Highly variable sequences in the env V3 region of HIV type 1 distributing among Thai carriers from 1995 to 1997

Molecular evolution of the HIV-1 Thai epidemic between the time of RV144 immunogen selection to the execution of the vaccine efficacy trial

The RV144 HIV-1 vaccine trial (Thailand, 2003 to 2009), using immunogens genetically matched to the regional epidemic, demonstrated the first evidence of efficacy for an HIV-1 vaccine. Here we studied the molecular evolution of the HIV-1 epidemic from the time of immunogen selection to the execution of the efficacy trial. We studied HIV-1 genetic diversity among 390 volunteers who were deferred from enrollment in RV144 due to preexisting HIV-1 infection using a multiregion hybridization assay, full-genome sequencing, and phylogenetic analyses. The subtype distribution was 91.7% CRF01_AE, 3.5% subtype B, 4.3% B/CRF01_AE recombinants, and 0.5% dual infections. CRF01_AE strains were 31% more diverse than the ones from the 1990s Thai epidemic. Sixty-nine percent of subtype B strains clustered with the cosmopolitan Western B strains. Ninety-three percent of B/CRF01_AE recombinants were unique; recombination breakpoint analysis showed that these strains were highly embedded within the larger network that integrates recombinants from East/Southeast Asia. Compared to Thai sequences from the early 1990s, the distance to the RV144 immunogens increased 52% to 68% for CRF01_AE Env immunogens and 12% to 29% for subtype B immunogens. Forty-three percent to 48% of CRF01_AE sequences differed from the sequence of the vaccine insert in Env variable region 2 positions 169 and 181, which were implicated in vaccine sieve effects in RV144. In conclusion, compared to the molecular picture at the early stages of vaccine development, our results show an overall increase in the genetic complexity of viruses in the Thai epidemic and in the distance to vaccine immunogens, which should be considered at the time of the analysis of the trial results.

Aberrant life cycle of human immunodeficiency virus type 1 CRF15_01B-like clinical isolates from Thailand in human CD4+ T-cell lines

Human immunodeficiency virus type 1 (HIV-1) is separated into several subtypes and circulating recombinant forms (CRFs). Here, infections of 4 clinical isolates (0-47-1, CU98-26, CU98-28, and CU98-31) from Thailand were examined in human CD4(+) T-cell lines, MT-4 and MOLT-4. The CU98-26 isolates in both cells and 0-47-1 in MT-4 established chronic infections, as in control 2 subtype B isolates from Japan, while 0-47-1 in MOLT-4 caused a latent infection. In contrast, CU98-28 and CU98-31 established aberrant infections in both cells. Integrated provirus was detected in all the chronic infections, including 0-47-1 in both cells. In contrast, extrachromosomal circular forms of HIV-1 DNA were detected in CU98-28- and CU98-31-infected cells, whereas the amount of the integrated form was below the limit of detection. Interestingly, phylogenetic trees and sequencing revealed that all the Thai isolates, except 0-47-1, displayed CRF15_01B-like mosaic structures of CRF01_AE with subtype B-like sequences in several regions that were apparently different from those of the inocula in peripheral blood mononuclear cells. Thus, in the infections of most of the above Thai isolates it was suggested that a minor population with mosaic patterns having multiple breakpoints between CRF01_AE and subtype B in the inocula could be selected by the T-cell lines.

Construction and characterization of an infectious molecular clone derived from the CRF01_AE primary isolate of HIV type 1

An infectious molecular clone (named p95TNIH022) was constructed using long-range polymerase chain reaction products derived from a clinical isolate (95TNIH022) of HIV-1 CRF01_AE obtained from an asymptomatic Thai carrier in 1995. The virus in the supernatant from p95TNIH022-transfected 293T cells showed infectivity in peripheral blood mononuclear cells (PBMCs) as well as in MAGIC5 cells, which express CD4 and CCR5, but not in the original MAGI cells, indicating that p95TNIH022 is an infectious molecular clone with CCR5 tropism. Interestingly, p95TNIH022-derived virus induced profound cell killing in infected PBMCs, as in cells infected with the parental isolate.

Ability to induce p53 and caspase-mediated apoptosis in primary CD4+ T cells is variable among primary isolates of human immunodeficiency virus type 1

Infection with human immunodeficiency virus type 1 (HIV-1) is associated with dramatic depletion of CD4(+) T cells, the major HIV-1-induced pathogenesis. Apoptosis has been suggested to play an important role for the T cell depletion and a number of mechanisms have been proposed for the apoptosis in T cells. Here, we compared the levels for apoptosis induction in primary peripheral blood mononuclear cells (PBMCs) among several laboratory strains and primary isolates of the HIV-1 subtypes B and E. The results showed that apoptosis in infected PBMCs, preferentially in CD4+ T cell population, became detectable around the time for virus production by flow cytometric terminal transferase dUTP nick end labeling (TUNEL) technique and staining with the nuclear dye Hoechst 33342. The abilities to induce apoptosis in PBMCs were highly variable in individual isolates. The increase of p53 protein in infected PBMCs, which was initiated before virus production, was observed in infected PBMCs and the levels of p53 protein were almost proportional to the rates of the isolates to induced apoptosis. The cells infected and cultured in the presence of Z-VAD-FMK had significantly decreased cell mortalities, indicating that activated caspases also played a significant role in the apoptosis. Thus, HIV-1-induced apoptosis in primary T cells was accompanied by the p53 protein and caspase activation at varied levels in primary isolates.

Construction and in vitro characterization of a molecularly cloned human immunodeficiency virus type 1 library

Development of a safe and effective vaccine against human immunodeficiency virus (HIV) is urgent, but many concerns regarding the safety and efficacy of the currently developing vaccines remain. A major hindrance in HIV vaccine development is the genetic diversity, a hallmark of HIV biology, and a poor understanding of how HIV vaccine prevents the emergence of escape variants during infection and progression of AIDS. Here, we developed a method to construct a molecularly cloned viral library. This technique employs a long-range polymerase chain reaction (PCR) to amplify a virtually full-length HIV type 1 (HIV-1) provirus genome from peripheral blood mononuclear cells (PBMCs) infected with CRF01_AE (subtype E) Thai primary isolate. Among randomly selected 93 clones, 41 with a full-length sequence were able to replicate in PBMCs, 5 of which induced strong cytopathic effects. Replication kinetics also showed that the parental virus was intermediate among the clones. Thus, the molecular library prepared by this method showed the quasi-species in infected cells and this method could provide a new possibility for the development of an order-made therapeutic vaccine against HIV-1.

Full-length sequences of two CRF01_ae (subtype e) HIV type 1 isolates from 1995 samples of patients with sexually transmitted diseases in Thailand

We isolated two CRF01_AE human immunodeficiency virus type 1 (95TNIH022 and 95TNIH047) from the 1995 blood samples derived from asymptomatic carriers in Ubonratchatani province of northeastern Thailand. Both isolates can replicate in peripheral blood mononuclear cells, but not in several T cell lines examined. The full-length sequences recovered from proviruses in infected cells by long-range polymerase chain reaction were determined. Phylogenetic analyses of these sequences at individual genes showed them to be closely related to those of reported CRF01_AE HIV-1, such as 1990 isolate CM240 and 1993 isolate 93TH253. Two isolates in this study also showed a similar pattern of CRF01_AE mosaicism and a similar structure at the long terminal repeat, i.e., a copy number of NF-kappaB binding sites, sequence at the TATA box, and the putative secondary structure of stem-loop in the transactivation response region. Our results showed that 1995 Thai E isolates could contribute to our understanding of the epidemiology, pathogenesis, and diagnostics of HIV-1 CRF01_AE and further to vaccine development.

Variable sequences in the long terminal repeat and Its downstream region of some of HIV Type 1 CRF01_AE recently distributing among Thai carriers

Human immunodeficiency virus type 1 (HIV-1) proviral DNA sequences in and downstream of the 5' long terminal repeat (LTR) were compared among samples obtained from 13 HIV-1 CRF01_AE-infected individuals in Thailand from 1998 to 1999. Eleven individuals had highly conserved sequences compared with previously reported CRF01_AE viruses. However, T cell-specific factor (TCF)-1alpha motif, which is located just beside the 3' terminus of the nef sequence, was duplicated in 2 out of the 13 subjects, one of whom had also lost the 24 nucleotides next to the 3' of the primer-binding site. Thus, several characteristics of CRF01_AE LTR and gag-leader sequence were identified in some samples recently obtained in Thailand.

Low or no antibody responses to human immunodeficiency virus type 1 Nef in infected carriers with subtype E, in contrast to subtype B that showed antibodies preferentially recognizing subtype-specific Nef epitopes

The viral accessory gene product Nef has been shown to play an important role in human immunodeficiency virus type 1 (HIV-1)-induced pathogenesis. Only little information is available regarding the differences in the host immune responses against Nef protein and its function in vivo among different subtypes of HIV-1. In the present study, we showed marked differences in the immune responses to Nef protein between subtypes B and E. The amino acid sequence in subtype E Nef showed 72% homology with that in subtype B. Most murine monoclonal antibodies obtained by immunization with subtype B or E Nef protein showed cross-reactivity with both Nef proteins (80 and 67%, respectively). Next, we focused on the immune responses among infected Japanese and Thai individuals. Subtyping of the individuals into B and E was carried out by enzyme-linked immunosorbent assay (ELISA) using synthetic peptides corresponding to the V3 loop representing the principal neutralizing domain. Most of the sera from these individuals reacted strongly with Gag p24 proteins derived from subtypes B and E at similar levels. However, the immune responses among these individuals to Nef protein were markedly different. Some subtype B-infected Japanese and Thai individuals (40 and 35%, respectively) showed higher levels of anti-Nef antibodies, although these antibodies preferentially recognized epitopes specific to subtype B. On the other hand, most of the subtype E-infected Japanese and Thai individuals showed low or no antibody responses to Nef proteins. Thus, immune responses to Nef were markedly different between subtypes B- and E-infected carriers, suggesting different function(s) for Nef in AIDS pathogenesis. Further, vaccine design must take into account the different subtypes of HIV-1.