Sequence variability in human immunodeficiency viruses

Viral vectors as vaccine carriers

This chapter reviews the performance of viral vectors based on adenoviruses or adeno-associated virus as vaccine carriers for infectious diseases. Replication-defective adenovirus vectors based on multiple human or non-human serotypes have consistently induced potent transgene product-specific B and T cell responses and are increasingly being explored in human clinical trials. The immunogenicity of most vectors based on adeno-associated virus vectors has been poor with the exception of a recently described hybrid vector from rhesus macaques that due to its ability to induce potent responses in mice warrant further investigation.

Characterization of gag and pol sequences from long-term survivors of human immunodeficiency virus type 1 infection

We previously identified a group of 10 long-term survivors (LTS) of human immunodeficiency virus type 1 (HIV-1) infection. Extensive biological analysis revealed that some of these individuals do well, at least in part, because they possess weakened or attenuated viruses. Also, previously, to determine the genotype associated with the attenuated phenotype in vivo, we characterized nef, vif, vpr, vpu, env, and LTR in our cohort of LTS. In this study, we analyzed gag and pol genes derived from eight individuals in our cohort. For each subject multiple full-length gag and pol clones were obtained for analysis. In most cases, the sequences derived from the LTS had an intact open reading frame. At the protein level, there were no discernible differences between the sequences derived from LTS and those derived from patients with AIDS. Thus, no common defect in gag and pol was found in our cohort. One individual (subject SF), however, had only Gag-defective proviral sequences (10 of 10) in his peripheral blood mononuclear cells. Furthermore, longitudinal studies of the samples collected from SF over a 2-year period showed that all p17 gag clones sequenced (24 of 24) were defective due to G-to-A hypermutations. This viral defect in Gag may provide the molecular basis for this individual's extremely low viral load and long-term asymptomatic state. These results, together with previous findings in our LTS cohort, reinforce the notion that it is unlikely that a single common viral genetic determinant accounts for the lack of disease progression in all cases. Multiple host and viral factors undoubtedly contribute to the well-being of LTS of HIV-1 infection.

Genotypic and phenotypic characterization of long terminal repeat sequences from long-term survivors of human immunodeficiency virus type 1 infection

Human immunodeficiency virus type 1 (HIV-1)-infected individuals who remain asymptomatic despite prolonged infection present a unique opportunity to understand virologic and immunologic factors involved in the pathogenesis of AIDS. We have previously identified a group of long-term survivors (LTS) who are clinically healthy and immunologically normal despite 13 to 15 years of HIV-1 infection. In this study, we examined the 5' long terminal repeat (5' LTR) sequences in eight of these LTS. A total of 29 nucleotide sequences were obtained from their peripheral blood mononuclear cells (PBMC). Analysis of these sequences revealed no gross deletions within the 5' LTR. Seven of the eight subjects shared nearly identical consensus sequences in the binding sites for NF-kappaB, Sp1, and the viral trans-activator Tat. In multiple samples from one individual (Pt 5), however, G-to-A hypermutations were found throughout the entire region, suggesting a genetically defective 5' LTR. The effects of the observed genetic variations on LTR transcription were studied by transient transfection of an LTR-driven luciferase reporter gene and by infection with a full-length recombinant HIV-1 containing a luciferase reporter (HIVHXBLTRluc). A wide range of basal and Tat-induced transcriptional activities was found among the 5' LTR from seven of the eight LTS in both transfected 293 cells and donor PBMC, suggesting a functionally intact 5' LTR in these individuals. It is therefore unlikely that defects in the 5' LTR are the underlying explanation for the benign clinical course associated with these seven individuals. However, functional abnormalities were found in the LTR from Pt 5 in directing both heterologous and viral gene expression, providing a possible genetic explanation for the low viral load and prolonged asymptomatic state of this individual. Last, a similar overall degree of genetic diversity was found among viruses from the LTS compared to those from patients with AIDS, reinforcing the notion that a strong correlation between the degree of genetic diversity and the rate of disease progression is unlikely.

Genetic characterization of vif, vpr, and vpu sequences from long-term survivors of human immunodeficiency virus type 1 infection

The identification of HIV-1-infected individuals who remain asymptomatic despite prolonged infection presents a unique opportunity to understand virologic and host factors involved in the pathogenesis of AIDS. We have previously identified 10 long-term survivors (LTS) who are clinically healthy and immunologically normal despite 13 to 15 years of HIV-1 infection. In this study, we examined three accessory genes of HIV-1, vif, vpr, and vpu, in these LTS. A total of 52 vif, 54 vpr, and 55 vpu nucleotide sequences were obtained from the peripheral blood mononuclear cells of these patients. Analysis of these sequences revealed no gross deletions or insertions. Most of the clones were full-length with an intact open reading frame. Phylogenetic analyses of the vif, vpr, and vpu sequences from the LTS suggested that the HIV-1 strains found in the study subjects are not significantly different from those found in patients with AIDS and that the viruses in the LTS are unlikely to share a common genetic origin. Furthermore, a similar degree of overall genetic diversity between viruses from the LTS and AIDS patients suggests that there is unlikely a significant correlation between the degree of genetic diversity and the rate of disease development. Factors other than genetic divergence, such as viral load and phenotype, are likely to impact more on disease status.

HIV-1 pol sequences from India fit distinct subtype pattern

HIV-1 isolates are classified phylogenetically in several subtypes or clades according to env and gag coding sequences. Viral subtypes tend to cluster geographically. DNA sequences encoding the p51 subunit of reverse transcriptase were obtained by nested polymerase chain reaction from peripheral blood mononuclear cells of two HIV-1-seropositive individuals from New Delhi and three from Pune, in northern and western India, respectively. These isolates were previously characterized as subtype C according to their env sequences. Based on phylogenetic analysis, the reverse transcriptase coding region of these isolates is distinct from those of subtype A, subtype B, subtype D, and group O of HIV-1 viruses. The nucleotide divergence of these Indian pol sequences (3.3%) is similar to that of existing sequences for subtype B and subtype D viruses. This result supports the epidemiologic data of a more recently introduced HIV-1 epidemic in India. Based on the corresponding env sequences, the pol sequences described in this report are subtype C.

Genetic variation of HIV type 1 in four World Health Organization-sponsored vaccine evaluation sites: generation of functional envelope (glycoprotein 160) clones representative of sequence subtypes A, B, C, and E. WHO Network for HIV Isolation and Characterization

As part of the WHO Network for HIV Isolation and Characterization, we PCR amplified, cloned, and sequenced gp120 and gp160 genes from 12 HIV-1 isolates collected in four WHO-sponsored vaccine evaluation sites (Brazil, Rwanda, Thailand, Uganda). Envelope clones were derived from PBMC-grown isolates obtained from asymptomatic individuals within 2 years of seroconversion. Analysis of their deduced amino acid sequences identified all but one to contain an uninterrupted open reading frame. Transient expression and biological characterization of selected gp160 constructs identified six clones to encode full length and functional envelope glycoproteins. Phylogenetic analysis of their nucleotide sequences revealed that they represent HIV-1 subtypes A, B, C, and E. Since current knowledge of HIV-1 envelope immunobiology is almost exclusively derived from subtype B viruses, these reagents should facilitate future envelope structure, function and antigenicity studies on a broader spectrum of viruses. This should assist in the design and evaluation of effective vaccines against HIV-1.

The induction of in vivo superinfection and recombination using feline immunodeficiency virus as the model

This study investigated the hypothesis that under certain conditions, superinfection of cats with feline immunodeficiency virus (FIV), may occur. One FIV isolate (T91) was used to inoculate three FIV and FeLV-free cats. Blood from an FIV-infected cat (N), which contained two variants and differed from T91 by at least 5% in nucleotide sequence in the env gene, was inoculated into a fourth cat. Both T91 and blood from N were inoculated simultaneously into a fifth cat. After 22 weeks, two of the three cats initially infected with T91 were challenged with blood from N. At 30 weeks following initial infection, peripheral blood mononuclear cells were obtained from all cats, DNA was extracted, and a segment of the env gene was PCR amplified, cloned and sequenced. Nucleotide sequence analysis of the cloned PCR product showed that virus strains used in initial infection were recovered from cats not challenged with a second variant. Challenge of cats with the blood of N following initial infection with T91 resulted in superinfection occurring in one cat and recombination occurring in the other. Furthermore, the use of blood as a source of challenge, in cats where superinfection and simultaneous infections were attempted, may have induced the appearance of variants which more closely resembled the most heterologous strain present in the infectious source.

HIV-1 variation: consequences for disease progression and vaccine strategies

HIV-1 displays a high degree of biological heterogeneity in vitro, differing in tropism, kinetics of replication, cytopathogenicity, resistance to antiviral drugs and susceptibility to serum neutralization. Some of these properties can be linked to pathogenesis in the host. HIV variation is a major challenge to the development of effective vaccine or antiviral therapies.

The needs and hopes for an AIDS vaccine

This article reviews the many difficulties met in the development of an effective vaccine against human immunodeficiency virus (HIV), including the considerable antigenic variability of the virus, its intracellular mode of transmission, its mucosal port of entry, and the persistent nature of the infection. Progresses in the development of prototype vaccines in animal models are discussed together with the results of initial clinical trials in human volunteers.

Development of a vaccine for the prevention of AIDS, a critical appraisal

The pathogenesis and clinical expression of HIV-1 infection in humans is considered in terms of classical pathogenetic studies of viral infections for which successful vaccines have been produced. The unique features of HIV pathogenesis are defined, and gaps in knowledge identified as a framework for considering designs for immune intervention. Envelope-derived candidate vaccines have been used in immunization and challenge experiments in SIV/macaque or HIV/chimpanzee models, presented either as vaccinia recombinant vectors or as subunits, singly or in sequence. These studies have been paralleled by clinical trials for safety and immunogenicity in seronegative individuals. Data generated will permit comparison of immune responses to specific antigens and delivery systems in animal models and in humans. In limited studies conducted under optimized conditions, non-human primates have been protected against virus challenge when immunized with some candidate vaccines or following passive transfer of high-titred antibody. Consideration of current information suggests that in order to prevent HIV infection it may be necessary to devise new strategies capable of inducing and maintaining high threshold titres of biologically relevant antibody as well as persistence of active cytotoxic T cells recognizing multiple epitopes.