Impact of the Analytical Approach on the Reliability of MRI-Based Assessment of Hepatic Fat Content.

MRI is a popular noninvasive method for the assessment of liver fat content. After MRI scan acquisition, there is currently no standardized image analysis procedure for the most accurate estimate of liver fat content. We determined intraindividual reliability of MRI-based liver fat measurement using 10 different MRI slice analysis methods in normal-weight, overweight, and obese individuals who underwent 2 same-day abdominal MRI scans. We also compared the agreement in liver fat content between analytical methods and assessed the variability in fat content across the entire liver. Our results indicate that liver fat content varies across the liver, with some slices averaging 54% lower and others 75% higher fat content than the mean of all slices (gold standard). Our data suggest that the entire liver should be contoured on at least every 10th slice to achieve close agreement with the gold standard.

Consuming glucose-sweetened, not fructose-sweetened, beverages increases fasting insulin in healthy humans.

Fructose-, compared to glucose-, sweetened beverages increase liver triglyceride content in the short-term, prior to weight gain. In secondary analyses of a randomized cross-over design study during which 24 healthy adults consumed 25% of their estimated energy requirement in the form of glucose-, fructose-, and high-fructose corn syrup-sweetened beverages in addition to an identical ad libitum diet for three periods of 8 days each, we investigated the hypothesis that fructose in sweetened beverages also triggers insulin resistance in the short term. Total energy intake, body weight, and fasting glucose did not differ among diet phases. However, there was a significant trend for higher fasting insulin (p = 0.042 for trend) and, among normal-weight participants, homeostasis model assessment index of insulin resistance (p = 0.034 for diet × adiposity interaction) according to the glucose content of the beverages. In conclusion, in contrast to our hypothesis, insulin resistance was increased with higher glucose vs. fructose content of the beverages in this short-term trial.

Intraindividual Variation in Markers of Intestinal Permeability and Adipose Tissue Inflammation in Healthy Normal-Weight to Obese Adults.

BACKGROUND: Intestinal permeability and adipose tissue inflammation are considered mechanistic links in the relationship between diet, obesity, and chronic disease. However, methods to measure both are not well standardized, and the reliability of commonly used measures is not known. METHODS: We calculated the intraclass correlation coefficient (ICC) for several common measures of intestinal permeability and adipose tissue inflammation from a randomized clinical trial of cross-over design in which normal-weight (n = 12) or overweight/obese (n = 12) individuals each completed three 8-day dietary intervention periods. RESULTS: For biomarkers of intestinal permeability, plasma zonulin, and lipopolysaccharide-binding protein, ICCs were "excellent" (i.e., >0.9). The direct measure of intestinal permeability, the lactulose/mannitol test, exhibited "fair" reliability (ICC = 0.53). A wider range of ICCs (0.6-0.9), suggesting "good" to "excellent" reliability, were obtained for measures of adipose tissue expression of genes encoding major mediators of inflammation. Similarly, individual immune cell populations isolated from adipose tissue, expressed as a percentage of all CD45+ cells, also had "good" to "excellent" ICCs. However, when these populations were expressed as number of cells per gram of tissue, ICC values were "fair," falling below 0.6. CONCLUSIONS: Due to the repeated measures design, our study offered a unique opportunity to assess reliability of commonly used biomarkers of intestinal permeability and adipose tissue inflammation. Our findings suggest that these measures were generally highly reliable in the short-term. IMPACT: Along with other factors, particularly validity, the demonstrated reliabilities can help inform the choice of endpoints in studies of intestinal permeability and adipose tissue inflammation.

Stress Among Latinos: Does it Vary by Occupation and Agricultural Season?

OBJECTIVE: Stress is pervasive among Latino immigrants. We identified seasonal and occupational patterns in stress among rural Latino immigrants. METHODS: During three agricultural periods, farmworker and non-farmworker participants responded to a 24-item stress questionnaire (Snipes et al, 2007). We measured the associations of stress with occupation, with season, and occupation within season, adjusting for demographic variables. RESULTS: The highest levels of stress were observed in the pre-thinning season when pruning takes place among farmworkers. Stress is significantly higher in farmworkers compared with non-farmworkers only in the non-spray season when crops are dormant. Higher income was associated with decreased stress in the pre-thinning and thinning seasons when buds and small fruit are removed from orchards. CONCLUSIONS: Identification of strategies to reduce stress in Latino migrants is warranted. Although some sources of stress may be intractable, others may be amenable to intervention.

Results of a randomized controlled trial to increase cervical cancer screening among rural Latinas.

BACKGROUND: Latinas have the highest rates of cervical cancer in the United States and the second highest rate of cervical cancer mortality. One factor in the disparity is the relatively low rate of screening for cervical cancer in this population. METHODS: Eligible women who were out of adherence with cervical cancer screening (>3 years since their last Papanicolaou [Pap] test) were identified via medical record review by a federally qualified local health center. The effects of a low-intensity intervention (video delivered to participants' homes; n = 150) and a high-intensity intervention (video plus a home-based educational session; n = 146) on cervical cancer screening uptake in comparison with a control arm (usual care; n = 147) were investigated. A cost-effectiveness analysis of the interventions was conducted: all intervention costs were calculated, and the incremental cost-effectiveness ratio was computed. Finally, women with positive Pap tests were provided navigation by a community health educator to ensure that they received follow-up care. RESULTS: A total of 443 Latinas participated. Seven months after randomization, significantly more women in the high-intensity arm received a Pap test (53.4%) in comparison with the low-intensity arm (38.7%; P < .001) and the usual-care arm (34.0%; P < .01). The incremental cost-effectiveness ratio for high-intensity women versus the control group amounted to $4.24. Twelve women had positive Pap tests, which encompassed diagnoses ranging from atypical squamous cells of unknown significance to invasive cancer; these women received navigation for follow-up care. CONCLUSIONS: A culturally appropriate, in-home, promotora-led educational intervention was successful in increasing cervical cancer screening among Latinas. Cancer 2017;123:666-674. © 2016 American Cancer Society.

No differential effect of beverages sweetened with fructose, high-fructose corn syrup, or glucose on systemic or adipose tissue inflammation in normal-weight to obese adults: a randomized controlled trial.

BACKGROUND: Sugar-sweetened beverage (SSB) consumption and low-grade chronic inflammation are both independently associated with type 2 diabetes and cardiovascular disease. Fructose, a major component of SSBs, may acutely trigger inflammation, which may be one link between SSB consumption and cardiometabolic disease. OBJECTIVE: We sought to determine whether beverages sweetened with fructose, high-fructose corn syrup (HFCS), and glucose differentially influence systemic inflammation [fasting plasma C-reactive protein and interleukin-6 (IL-6) as primary endpoints] acutely and before major changes in body weight. Secondary endpoints included adipose tissue inflammation, intestinal permeability, and plasma fetuin-A as potential mechanistic links between fructose intake and low-grade inflammation. DESIGN: We conducted a randomized, controlled, double-blind, crossover design dietary intervention (the Diet and Systemic Inflammation Study) in 24 normal-weight to obese adults without fructose malabsorption. Participants drank 4 servings/d of fructose-, glucose-, or HFCS-sweetened beverages accounting for 25% of estimated calorie requirements while consuming a standardized diet ad libitum for three 8-d periods. RESULTS: Subjects consumed 116% of their estimated calorie requirement while drinking the beverages with no difference in total energy intake or body weight between groups as reported previously. Fasting plasma concentrations of C-reactive protein and IL-6 did not differ significantly at the end of the 3 diet periods. We did not detect a consistent differential effect of the diets on measures of adipose tissue inflammation except for adiponectin gene expression in adipose tissue (P = 0.005), which was lowest after the glucose phase. We also did not detect consistent evidence of a differential impact of these sugars on measures of intestinal permeability (lactulose:mannitol test, plasma zonulin, and plasma lipopolysaccharide-binding protein). CONCLUSION: Excessive amounts of fructose, HFCS, and glucose from SSBs consumed over 8 d did not differentially affect low-grade chronic systemic inflammation in normal-weight to obese adults. This trial was registered at clinicaltrials.gov as NCT01424306.

A Pilot Study of Raltegravir Plus Combination Antiretroviral Therapy in Early Human Immunodeficiency Virus Infection: Challenges and Lessons Learned.

Availability of integrase strand transfer inhibitors created interest in determining whether their use would decrease persistently infected cell numbers. This study hypothesized that adding raltegravir (RAL) to standard antiretroviral therapy (ART) would decrease human immunodeficiency virus (HIV)-infected CD4(+) T cells more than standard combination ART. This was a pilot, randomized study comparing open-label standard triple ART to standard triple ART plus RAL over 96 weeks in ART-naive adults with early HIV infection. The primary objective was to compare quantity and trajectory of HIV DNA. Eighty-two persons were referred. A diverse set of reasons precluded the enrollment of all but 10. Those who enrolled and completed the study had an estimated median duration of HIV infection of 74 days at ART start. The groups had similar baseline characteristics. The RAL group had more rapid first phase plasma HIV RNA decay (0.67 log10 copies/mL/day) than with combination ART (0.34 log10copies/mL/day), p = 0.037. Second phase HIV RNA decay, residual viremia, cell-associated RNA, HIV DNA, CD4(+) T-cells with replication-competent virus, and 2LTR circle levels did not differ between groups. Among those with entry plasma HIV RNA levels above the median, 2LTR circles were significantly lower over time than in those with lower entry HIV RNA levels (p = 0.02). Our results suggest homogeneity of responses in cell-associated RNA, HIV DNA, CD4(+) T-cells with replication-competent virus, and 2LTR circles with early HIV in both ART groups. The kinetics of 2LTR DNA did not reflect the kinetics of plasma HIV RNA decline following ART initiation.

Symmetric Directional False Discovery Rate Control.

This research is motivated from the analysis of a real gene expression data that aims to identify a subset of "interesting" or "significant" genes for further studies. When we blindly applied the standard false discovery rate (FDR) methods, our biology collaborators were suspicious or confused, as the selected list of significant genes was highly unbalanced: there were ten times more under-expressed genes than the over-expressed genes. Their concerns led us to realize that the observed two-sample t-statistics were highly skewed and asymmetric, and thus the standard FDR methods might be inappropriate. To tackle this case, we propose a symmetric directional FDR control method that categorizes the genes into "over-expressed" and "under-expressed" genes, pairs "over-expressed" and "under-expressed" genes, defines the p-values for gene pairs via column permutations, and then applies the standard FDR method to select "significant" gene pairs instead of "significant" individual genes. We compare our proposed symmetric directional FDR method with the standard FDR method by applying them to simulated data and several well-known real data sets.

No difference in ad libitum energy intake in healthy men and women consuming beverages sweetened with fructose, glucose, or high-fructose corn syrup: a randomized trial.

BACKGROUND: Increased energy intake is consistently observed in individuals consuming sugar-sweetened beverages (SSBs), likely mainly because of an inadequate satiety response to liquid calories. However, SSBs have a high content of fructose, the consumption of which acutely fails to trigger responses in key signals involved in energy homeostasis. It is unclear whether the fructose content of SSBs contributes to the increased energy intake in individuals drinking SSBs. OBJECTIVE: We investigated whether the relative amounts of fructose and glucose in SSBs modifies ad libitum energy intake over 8 d in healthy adults without fructose malabsorption. DESIGN: We conducted 2 randomized, controlled, double-blind crossover studies to compare the effects of consuming 4 servings/d of a fructose-, glucose-, or aspartame-sweetened beverage (study A; n = 9) or a fructose-, glucose-, or high-fructose corn syrup (HFCS)-sweetened beverage (study B; n = 24) for 8 d on overall energy intake. SSBs were provided at 25% of estimated energy requirement, or an equivalent volume of the aspartame-sweetened beverage, and consumption was mandatory. All solid foods were provided at 125% of estimated energy requirements and were consumed ad libitum. RESULTS: In study A, ad libitum energy intake was 120% ± 10%, 117% ± 12%, and 102% ± 15% of estimated energy requirements when subjects consumed the fructose-, glucose-, and aspartame-sweetened beverages. Energy intake was significantly higher in the fructose and glucose phases than in the aspartame phase (P < 0.003 for each), with no difference between the fructose and glucose phases (P = 0.462). In study B, total energy intake during the fructose, HFCS, and glucose phases was 116% ± 14%, 116% ± 16%, and 116% ± 16% of the subject's estimated total energy requirements (P = 0.880). CONCLUSIONS: In healthy adults, total 8-d ad libitum energy intake was increased in individuals consuming SSBs compared with aspartame-sweetened beverages. The energy overconsumption observed in individuals consuming SSBs occurred independently of the relative amounts of fructose and glucose in the beverages. These trials were registered at clinicaltrials.gov as NCT00475475 and NCT01424306.

HIV-1 shedding from the female genital tract is associated with increased Th1 cytokines/chemokines that maintain tissue homeostasis and proportions of CD8+FOXP3+ T cells.

BACKGROUND: HIV-1 shedding from the female genital tract is associated with increased sexual and perinatal transmission and has been broadly evaluated in cross-sectional studies. However, few longitudinal studies have evaluated how the immune microenvironment effects shedding. METHODS: Thirty-nine HIV-1-infected women had blood, cervicovaginal lavage, and biopsies of the uterine cervix taken quarterly for up to 5 years. Cytokines/chemokines were quantified by Luminex assay in cervicovaginal lavage, and cellular phenotypes were characterized using immunohistochemistry in cervical biopsies. Comparisons of cytokine/chemokine concentrations and the percent of tissue staining positive for T cells were compared using generalized estimating equations between non-shedding and shedding visits across all women and within a subgroup of women who intermittently shed HIV-1. RESULTS: Genital HIV-1 shedding was more common when plasma HIV-1 was detected. Cytokines associated with cell growth (interleukin-7), Th1 cells/inflammation (interleukin-12p70), and fractalkine were significantly increased at shedding visits compared with non-shedding visits within intermittent shedders and across all subjects. Within intermittent shedders and across all subjects, FOXP3 T cells were significantly decreased at shedding visits. However, there were significant increases in CD8 cells and proportions of CD8FOXP3 T cells associated with HIV-1 shedding. CONCLUSIONS: Within intermittent HIV-1 shedders, decreases in FOXP3 T cells at the shedding visit suggests that local HIV-1 replication leads to CD4 T-cell depletion, with increases in the proportion of CD8FOXP3 cells. HIV-1-infected cell loss may promote a cytokine milieu that maintains cellular homeostasis and increases immune suppressor cells in response to HIV-1 replication in the cervical tissues.

Antibodies to PfSEA-1 block parasite egress from RBCs and protect against malaria infection.

Novel vaccines are urgently needed to reduce the burden of severe malaria. Using a differential whole-proteome screening method, we identified Plasmodium falciparum schizont egress antigen-1 (PfSEA-1), a 244-kilodalton parasite antigen expressed in schizont-infected red blood cells (RBCs). Antibodies to PfSEA-1 decreased parasite replication by arresting schizont rupture, and conditional disruption of PfSEA-1 resulted in a profound parasite replication defect. Vaccination of mice with recombinant Plasmodium berghei PbSEA-1 significantly reduced parasitemia and delayed mortality after lethal challenge with the Plasmodium berghei strain ANKA. Tanzanian children with antibodies to recombinant PfSEA-1A (rPfSEA-1A) did not experience severe malaria, and Kenyan adolescents and adults with antibodies to rPfSEA-1A had significantly lower parasite densities than individuals without these antibodies. By blocking schizont egress, PfSEA-1 may synergize with other vaccines targeting hepatocyte and RBC invasion.

Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time.

BACKGROUND: Whether unique human immunodeficiency type 1 (HIV) genotypes occur in the genital tract is important for vaccine development and management of drug resistant viruses. Multiple cross-sectional studies suggest HIV is compartmentalized within the female genital tract. We hypothesize that bursts of HIV replication and/or proliferation of infected cells captured in cross-sectional analyses drive compartmentalization but over time genital-specific viral lineages do not form; rather viruses mix between genital tract and blood. METHODS: Eight women with ongoing HIV replication were studied during a period of 1.5 to 4.5 years. Multiple viral sequences were derived by single-genome amplification of the HIV C2-V5 region of env from genital secretions and blood plasma. Maximum likelihood phylogenies were evaluated for compartmentalization using 4 statistical tests. RESULTS: In cross-sectional analyses compartmentalization of genital from blood viruses was detected in three of eight women by all tests; this was associated with tissue specific clades containing multiple monotypic sequences. In longitudinal analysis, the tissues-specific clades did not persist to form viral lineages. Rather, across women, HIV lineages were comprised of both genital tract and blood sequences. CONCLUSIONS: The observation of genital-specific HIV clades only in cross-sectional analysis and an absence of genital-specific lineages in longitudinal analyses suggest a dynamic interchange of HIV variants between the female genital tract and blood.

HIV-1 RNA may decline more slowly in semen than in blood following initiation of efavirenz-based antiretroviral therapy.

OBJECTIVES: Antiretroviral therapy (ART) decreases HIV-1 RNA levels in semen and reduces sexual transmission from HIV-1-infected men. Our objective was to study the time course and magnitude of seminal HIV-1 RNA decay after initiation of efavirenz-based ART among 13 antiretroviral-naïve Kenyan men. METHODS: HIV-1 RNA was quantified (lower limit of detection, 120 copies/mL) in blood and semen at baseline and over the first month of ART. Median log(10) HIV-1 RNA was compared at each time-point using Wilcoxon Signed Rank tests. Perelson's two-phase viral decay model and nonlinear random effects were used to compare decay rates in blood and semen. RESULTS: Median baseline HIV-1 RNA was 4.40 log(10) copies/mL in blood (range, 3.20-5.08 log(10) copies/mL) and 3.69 log(10) copies/mL in semen (range, <2.08-4.90 log(10) copies/mL). The median reduction in HIV-1 RNA by day 28 was 1.90 log(10) copies/mL in blood (range, 0.56-2.68 log(10) copies/mL) and 1.36 log(10) copies/mL in semen (range, 0-2.66 log(10) copies/mL). ART led to a decrease from baseline by day 7 in blood and day 14 in semen (p = 0.005 and p = 0.006, respectively). The initial modeled decay rate was slower in semen than in blood (p = 0.06). There was no difference in second-phase decay rates between blood and semen. CONCLUSIONS: Efavirenz-based ART reduced HIV-1 RNA levels more slowly in semen than in blood. Although this difference was of borderline significance in this small study, our observations suggest that there is suboptimal suppression of seminal HIV-1 RNA for some men in the early weeks of treatment.

Do workplace and home protective practices protect farm workers? Findings from the "For Healthy Kids" study.

OBJECTIVE: To assess associations of protective workplace and home practices with pesticide exposure levels. METHODS: Using data from orchard workers in the Yakima Valley, Washington, we examined associations of workplace and home protective practices with (1) urinary metabolite concentrations of dimethylthiophosphate (DMTP) in adults and children aged 2 to 6 years and (2) azinphos-methyl levels in house and vehicle dust. RESULTS: Data were collected from 95 orchard workers and 94 children. Contrary to expectation, adult farm workers who wore boots or washed hands using hand sanitizer had higher concentrations of DMTP than those who did not. Children who attended daycare had higher DMTP concentrations than children who did not. CONCLUSIONS: Few workplace or home practices were associated with pesticide exposure levels; workers who used hand sanitizer had higher concentrations of DMTP, as did children who attended daycare.

Post-prostatic massage fluid/urine as an alternative to semen for studying male genitourinary HIV-1 shedding.

OBJECTIVES: Genitourinary tract samples are required to investigate male HIV-1 infectivity. Because semen collection is often impractical, the acceptability, feasibility and validity of post-prostatic massage fluid/urine (post-PMF/U) was evaluated for studying male genitourinary HIV-1 shedding. METHODS: HIV-1-seropositive men were evaluated after 48 h of sexual abstinence. At each visit, a clinician performed prostatic massage, then post-PMF/U and blood were collected. Participants provided semen specimens 1 week later. An audio computer-assisted self-interview (ACASI) administered after each specimen collection evaluated acceptability, adherence to instructions and recent genitourinary symptoms. HIV-1 RNA was quantified using a real-time PCR assay. Detection and quantitation of HIV-1 RNA and stability over visits were compared for semen, post-PMF/U and blood. RESULTS: Post-PMF/U was successfully obtained at 106 visits (64%) and semen at 136 visits (81%, p<0.001). In ACASI, discomfort was rated higher for post-PMF/U collection (p=0.003), but there was no significant difference in acceptability. Detection of HIV-1 RNA in post-PMF/U was associated with detection in semen (p=0.02). Semen and post-PMF/U HIV-1-RNA levels were correlated (ρ=0.657, p<0.001). Concordance of results at repeat visits was 78.9% for post-PMF/U (κ=0.519, p=0.02) and 89.5% for both blood and semen (κ=0.774, p=0.001). CONCLUSIONS: Although semen collections were more successful, both post-PMF/U and semen collections were acceptable to many participants. HIV-1 RNA detection and levels were closely associated in semen and post-PMF/U, and results were relatively stable across visits. To assess male HIV-1 infectivity, post-PMF/U may represent a valid alternative when semen cannot be obtained.

The effect of mental illness, substance use, and treatment for depression on the initiation of highly active antiretroviral therapy among HIV-infected individuals.

Information regarding the prevalence of mental illness and substance use among HIV-infected patients and the effect of these problems on HIV treatment is needed. We conducted an observational study of patients in the University of Washington (UW) HIV Cohort to determine prevalence rates for mental illness and substance use. Cox regression analyses were used to examine the relationship between mental illness and substance use, pharmacologic treatment for depression/anxiety, and initiation of highly active antiretroviral therapy (HAART) within 9 months of becoming eligible for HAART. Among 1774 patients in the UW HIV cohort during 2004, 63% had a mental illness (including mood, anxiety, psychotic, or personality disorders), 45% had a substance use disorder, and 38% had both. There were 278 patients who met criteria for HAART eligibility. After controlling for other factors, patients with depression and/or anxiety were significantly less likely to initiate HAART compared with patients without a mental illness (hazard ratio [HR] 0.4, p = 0.02). However, patients with depression/anxiety who received antidepressant/antianxiety medications were equally likely to initiate HAART as patients without a mental illness (HR 0.9, p = 0.5). We found that patients with mental illness or substance use disorders receive HAART at lower CD4+ cell counts and higher HIV-1 RNA levels than patients without these disorders. However, HAART initiation among patients who receive treatment for depression/anxiety is associated with no delay. Screening for these disorders in primary care settings and access to appropriate treatment are increasingly important components of providing care to HIV-infected patients.

Sentinel surveillance of sexually transmitted infections/HIV and risk behaviors in vulnerable populations in 5 Central American countries.

In El Salvador, Guatemala, Honduras, Nicaragua, and Panama, we recruited 2466 female sex workers (FSWs) by probabilistic or comprehensive sampling and 1418 men who have sex with men (MSM) by convenience sampling to measure sociobehavioral risk and sexually transmitted infections. For MSM, HIV seroprevalence ranged from 7.6% in Nicaragua to 15.3% in El Salvador, and estimated HIV seroincidence per 100 person-years ranged from 2.7 in Panama to 14.4 in Nicaragua; 61% reported using condoms consistently with casual male partners, 29% reported exposure to behavioral interventions, and 22% reported recent sex with male and female partners. For FSWs, HIV seroprevalence ranged from 0.2% in Nicaragua and Panama to 9.6% in Honduras, where estimated HIV seroincidence was also highest (3.2 per 100 person-years); 77% and 72% of FSWs reported using condoms consistently with new and regular clients. Herpes simplex virus (HSV)-2 seroprevalence averaged 85.3% in FSWs and 48.2% in MSM, and syphilis seropositivity averaged 9.6% in FSWs and 8.3% in MSM. Chlamydia trachomatis and Neisseria gonorrhoeae prevalences in FSWs averaged 20.1% and 8.1%, and Trichomonas vaginalis and bacterial vaginosis prevalences averaged 11.0% and 54.8%. An ongoing HIV epidemic involves Central American MSM with potential bridging to women. In FSWs, HSV-2 infection was associated with HIV infection (odds ratio = 11.0, 95% confidence interval: 2.9 to 7.9). For these vulnerable populations, prevention must incorporate acceptable and effective sexual health services, including improved condom access and promotion.

Initiation of antiretroviral therapy leads to a rapid decline in cervical and vaginal HIV-1 shedding.

BACKGROUND: Antiretroviral therapy (ART) may decrease HIV-1 infectivity in women by reducing genital HIV-1 shedding. OBJECTIVES: To evaluate the time course and magnitude of decay in cervical and vaginal HIV-1 shedding as women initiate ART. METHODS: This prospective, observational study of 20 antiretroviral-naive women initiating ART with stavudine, lamivudine, and nevirapine measured HIV-1 RNA in plasma, cervical secretions, and vaginal secretions. Qualitative polymerase chain reaction estimated HIV-1 DNA in cervical and vaginal samples. Perelson's two-phase viral decay model and non-linear random effects were used to compare RNA decay rates. Decreases in proviral DNA were evaluated using logistic regression and generalized estimating equations. RESULTS: Significant decreases in the quantity of HIV-1 RNA were observed by day 2 in plasma (P < 0.001), day 2 in cervical secretions (P = 0.001), and day 4 in vaginal secretions (P < 0.001). Modeled initial and subsequent RNA decay rates in plasma, cervical secretions, and vaginal secretions were 0.6, 0.8, and 1.2 log10 virions/day, and 0.04, 0.05, and 0.06 log10 virions/day, respectively. The initial decay rate for vaginal HIV-1 RNA was more rapid than for plasma RNA (P = 0.02). Detection of HIV-1 DNA decreased significantly in vaginal secretions during the first week (P < 0.001). At day 28, 10 women had detectable HIV-1 RNA or proviral DNA in genital secretions. CONCLUSIONS: Genital HIV-1 shedding decreased rapidly after ART initiation, consistent with a rapid decrease in infectivity. However, incomplete viral suppression in half of these women may indicate an ongoing risk of transmission.

Selection on the human immunodeficiency virus type 1 proteome following primary infection.

Typically during human immunodeficiency virus type 1 (HIV-1) infection, a nearly homogeneous viral population first emerges and then diversifies over time due to selective forces that are poorly understood. To identify these forces, we conducted an intensive longitudinal study of viral genetic changes and T-cell immunity in one subject at < or =17 time points during his first 3 years of infection, and in his infecting partner near the time of transmission. Autologous peptides covering amino acid sites inferred to be under positive selection were powerful for identifying HIV-1-specific cytotoxic-T-lymphocyte (CTL) epitopes. Positive selection and mutations resulting in escape from CTLs occurred across the viral proteome. We detected 25 CTL epitopes, including 14 previously unreported. Seven new epitopes mapped to the viral Env protein, emphasizing Env as a major target of CTLs. One-third of the selected sites were associated with epitopic mutational escapes from CTLs. Most of these resulted from replacement with amino acids found at low database frequency. Another one-third represented acquisition of amino acids found at high database frequency, suggesting potential reversions of CTL epitopic sites recognized by the immune system of the transmitting partner and mutation toward improved viral fitness in the absence of immune targeting within the recipient. A majority of the remaining selected sites occurred in the envelope protein and may have been subjected to humoral immune selection. Hence, a majority of the amino acids undergoing selection in this subject appeared to result from fitness-balanced CTL selection, confirming CTLs as a dominant selective force in HIV-1 infection.

Density-dependent decay in HIV-1 dynamics.

The decay of HIV-1-infected cell populations after treatment with antiretroviral therapy has been measured using simple exponential decay models. These models are unlikely to be realistic over periods longer than a few months, however, because the population dynamics of HIV are complex. We considered an alternate model developed by Perelson and colleagues that extends the standard model for biphasic viral load decline and allows for nonlinear log decay of infected cell populations. Using data from 6 children on highly active antiretroviral therapy (HAART) and a single parameter in the new model, the assumption of log linear decay of infected cell populations is tested. Our analysis indicates that the short-lived and long-lived infected cell populations do not decay according to a simple exponential model. Furthermore, the resulting estimates of time to eradication of infected cell compartments are dramatically longer than those previously reported (eg, decades vs. years for long-lived infected cell populations and years vs. weeks for short-lived infected cell populations). Furthermore, estimates of the second-phase decay rates are significantly different than 0 for most children when obtained using the Perelson biphasic decay model. In contrast, this rate is not significantly different than 0 when the density-dependent decay model is used for parameter estimation and inference. Thus, the density-dependent decay model but not the simple exponential decay model is consistent with recent data showing that even under consistent HAART-mediated suppression of viral replication, decay rates of infected cell reservoirs decay little over several years. This suggests that conclusions about long-term viral dynamics of HIV infection based on simple exponential decay models should be carefully re-evaluated.