10.1093/infdis/jis659
PMCID: PMC3532826  PMID: 23129760
HIV; incidence testing; United States; epidemiology
25.  Strong Relationship between Oral Dose and Tenofovir Hair Levels in a Randomized Trial: Hair as a Potential Adherence Measure for Pre-Exposure Prophylaxis (PrEP) 
PLoS ONE  2014;9(1):e83736.
Background
Pre-exposure prophylaxis (PrEP) trials using tenofovir-based regimens have demonstrated that high levels of adherence are required to evaluate efficacy; the incorporation of objective biomarkers of adherence in trial design has been essential to interpretation, given the inaccuracy of self-report. Antiretroviral measurements in scalp hair have been useful as a marker of long-term exposure in the HIV treatment setting, and hair samples are relatively easy and inexpensive to collect, transport, and store for analysis. To evaluate the relationship between dose and tenofovir concentrations in hair, we examined the dose proportionality of tenofovir in hair in healthy, HIV-uninfected adults.
Methods
A phase I, crossover pharmacokinetic study was performed in 24 HIV-negative adults receiving directly-observed oral tenofovir tablets administered 2, 4, and 7 doses/week for 6 weeks, with a ≥3-week break between periods. Small samples of hair were collected after each six-week period and analyzed for tenofovir concentrations. Geometric-mean-ratios compared levels between each pair of dosing conditions. Intensive plasma pharmacokinetic studies were performed during the daily-dosing period to calculate areas-under-the-time-concentration curves (AUCs).
Results
Over 90% of doses were observed per protocol. Median tenofovir concentrations in hair increased monotonically with dose. A log-linear relationship was seen between dose and hair levels, with an estimated 76% (95% CI 60–93%) increase in hair level per 2-fold dose increase. Tenofovir plasma AUCs modestly predicted drug concentrations in hair.
Conclusions
This study found a strong linear relationship between frequency of dosing and tenofovir levels in scalp hair. The analysis of quantitative drug levels in hair has the potential to improve adherence measurement in the PrEP field and may be helpful in determining exposure thresholds for protection and explaining failures in PrEP trials. Hair measures for adherence monitoring may also facilitate adherence measurement in real-world settings and merit further investigation in upcoming PrEP implementation studies and programs.
Trial Registration
ClinicalTrials.gov +NCT00903084.
doi:10.1371/journal.pone.0083736
PMCID: PMC3885443  PMID: 24421901

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