Analyzing time-to-event data in a clinical trial when an unknown proportion of subjects has experienced the event at entry

In some clinical trials, where the outcome is the time until development of a silent event, an unknown proportion of subjects who have already experienced the event will be unknowingly enrolled due to the imperfect nature of the diagnostic tests used to screen potential subjects. For example, commonly used diagnostic tests for evaluating HIV infection status in infants, such as DNA PCR and HIV Culture, have low sensitivity when given soon after infection. This can lead to the inclusion of an unknown proportion of HIV-infected infants into clinical trials aimed at the prevention of transmission from HIV-positive mothers to their infants through breastfeeding. The infection status of infants at the end of the trial, when they are more than a year of age, can be determined with certainty. For those infants found to be infected with HIV at the end of the trial, it cannot be determined whether this occurred during the study or whether they were already infected when they were enrolled. In these settings, estimates of the cumulative risk of the event by the end of the study will overestimate the true probability of event during the study period and hypothesis tests comparing two or more intervention strategies can also be biased. We present inference methods for the distribution of time until the event of interest in these settings, and investigate issues in the design of such trials when there is a choice of using both imperfect and perfect diagnostic tests.     

Modeling Maternal-Infant HIV Transmission in the Presence of Breastfeeding with an Imperfect Test

An important public health question is to determine the probabilities of perinatal HIV transmission and when it occurs, whether antepartum, intrapartum, or postpartum through breastfeeding. However, this is a difficult problem because the presence of HIV infection in an infant can only be ascertained through viral assays in the postpartum period. We propose a model that simultaneously estimates the risks of antepartum, intrapartum, and postpartum transmissions together with the sensitivity of the screening tests for HIV infection. The model allows estimating of infectivity through breast milk during postpartum periods. The methods are illustrated on a South African randomized clinical trial of extended AZT versus a short course of nevirapine in infants whose mothers had no access to antenatal antiretroviral therapy.     

Drugs of abuse and HIV infection/replication: implications for mother-fetus transmission

Human immunodeficiency virus (HIV) infection and progression of acquired immunodeficiency syndrome (AIDS) can be modulated by a number of cofactors, including drugs of abuse. Opioids, cocaine, cannabinoids, methamphetamine (METH), alcohol, and other substances of abuse have been implicated as risk factors for HIV infection, as they all have the potential to compromise host immunity and facilitate viral replication. Although epidemiologic evidence regarding the impact of drugs of abuse on HIV disease progression is mixed, in vitro studies as well as studies using in vivo animal models have indicated that drugs of abuse have the ability to enhance HIV infection/replication. Drugs of abuse may also be a risk factor for perinatal transmission of HIV. Because high levels of viral load in maternal blood are associated with increased risk of HIV vertical transmission, it is likely that drugs of abuse play an important role in promoting mother-fetus transmission. Furthermore, because the neonatal immune system differs qualitatively from the adult system, it is possible that maternal exposure to drugs of abuse would exacerbate neonatal immunity defects, facilitating HIV infection of neonate immune cells and promoting HIV vertical transmission. The availability and use of antiretroviral therapy for women infected with HIV increase, there is an increasing interest in determining the impact of drug abuse on efficacy of AIDS Clinical Trials Group (ACTG)-standardized treatment regimens for woman infected with HIV in the context of HIV vertical transmission.     

Needle exchange programs: an economic evaluation of a local experience

OBJECTIVE: To determine whether providing a needle exchange program to prevent HIV transmission among injection drug users would cost less than the health care consequences of not having such a program. DESIGN: Incidence outcome model to estimate the number of cases of HIV infection that this program would prevent over 5 years, assuming that the HIV incidence rate would be 2% with the program and 4% without it, and that an estimated 275 injection drug users would use the service over this time. SETTING: Hamilton, Ont. OUTCOME MEASURES: Estimated number of cases of HIV infection expected to be prevented with and without the program over 5 years; estimated lifetime health care costs of treating an AIDS patient. The indirect costs of AIDS to society (e.g., lost productivity and informal caregiving) were not included. Projected costs were adjusted (discounted) to reflect their present value. In a sensitivity analysis, 3 parameters were varied: the estimate of the HIV transmission rate if no needle exchange program were provided, the number of injection drug users participating in the program, and the discount rate. RESULTS: With very conservative estimates, it was predicted that the Hamilton needle exchange program will prevent 24 cases of HIV infection over 5 years, thereby providing cost savings of $1.3 million after the program costs are taken into account. This translates into a ratio of cost savings to costs of 4:1. The sensitivity analysis confirmed that these findings are robust. CONCLUSION: Needle exchange programs are an efficient use of financial resources.     

Mother-to-child transmission of HIV in Botswana: an ethical perspective on mandatory testing

Mother-to-child transmission (MTCT) of HIV represents a particularly dramatic aspect of the HIV epidemic with an estimated 600,000 newborns infected yearly, 90% of them living in sub-Saharan Africa. Since the beginning of the HIV epidemic, an estimated 5.1 million children worldwide have been infected with HIV. MTCT is responsible for 90% of these infections. Two-thirds of the MTCT are believed to occur during pregnancy and delivery, and about one-third through breastfeeding. As the number of women of child bearing age infected with HIV rises, so does the number of infected children. It is apparent that voluntary testing in Botswana has made some valuable inroads in decreasing perinatal HIV transmission, but the statistics showing the increased rate of HIV infection among women 15-24 years of age are not very promising. After reviewing all the pertinent scientific data it is clear that mandatory HIV testing of all pregnant women in conjunction with the implementation of a full package of interventions would save thousands of lives -- mothers, newborns and others who could be infected as a result of these women not being aware of their HIV status. If the protection and preservation of human life is a priority in Botswana, then it is time to allow for mandatory HIV testing of all pregnant women, before it is too late for those who are the most vulnerable. To do less would be medically inappropriate and ethically irresponsible.     

Sensitivity analysis for the assessment of causal vaccine effects on viral load in HIV vaccine trials

Vaccines with limited ability to prevent HIV infection may positively impact the HIV/AIDS pandemic by preventing secondary transmission and disease in vaccine recipients who become infected. To evaluate the impact of vaccination on secondary transmission and disease, efficacy trials assess vaccine effects on HIV viral load and other surrogate endpoints measured after infection. A standard test that compares the distribution of viral load between the infected subgroups of vaccine and placebo recipients does not assess a causal effect of vaccine, because the comparison groups are selected after randomization. To address this problem, we formulate clinically relevant causal estimands using the principal stratification framework developed by Frangakis and Rubin (2002, Biometrics 58, 21-29), and propose a class of logistic selection bias models whose members identify the estimands. Given a selection model in the class, procedures are developed for testing and estimation of the causal effect of vaccination on viral load in the principal stratum of subjects who would be infected regardless of randomization assignment. We show how the procedures can be used for a sensitivity analysis that quantifies how the causal effect of vaccination varies with the presumed magnitude of selection bias.     

Human immunodeficiency virus (HIV) vaccine trials: a novel assay for differential diagnosis of HIV infections in the face of vaccine-generated antibodies

All current human immunodeficiency virus (HIV) vaccine candidates contain multiple viral components and elicit antibodies that react positively in licensed HIV diagnostic tests, which contain similar viral products. Thus, vaccine trial participants could be falsely diagnosed as infected with HIV. Additionally, uninfected, seropositive vaccinees may encounter long-term social and economic harms. Moreover, this also interferes with early detection of true HIV infections during preventive HIV vaccine trials. An HIV-seropositive test result among uninfected vaccine trial participants is a major public health concern for volunteers who want to participate in future HIV vaccine trials. Based on the increased number of HIV vaccines being tested globally, it is essential to differentiate vaccine- from virus-induced antibodies. Using a whole-HIV-genome phage display library, we identified conserved sequences in Env-gp41 and Gag-p6 which are recognized soon after infection, do not contain protective epitopes, and are not part of most current HIV vaccines. We established a new HIV serodetection assay based on these peptides. To date, this assay, termed HIV-SELECTEST, demonstrates >99% specificity and sensitivity. Importantly, in testing of plasma samples from multiple HIV vaccine trials, uninfected trial participants scored negative, while all intercurrent infections were detected within 1 to 3 months of HIV infection. The new HIV-SELECTEST is a simple but robust diagnostic tool for easy implementation in HIV vaccine trials and blood banks worldwide.     

Immunologic basis for revaccination of HIV-infected children receiving HAART

With increasing access to antiretroviral therapy for children infected with HIV, especially in sub-Saharan Africa, better understanding of the development and maintenance of memory T- and B-cell responses to pathogens after immune reconstitution is needed to assess the risk of infection. Knowledge of long-term immune responses after starting HAART is of particular importance for policies on revaccination of HIV-infected children, who may lose protective immunity to prior infections and immunizations. We review normal development of T- and B-cell memory responses to viruses and vaccines against viral pathogens, and contrast the immunological effects of perinatal HIV transmission with HIV infection acquired later in life. We then explore the potential benefits of antiretroviral therapy and revaccination, using measles virus as a model.     

Bayesian Estimation of the Time‐Varying Sensitivity of a Diagnostic Test with Application to Mother‐to‐Child Transmission of HIV

Summary We present a Bayesian model to estimate the time‐varying sensitivity of a diagnostic assay when the assay is given repeatedly over time, disease status is changing, and the gold standard is only partially observed. The model relies on parametric assumptions for the distribution of the latent time of disease onset and the time‐varying sensitivity. Additionally, we illustrate the incorporation of historical data for constructing prior distributions. We apply the new methods to data collected in a study of mother‐to‐child transmission of HIV and include a covariate for sensitivity to assess whether two different assays have different sensitivity profiles.     

HIV in Children in a General Population Sample in East Zimbabwe: Prevalence,Causes and Effects

Background

There are an estimated half-million children living with HIV in sub-Saharan Africa. The predominant source of infection is presumed to be perinatal mother-to-child transmission, but general population data about paediatric HIV are sparse. We characterise the epidemiology of HIV in children in sub-Saharan Africa by describing the prevalence, possible source of infection, and effects of paediatric HIV in a southern African population.

Methods

From 2009 to 2011, we conducted a household-based survey of 3389 children (aged 2–14 years) in Manicaland, eastern Zimbabwe (response rate: 73.5%). Data about socio-demographic correlates of HIV, risk factors for infection, and effects on child health were analysed using multi-variable logistic regression. To assess the plausibility of mother-to-child transmission, child HIV infection was linked to maternal survival and HIV status using data from a 12-year adult HIV cohort.

Results

HIV prevalence was (2.2%, 95% CI: 1.6–2.8%) and did not differ significantly by sex, socio-economic status, location, religion, or child age. Infected children were more likely to be underweight (19.6% versus 10.0%, p = 0.03) or stunted (39.1% versus 30.6%, p = 0.04) but did not report poorer physical or psychological ill-health. Where maternal data were available, reported mothers of 61/62 HIV-positive children were deceased or HIV-positive. Risk factors for other sources of infection were not associated with child HIV infection, including blood transfusion, vaccinations, caring for a sick relative, and sexual abuse. The observed flat age-pattern of HIV prevalence was consistent with UNAIDS estimates which assumes perinatal mother-to-child transmission, although modelled prevalence was higher than observed prevalence. Only 19/73 HIV-positive children (26.0%) were diagnosed, but, of these, 17 were on antiretroviral therapy.

Conclusions

Childhood HIV infection likely arises predominantly from mother-to-child transmission and is associated with poorer physical development. Overall antiretroviral therapy uptake was low, with the primary barrier to treatment appearing to be lack of diagnosis.     

gp340 expressed on human genital epithelia binds HIV-1 envelope protein and facilitates viral transmission

During sexual transmission of HIV in women, the first cells likely to be infected are submucosal CD4(+) T cells and dendritic cells of the lower genital tract. HIV is segregated from these target cells by an epithelial cell layer that can be bypassed even when healthy and intact. To understand how HIV penetrates this barrier, we identified a host protein, gp340, that is expressed on genital epithelium and binds the HIV envelope via a specific protein-protein interaction. This binding allows otherwise subinfectious amounts of HIV to efficiently infect target cells and allows this infection to occur over a longer period of time after binding. Our findings suggest a mechanism of viral entry during heterosexual transmission where HIV is bound to intact genital epithelia, which then promotes the initial events of infection. Understanding this step in the initiation of infection will allow for the development of tools and methods for blocking HIV transmission.     

Performance of risk-based criteria for targeting acute HIV screening in San Francisco

Background

Federal guidelines now recommend supplemental HIV RNA testing for persons at high risk for acute HIV infection. However, many rapid HIV testing sites do not include HIV RNA or p24 antigen testing due to concerns about cost, the need for results follow-up, and the impact of expanded venipuncture on clinic flow. We developed criteria to identify patients in a municipal STD clinic in San Francisco who are asymptomatic but may still be likely to have acute infection.

Methods

Data were from patients tested with serial HIV antibody and HIV RNA tests to identify acute HIV infection. BED-CEIA results were used to classify non-acute cases as recent or longstanding. Demographics and self-reported risk behaviors were collected at time of testing. Multivariate models were developed and preliminarily evaluated using predictors associated with recent infection in bivariate analyses as a proxy for acute HIV infection. Multivariate models demonstrating ≥70% sensitivity for recent infection while testing ≤60% of patients in this development dataset were then validated by determining their performance in identifying acute infections.

Results

From 2004–2007, 137 of 12,622 testers had recent and 36 had acute infections. A model limiting acute HIV screening to MSM plus any one of a series of other predictors resulted in a sensitivity of 83.3% and only 47.6% of patients requiring testing. A single-factor model testing only patients reporting any receptive anal intercourse resulted in 88.9% sensitivity with only 55.2% of patients requiring testing.

Conclusions

In similar high risk HIV testing sites, acute screening using “supplemental” HIV p24 antigen or RNA tests can be rationally targeted to testers who report particular HIV risk behaviors. By improving the efficiency of acute HIV testing, such criteria could facilitate expanded acute case identification.     

The use of PCR analysis for the diagnosis of HIV infection in infants in the 1st months of life

In this review the data of contemporary studies of dynamic changes in serological and virological markers in the course of HIV infection in infants aged 0-18 months, aimed at finding out the comparative value of different tests made with a view to established exact diagnosis, are discussed. The results of the study of the sensitivity and specificity of the RNA and DNA polymerase chain reaction in the diagnostics of HIV infection in infants during the first months of life, as well as the recommended time of testing, have been analyzed in detail. On the basis of the data presented in this review the author has formulated the scheme of the algorithm for diagnosing HIV infection in infants born of HIV-infected mothers with the following variants of the diagnosis: "possible infection", "seroversion" (marking it possible to exclude the presence of the infection) and "HIV infection". The proposed scheme has the character of recommendation, but under the conditions of the rapid spread of HIV infection with the involvement of infants into the process this scheme may be useful in pediatric practice.     

Excluding blood donors at high risk of HIV infection in a west African city.

OBJECTIVE--To examine the potential impact of deferral of blood donors at high risk of HIV infection in a west African city where blood is screened for HIV antibodies but no other special measures are taken to protect the blood supply. DESIGN--Cross sectional study. SETTING--National Blood Transfusion Centre and Project RETRO-CI, an international collaborative AIDS research project, Abidjan, Côte d''Ivoire. SUBJECTS--1257 male first time blood donors. INTERVENTIONS--Blood donors were interviewed about demographic and behavioural characteristics and tested for HIV antibodies by enzyme immunoassay and, if positive, synthetic peptide based tests. MAIN OUTCOME MEASURES--HIV antibody status in relation to presence of behavioural risk factors; calculation of sensitivity, specificity, and predictive values of specific criteria for excluding HIV infected donors. RESULTS--The overall prevalence of HIV infection was 11.4%. The most important risk factors for HIV positivity were prostitute contact and being aged 30-39 years. For identifying seropositive donors individual criteria had sensitivity, specificity, and positive predictive values ranging from 15% to 98%, 38% to 91%, and 17% to 30% respectively. Prostitute contact in the past five years would have excluded 31% of all donors and 73% of HIV infected donors. 27% of those excluded would have been HIV positive. CONCLUSIONS--The widespread assumption that donor deferral is not feasible in sub-Saharan Africa needs reassessment. In Abidjan this approach was well accepted and potentially effective. Donor deferral requires evaluation as a strategy for improving blood safety in resource poor areas with high rates of HIV infection.     

Persistence of infectious HIV on follicular dendritic cells

Follicular dendritic cells (FDCs) trap Ags and retain them in their native state for many months. Shortly after infection, HIV particles are trapped on FDCs and can be observed until the follicular network is destroyed. We sought to determine whether FDCs could maintain trapped virus in an infectious state for long periods of time. Because virus replication would replenish the HIV reservoir and thus falsely prolong recovery of infectious virus, we used a nonpermissive murine model to examine maintenance of HIV infectivity in vivo. We also examined human FDCs in vitro to determine whether they could maintain HIV infectivity. FDC-trapped virus remained infectious in vivo at all time points examined over a 9-mo period. Remarkably, as few as 100 FDCs were sufficient to transmit infection throughout the 9-mo period. Human FDCs maintained HIV infectivity for at least 25 days in vitro, whereas virus without FDCs lost infectivity after only a few days. These data indicate that HIV retained on FDCs can be long lived even in the absence of viral replication and suggest that FDCs stabilize and protect HIV, thus providing a long-term reservoir of infectious virus. These trapped stores of HIV may be replenished with replicating virus that persists even under highly active antiretroviral therapy and would likely be capable of causing infection on cessation of drug therapy.     

Bifunctional recombinant fusion proteins for rapid detection of antibodies to both HIV-1 and HIV-2 in whole blood

Background  

Availability of accurate diagnostic tests has been helpful in curtailing the spread of HIV infection. Among these, simple, point of care, inexpensive tests which require only a drop of blood from finger-prick and give reliable results within minutes are a must for expansion of testing services and for reaching mobile and marginalised populations. Such tests will not only be a boon for the infrastructure-starved developing and underdeveloped countries but will also be extremely useful in developed countries where post-testing compliance is a major problem. Our laboratory has been involved in developing reagents for heamagglutination-based rapid detection of antibodies to HIV in whole blood using recombinant molecules specific for either HIV-1 or HIV-2. Since it is not required of a screening test to differentially detect HIV and HIV-2, it would useful to create a single molecule capable of simultaneous detection of both HIV-1 and HIV-2 in a drop of blood.     

Inferring the Source of Transmission with Phylogenetic Data

Identifying the source of transmission using pathogen genetic data is complicated by numerous biological, immunological, and behavioral factors. A large source of error arises when there is incomplete or sparse sampling of cases. Unsampled cases may act as either a common source of infection or as an intermediary in a transmission chain for hosts infected with genetically similar pathogens. It is difficult to quantify the probability of common source or intermediate transmission events, which has made it difficult to develop statistical tests to either confirm or deny putative transmission pairs with genetic data. We present a method to incorporate additional information about an infectious disease epidemic, such as incidence and prevalence of infection over time, to inform estimates of the probability that one sampled host is the direct source of infection of another host in a pathogen gene genealogy. These methods enable forensic applications, such as source-case attribution, for infectious disease epidemics with incomplete sampling, which is usually the case for high-morbidity community-acquired pathogens like HIV, Influenza and Dengue virus. These methods also enable epidemiological applications such as the identification of factors that increase the risk of transmission. We demonstrate these methods in the context of the HIV epidemic in Detroit, Michigan, and we evaluate the suitability of current sequence databases for forensic and epidemiological investigations. We find that currently available sequences collected for drug resistance testing of HIV are unlikely to be useful in most forensic investigations, but are useful for identifying transmission risk factors.     

Evolution of Cryptococcal Antigen Testing: What Is New?

Over the last decade, an upsurge in both the frequency and severity of fungal infections due to the HIV/AIDS epidemic and the use of immunosuppressive therapy has occurred. Even diagnostic methods like culture and microscopy, which have low sensitivity and longer turnaround times, are not widely available, leading to delays in timely antifungal therapy and detrimental patient outcomes. The evolution of cryptococcal antigen (CrAg) testing to develop inexpensive and more sensitive methods to detect cryptococcal antigen is significant. These newer tests employ immunoassays as part of point-of-care platforms, which do not require complex laboratory infrastructure, and they have the potential to detect early disease and reduce time to diagnosis of cryptococcal infection. Advocacy for widely available and efficacious life-saving antifungal treatment should be the only remaining challenge.     

The usefulness of defined clinical features in the diagnosis of HIV/AIDS infection in Sierra Leone.

Sierra Leone ranks at the bottom of the global World Bank Development Index based on multiple health and economic indices and lacks the resources to purchase HIV diagnostic kits. Our study has defined some common clinical features presenting HIV infection that could form clinical algorithms for the diagnosis and recognition of HIV infection by health workers in Sierra Leone. In a private clinic in Freetown, Sierra Leone, West Africa, 106 out of a total of 124 patients presenting with various symptoms and strong clinical suspicion of HIV infection within a two-year period (1999 and 2000), were deemed positive by two different ELISA tests. The prevalence of HIV infection seen in this private clinic in Freetown in 2000 was 14.89% as compared to 9.25% in 1999. The positive predictive value of our clinical diagnosis of HIV/AIDS infection was 85.5%. The male:female ratio of the patients in our series was 1:1.9, with a mean age of 39 years for males and 28 years for females. HIV infection was found in a cross-section of the population that we examined. Heterosexual contact appeared to be the major mode of transmission amongst our patients and there seemed to be a significant epidemiological risk of HIV infection amongst those who traveled to other countries in the West African sub region. Common clinical features in decreasing frequency were fever (92.5%), weight loss (84.1%), lymphadenopathy (78.3%), cough (48.1%), diarrhea (37.7%), candidiasis (32.1%) and body aches (30.1%).