The WHO and why of HIV vaccine trials

A brief history of the global effort to develop a preventive HIV vaccine

Soon after HIV was discovered as the cause of AIDS in 1983-1984, there was an expectation that a preventive vaccine would be rapidly developed. In trying to achieve that goal, three successive scientific paradigms have been explored: induction of neutralizing antibodies, induction of cell mediated immunity, and exploration of combination approaches and novel concepts. Although major progress has been made in understanding the scientific basis for HIV vaccine development, efficacy trials have been critical in moving the field forward. In 2009, the field was reinvigorated with the modest results obtained from the RV144 trial conducted in Thailand. Here, we review those vaccine development efforts, with an emphasis on events that occurred during the earlier years. The goal is to provide younger generations of scientists with information and inspiration to continue the search for an HIV vaccine.

Application and impact of population pharmacokinetics in the assessment of antiretroviral pharmacotherapy

Population pharmacokinetics has been an important technique used to explore and define relevant sources of variation in drug exposure and response in patient populations. This has been especially true in the area of antiretroviral therapy where the assurance of adequate and sustained drug exposure of multiple agents is highly correlated with therapeutic success. Population pharmacokinetic analyses across the four drug classes and 20 US FDA-approved products used to treat HIV have been published to date. The published reports were predominantly based on actual clinical trials conducted in HIV-infected patients with one or more agents administered. Modelling and simulation approaches have been used in the evaluation of antiretroviral agent outcomes incorporating problematic design and analysis factors such as sparse plasma sampling, data imbalance and censored data. Additional benefits of population modelling approaches applied to the investigation of antiretroviral agents include the ability to assess dosing compliance, understanding and quantifying drug-drug interactions in order to select dosing regimens and the screening of new drug candidates. Pharmacokinetic/pharmacodynamic models have been used to characterise the relationship between drug exposure and virological and immunological response, and to predict clinical outcome. These models offer the best opportunity for individualising and optimising patient therapy, particularly when adjusted for adherence/compliance. The impact of population pharmacokinetics in the area of antiretroviral therapy can be directly assessed by its role in the validation of surrogate markers such as viral RNA load, therapeutic drug monitoring and the management of individual patient outcomes via exposure-toxicity relationships. Each of these population pharmacokinetic outcomes has contributed to the current regulatory environment, specifically in the area of accelerated approval of new antiretroviral agents.

Potential Public Health Impact of Imperfect HIV Type 1 Vaccines

The potential public health impact of imperfect human immunodeficiency virus (HIV) type 1 vaccines was examined by use of deterministic mathematical models of virus transmission. Imperfect vaccines are defined as those that act to favorably alter the typical clinical course of disease in those immunized who acquire infection. The properties examined include a lengthened incubation period; reduced virus load, which acts to lower infectiousness; reduced susceptibility on exposure to infection; and an increase in risk behaviors by those vaccinated. Analyses suggest that, although imperfect vaccines would struggle to block transmission via cohort vaccination of those entering the sexually active age classes, they could have a substantial public health impact, as measured by reduced prevalence and mortality induced by acquired immunodeficiency syndrome (AIDS), provided the case reproductive number of HIV-1 among vaccinated individuals (R(0v)) was less than that among unvaccinated individuals (R(0)). This requires that any lengthening in the incubation period and, hence, the time period over which an infected vaccine recipient can transmit to susceptible sex partners, as well as any increase in risk behaviors, are more than offset by other effects, such as reduced susceptibility to infection and reduced infectiousness. Numerical studies based on a more complex model, which included representation of age, sex, heterogeneity in sexual activity, variable infectiousness, and different mixing patterns between risk groups, were used to confirm the general insights gained from a simple deterministic model.

Reanalysis of the HIV-1 circulating recombinant form A/E (CRF01_AE): evidence of A/E/G recombination

Circulating recombinant form (CRF) 01_AE caused an extensive HIV-1 epidemic in Thailand and Southeast Asia. Reanalysis of the recombination pattern of CRF01_AE suggested a more complicated pattern of mosaicism consisting of subtypes A, G, and E. These findings provide evidence that CRF01_AE originated from recombination between at least three different subtypes.

The Biology and Evolution of HIV

▪ Abstract  This review examines the current state of knowledge about HIV/AIDS in terms of its origins, pathogenesis, genetic variation, and evolutionary biology. The HIV virus damages the host's immune system, resulting in AIDS, which is characterized by immunodeficiency, opportunistic infections, neoplasms, and neurological problems. HIV is a complex retrovirus with a high mutation rate. This mutation rate allows the virus to evade host immune responses, and evidence indicates that selection favors more virulent strains with rapid replication. While a number of controversial theories attempt to explain the origin of HIV/AIDS, phylogenetic evidence suggests a zoonotic transmission of HIV to humans and implicates the chimpanzee (Pan troglodytes troglodytes) as the source of HIV-1 infection and the sooty mangabey as the source of HIV-2 infection in human populations. New therapies provide hope for increased longevity among people living with AIDS, but the biology of HIV presents significant obstacles to finding a cure and/or vaccine. HIV continues to be a threat to the global population because of its fast mutation rate, recombinogenic effect, and its use of human defenses to replicate itself.

Omnibus tests for comparison of competing risks with adjustment for covariate effects

This article develops omnibus tests for comparing cause-specific hazard rates and cumulative incidence functions at specified covariate levels. Confidence bands for the difference and the ratio of two conditional cumulative incidence functions are also constructed. The omnibus test is formulated in terms of a test process given by a weighted difference of estimates of cumulative cause-specific hazard rates under Cox proportional hazards models. A simulation procedure is devised for sampling from the null distribution of the test process, leading to graphical and numerical technques for detecting significant differences in the risks. The approach is applied to a cohort study of type-specific HIV infection rates.

Comparison of competing risks failure time methods and time-independent methods for assessing strain variations in vaccine protection

In a preventive vaccine efficacy trial of a vaccine for a genotypically and phenotypically diverse pathogen, it is important to assess if and how vaccine protection against infection or disease varies with characteristics of the exposing pathogen. Gilbert, Self and Ashby developed statistical methods for this problem when the outcome data are counts of the number of vaccinated and unvaccinated trial participants infected by each pathogen strain. However, in many vaccine trials time-to-case information is available, and the extent to which this information improves investigation of differential vaccine protection is unclear. We describe how cause-specific proportional hazards models and other popular competing risks failure time techniques can be applied to this problem. This includes new results on the assumptions required for these methods to give valid inferences about strain-specific vaccine efficacy, and a comparison of theoretical and finite-sample properties between these methods and the time-independent methods. Theoretical considerations, a cholera vaccine trial example, and an extensive simulation study of a human immunodeficiency virus type 1 (HIV-1) vaccine trial show that information about failure times does not appreciably improve estimation or testing unless the pathogen has a high attack rate and the relative prevalence of pathogen strains shifts substantially during the trial follow-up period. An important implication is that practically optimal evaluation of strain-specific vaccine efficacy in HIV-1 vaccine trials will not require knowledge of infection times.

Molecular epidemiology of HIV type 1 in a rural community in southwest Uganda

The molecular epidemiology of a population-based cohort in a cluster of 15 villages in southwestern Uganda was investigated by sequencing part of the p24 gag gene and performing heteroduplex mobility assays (HMAs) of the V3 region of the env gene. Sequence and HMA data, obtained for 69 and 88 proviruses, respectively, showed that the clade A and D viruses were present at a ratio of about 0.67:1. No other clades were detected. Thirteen (22%) of 59 proviruses for which both gag and env data were obtained appeared to be recombinants. Although both clade A and D viruses were present in 13 of the villages, their distribution was unequal: for example, from env data 59% of clade A viruses were found in the eastern villages, compared with only 27% of clade D viruses. Phylogenetic (maximum likelihood) analysis of the p24 gag sequences showed a total of five clusters supported by bootstrap resampling values above or close to 75%. Four clusters were sexual partners, but there was no known sexual contact between the persons in the other cluster. The DNA sequences showed between 0.5 and 8.3% divergence from the cohort clade A or D consensus sequences. The sequences were not closely related to those published for other clade A or D proviruses.

Some important issues in the planning of phase III HIV vaccine efficacy trials

Given that interesting HIV vaccine candidates, including live preparations and DNA plasmids, exist and that the first phase III vaccine (AIDSVAX) testing is due to begin this summer, 1998, in the U.S., adequately addressing trial preparedness is a pressing issue. Despite double-blind randomized controlled clinical trial design, there may be difficulties with interpretation and use of the usual measures of vaccinal efficacy and calculation of sample size. Difficulties arise from vaccine characteristics (e.g. mode of action, time-lag, waning) and population heterogeneities (e.g. differences in susceptibility, sexual behaviour, mixing preferences) causing frailty effects that can exacerbate bias and time-dependent effects already known to exist in simple cases. Since vaccine properties, particularly mode of action, are unlikely to be known before the onset of clinical trials, choosing an efficacy measure and the associated analyses and sample size calculations will be problematic. Interim analyses designed to decide whether a study will be prolonged may be tenuous if based on a time-dependent measure and will influence sample size determination. Despite shortcomings, general recommendations can be made to minimise pernicious effects. The objectives of this paper are principally to review the current state of knowledge of the different stages in the preparation of large phase III HIV vaccine efficacy trials, the methodological difficulties related to their design, and the analysis of data collected from them. Mathematical models and trial simulations are used to demonstrate that further research is necessary to study the behaviour of vaccine efficacy measures under heterogeneous conditions of population, vaccine action, and trial design and identify a time-independent efficacy measure. Alternative methods to validate sample size calculations have to be developed in older to reduce the chances of unnecessary economic and human cost in phase III HIV vaccine trials.

Complex dynamic behaviours in the interaction between parasite population and the host's immune system

The paper describes recent progress in the development of a mathematical framework for the study of epidemiology, evolution, within-host parasite population growth and the control of parasitic infections. A major emphasis is placed on dynamic models of the interaction between the parasite population and the host's immune system that capture the effects of antigenic variation, parasite evolution in response of immunological attack and the control of population growth by chemotherapeutic agents.

Immunological and virological analyses of persons infected by human immunodeficiency virus type 1 while participating in trials of recombinant gp120 subunit vaccines

We have studied 18 participants in phase I/II clinical trials of recombinant gp120 (rgp120) subunit vaccines (MN and SF-2) who became infected with human immunodeficiency virus type 1 (HIV-1) during the course of the trials. Of the 18 individuals, 2 had received a placebo vaccine, 9 had been immunized with MN rgp120, and seven had been immunized with SF-2 rgp120. Thirteen of the 18 infected vaccinees had received three or four immunizations prior to becoming infected. Of these, two were placebo recipients, six had received MN rgp120, and five had received SF-2 rgp120. Only 1 of the 11 rgp120 recipients who had multiple immunizations failed to develop a strong immunoglobulin G antibody response to the immunogen. However, the antibody response to rgp120 was transient, typically having a half-life of 40 to 60 days. No significant neutralizing activity against the infecting strain was detected in any of the infected individuals at any time prior to infection. Antibody titers in subjects infected despite vaccination and in noninfected subjects were not significantly different. Envelope-specific cytotoxic T-lymphocyte responses measured after infection were infrequent and weak in the nine vaccinees who were tested. HIV-1 was isolated successfully from all 18 individuals. Sixteen of these strains had a non-syncytium-inducing (NSI) phenotype, while two had a syncytium-inducing (SI) phenotype. NSI strains used the CCR5 coreceptor to enter CD4+ cells, while an SI strain from one of the vaccinees also used CXCR4. Viruses isolated from the blood of rgp120 vaccinees were indistinguishable from viruses isolated from control individuals in terms of their inherent sensitivity to neutralization by specific monoclonal antibodies and their replication rates in vitro. Furthermore, genetic sequencing of the env genes of strains infecting the vaccinees did not reveal any features that clearly distinguished these viruses from contemporary clade B viruses circulating in the United States. Thus, despite rigorous genetic analyses, using various breakdowns of the data sets, we could find no evidence that rgp120 vaccination exerted selection pressure on the infecting HIV-1 strains. The viral burdens in the infected rgp120 vaccine recipients were also determined, and they were found to be not significantly different from those in cohorts of placebo-vaccinated and nonvaccinated individuals. In summary, we conclude that vaccination with rgp120 has had,to date, no obvious beneficial or adverse effects on the individuals we have studied.

Low-efficacy HIV vaccines: potential for community-based intervention programmes

To combat the spread of HIV, progress on vaccine development is eagerly awaited. Haynes in this series has described the progress made so far with various vaccine types. This article describes how mathematical modelling techniques can be used to predict the likely impact of low-efficacy vaccines in community transmission of the virus. The answers are often not what one would predict by intuition alone, and they have great bearing on the likely success of such vaccination strategies.

The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin

Since 1989, human immunodeficiency virus type 1 (HIV-1) has spread explosively through the heterosexual population in Thailand. This epidemic is caused primarily by viruses classified as "subtype E", which, on the basis of limited sequence comparisons, appear to represent hybrids of subtypes A (gag) and E (env). However, the true evolutionary origins of "subtype E" viruses are still obscure since no complete genomes have been analyzed, and only one full-length subtype A sequence has been available for phylogenetic comparison. In this study, we determined full-length proviral sequences for "subtype E" viruses from Thailand (93TH253) and the Central African Republic (90CR402) and for a subtype A virus from Uganda (92UG037). We also sequenced the long terminal repeat (LTR) regions from 16 virus strains representing clades A, C, E, F, and G. Detailed phylogenetic analyses of these sequences indicated that "subtype E" viruses do indeed represent A/E recombinants with multiple points of crossover along their genomes. The extracellular portion of env, parts of vif and vpr, as well as most of the LTR are of subtype E origin, whereas the remainder of the genome is of subtype A origin. The possibility that the discordant phylogenetic positions of "subtype E" viruses in gag- and env-derived trees are the result of unusual rates or patterns of evolution was also considered but was ruled out on the basis of two lines of evidence: (i) phylogenetic trees constructed for synonymous and nonsynonymous substitutions yielded the same discordant branching orders for "subtype E" gag and env gene sequences, thus excluding selection-driven evolution, and (ii) multiple crossovers in the viral genome are most consistent with the copy choice model of recombination and have been observed in other documented examples of HIV-1 intersubtype recombination. Thai and CAR "subtype E" viruses exhibited the same pattern of A/E mosaicism, indicating that the recombination event occurred in Africa prior to the spread of virus to Asia. Finally, all "subtype E" viruses were found to contain a distinctive two-nucleotide bulge in their transactivation response (TAR) elements. This feature was present only in viruses which also contained a subtype A 5' pol region (i.e., subtype A viruses or A/D and A/E recombinants), raising the possibility of a functional linkage between the TAR region and the polymerase. The implications of epidemic spread of a recombinant HIV-1 strain to viral natural history and vaccine development are discussed.

Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization

Present knowledge of human immunodeficiency virus type 1 (HIV-1) envelope immunobiology has been derived almost exclusively from analyses of subtype B viruses, yet such viruses represent only a minority of strains currently spreading worldwide. To generate a more representative panel of genetically diverse envelope genes, we PCR amplified, cloned, and sequenced complete gp160 coding regions of 35 primary (peripheral blood mononuclear cell-propagated) HIV-1 isolates collected at major epicenters of the current AIDS pandemic. Analysis of their deduced amino acid sequences revealed several important differences from prototypic subtype B strains, including changes in the number and distribution of cysteine residues, substantial length differences in hypervariable regions, and premature truncations in the gp41 domain. Moreover, transiently expressed glycoprotein precursor molecules varied considerably in both size and carbohydrate content. Phylogenetic analyses of full-length env sequences indicated that the panel included members of all major sequence subtypes of HIV-1 group M (clades A to G), as well as an intersubtype recombinant (F/B) from an infected individual in Brazil. In addition, all subtype E and three subtype G viruses initially classified on the basis of partial env sequences were found to cluster in subtype A in the 3' half of their gp41 coding region, suggesting that they are also recombinant. The biological activity of PCR-derived env genes was examined in a single-round virus infectivity assay. This analysis identified 20 clones, including 1 from each subtype (or recombinant), which expressed fully functional envelope glycoproteins. One of these, derived from a patient with rapid CD4 cell decline, contained an amino acid substitution in a highly conserved endocytosis signal (Y721C), as mediated virus entry with very poor efficiency, although they did not contain sequence changes predicted to alter protein function. These results indicate that the env genes of primary HIV-1 isolates collected worldwide can vary considerably in their genetic, phylogenetic, and biological properties. The panel of env constructs described here should prove valuable for future structure-function studies of naturally occurring envelope glycoproteins as well as AIDS vaccine development efforts targeted against a broader spectrum of viruses.

Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type 1 by using restriction fragment length polymorphism analysis

The simultaneous presence of multiple HIV-1 subtypes has become common in communities with the growth of the pandemic. As a consequence, the potentiality for an increased frequency of HIV-1 mixed infections caused by viruses of distinct subtypes could be expected. Thus, there is a need to estimate the prevalence and geographic distribution of infections caused by viruses of a singular subtype as well as coinfections caused by two or more HIV-1 strains of distinct subtypes. To address this need, we have developed a genetic method based on restriction fragment length polymorphism (RFLP) to screen for these two types of infections within infected populations. In this assay, restriction enzymes may be used to predict the phylogroup of HIV-1 infected samples. A 297 bp pol fragment spanning the entire viral protease gene and a 311 bp fragment of the p24 gag region are used for this analysis. The viral regions are amplified by nested PCR using DNA templates from uncultured peripheral blood mononuclear cells (PBMC) or virus culture. Classification of HIV-1 strains to well defined subtypes B, D, F, and A/C is done by sequential endonuclease restriction analysis of a PCR amplified-protease gene followed by analysis of the p24 gag region. The electrophoretic migration patterns visualized by ethidium bromide staining or by radiolabeled probes are then determined on a 10% polyacrylamide gel. In infections caused by viruses of a singular subtype, a single restriction pattern is detected, whereas in multiple infections caused by two or more viral strains of different subtypes, the combination of different digestion patterns are observed in infected individuals. Using this methodology we have screened for genetic variations in HIV-1 proviral DNA from thirty-three Brazilian samples. Our RFLP procedure classified thirty-two samples as single infections caused by viruses of subtypes B (31) and F (1), and one sample as dual infection caused by distinct viral strains. Subsequent sequence and phylogenetic analysis of the viral protease gene in lymphocytes of all these patients confirmed our RFLP findings in single infections, and demonstrated the existence of two distinct HIV-1 strains of subtypes F and D in a patient which lymphocytes showed the simultaneous presence of two different digestion patterns. As up to now, single infections caused by subtype D variants were not identified in Brazil, our data provide the first evidence of subtype D HIV-1 in this country. Because sequencing of HIV proviral DNA is not particularly practical for large-scale molecular epidemiological studies, the protease/gag-based RFLP screening method will be useful to predict the phylogroup of HIV-1, and to identify multiple infections caused by HIV-1 strains of distinct subtypes. We believe that this information is crucial for both evaluation of the HIV-1/AIDS pandemic and intervention strategies.

For her own good: protecting (and neglecting) women in research

In gender mythology woman is nature, the embodiment of life, destruction, and death. Semantically encoded in good and evil, the one conceptual stability woman represents is ambivalence. As a walled garden in which nature works its demonic sorcery, she turns a gob of refuse into a spreading web of sentient being, floating on the snaky umbilical by which she leashes every man. But as an ontological entity, woman is therealFirst Mover. The pregnant woman is devilishly complete. She needs nothing and no one.2 Confronted with the terrible sense of woman's power, man is forced to wrestle with her nature to gain his identity, never to fall back into her. Man is the essential, the norm, the absolute One without reciprocity. Woman is “the Other, posed by the One to define itself, the inessential who never goes back to being the essential and the absolute Other without reciprocity.

Potential impact of low efficacy HIV-1 vaccines in populations with high rates of infection

A safe and effective HIV vaccine to prevent infection and/or to moderate disease is urgently needed. Research progress has been slower than anticipated for a variety of reasons including uncertainty over which immunogen to use (i.e. recombinant subunit envelope proteins or whole HIV-1 products), confusion on which immunological markers best correlate with protection, the relevance of the HIV-1 chimpanzee model to infection in humans and the significance of the rapid evolution of HIV-1, with different clades of the virus emerging in different parts of the world. However, what some would interpret as encouraging results, from Phase I and II trials of recombinant envelope glycoprotein vaccines, have raised the question of whether the time is right to start Phase III trials in humans with immunogens that may have low to moderate efficacy. By using mathematical models and data from epidemiological studies, we examine the potential impact of such vaccines within heterosexual communities with high rates of infection. Analyses suggest that it will be difficult to block HIV-1 transmission even with very high levels of mass vaccination. The cost of sustaining high levels of herd immunity with a vaccine of short protection duration is likely to be high. However, assessments of impact over the long duration of an HIV-1 epidemic indicate that many cases of HIV infection and associated mortality can be prevented by immunogens with efficacy of 50% or less and a five year protection duration.(ABSTRACT TRUNCATED AT 250 WORDS)