Non-syncytium-inducing Research Articles

Identification of novel molecular determinants of co-receptor usage in HIV-1 subtype F V3 envelope sequences

HIV-1 determinants of coreceptor usage within the gp120 V3 loop have been broadly studied over the past years. This information has led to the development of state-of the-art bioinformatic tools that are useful to predict co-receptor usage based on the V3 loop sequence mainly of subtypes B, C and A. However, these methods show a poor performance for subtype F V3 loops, which are found in an increasing number of HIV-1 strains worldwide. In the present work we investigated determinants of viral tropisms in the understudied subtype F by looking at genotypic and structural information of coreceptor:V3 loop interactions in a novel group of 40 subtype F V3 loops obtained from HIV-1 strains phenotypically characterized either as syncytium inducing or non-syncytium inducing by the MT-2 assay. We provide novel information about estimated interactions energies between a set of V3 loops with known tropism in subtype F, that allowed us to improve predictions of the coreceptor usage for this subtype. Understanding genetic and structural features underlying HIV coreceptor usage across different subtypes is relevant for the rational design of preventive and therapeutic strategies aimed at limiting the HIV-1 epidemic worldwide.

Influence of HIV-1 Genetic Variability on Vertical Transmission and Pathogenesis

HIV-1 exists as a genetically heterogeneous population within infected individuals and in infected population. Genetic variability or viral heterogeneity plays an important role in transmission, pathogenesis, immune response, disease progression and therapy as well as is the most effective way for the virus to evade the host immune response and persists in infected individuals. We have used HIV-1 infected motherinfant pairs as a transmitter-recipient model to elucidate the role of the molecular and biological properties of HIV-1 associated with transmission and pathogenesis. HIV-1 sequences derived from infected mothers were more heterogeneous than their younger infected infants’ HIV-1 sequences. However, the infants’ HIV-1 sequences diversified as they grew older. HIV-1 infants’ sequences were different from each other but similar or closer to their mother’s sequences. We found that the minor genotypes of HIV-1 found in mothers were transmitted to their infants, which was initially maintained as a homogeneous population in infants and diversified as the infants grew older. In addition, the phenotype of these minor geno types was macrophage-tropic, nonsyncytium inducing (NSI) referred as R5 HIV-1. We also analyzed several other regions of HIV-1 genome, including env, gag p17 and NC, pol RT, tat, rev, vif, vpr, vpu and nef infected mother-infant pairs and found that there was a high functional conservation of these genes. These findings suggested that HIV-1 heterogenity plays an important role in vertical transmission and pathogenesis. The properties of transmitted viruses and those that are associated with disease progression should be targeted for the development of new strategies for prevention and treatment of HIV-1 infection. Research should focus utilizing these findings in the development of better strategies for prevention and treatment of HIV-1.

Subtype-specific differences in human immunodeficiency virus type 1 co-receptor usage in Northern Kenya

Background HIV-1 phenotype variability plays an important role in HIV-1 transmission and pathogenesis of AIDS. The basis of heterogeneity between the phenotypes is known to be the differential use of chemokine receptors as co-receptors for viral entry. Beta Chemokine receptor-5 (CCR5) using variants are associated with acute infections, macrophage tropism, non syncytium inducing (NSI) phenotype and slow progression to AIDS. Alpha chemokine receptor-4 (CXCR4) using variants evolve later in infection in about 50 % of the patients and are associated with T cell lines tropism, syncytium induction, accelerated T cell depletion and Rapid progression to AIDS. HIV-1 co-receptor usage and phenotypes are mapped in the third variable region (V3) of the gp120 env gene. Methods One hundred and thirty five (135) whole blood samples were collected from HIV-1 infected patients in Northern Kenya. Proviral DNA was extracted using DNazol and ethanol precipitation. HIV-1 V3 region was amplified by nested PCR using C2V3 primers. Amplicons were sequenced directly using Big Dye technology in the ABI Prism Genetic Analyzer to generate gp120 V3 loop sequences. Bioinformatics tools were used to determine co-receptor usage from the sequences obtained. Results CXCR4 usage was most dominant with 94 out of 135 samples(69.6 %) using this co-receptor compared to CCR5 which was used by 29 of the 135 (21.8 %) samples and dual co-receptor usage found in 12 of the 135(8.6%) samples tested. Conclusion Most patients were inferred to be in late stages of infection and likely to be rapidly progressing to AIDS. Based on these results from co-receptor usage data, HIV-1 incidence rate was likely to be low. Co-receptor usage was observed to be associated with HIV-1 subtypes. Poor alignment of the Northern Kenya sequences with the training data for the classifier software necessitates the need for development of Bioinformatic software relevant for locally circulating HIV-1 subtypes.

Isolation and Biological Characterization of Non-B HIV Type 1 from Kenya

The isolation and characterization of primary strains of human immunodeficiency virus (HIV) is a vital tool for assessing properties of viruses replicating in HIV-infected subjects. HIV-1 isolation was carried out from 30 HIV-1-infected patients from a Comprehensive Care Clinic (CCC) after informed consent. Virus was successfully isolated from 9 out of the 30 samples investigated. Seven of the isolates were from drug-naive patients while two were from patients on antiretroviral drugs. The isolates were biologically phenotyped through measurement of the syncytium-inducing capacity in MT2 cells. Six of the isolates exhibited syncytia induction (SI) associated with CXCR4 coreceptor usage while three of the isolates were non-syncytia-inducing (NSI) isolates associated with CCR5 coreceptor usage. In addition, the replication capacity of the isolates was further determined in established cell line CD4(+) C8166. Indirect immunofluorescence assay was used to check the antigen expression on the cells as a supplementary test. HIV-1 isolation success was 70% (7/10) and 20% (2/20) in naive and drug-experienced patients, respectively. The majority of the viral isolates obtained (6/9) were of the SI phenotype, though SI virus strains are rare among non-B subtypes. A significant correlation between virus isolation success and viral load was established. Coreceptor use data for heavily treatment-experienced patients with limited treatment options are scanty and this is the group with perhaps the most urgent need of novel antiretroviral agents.

Performance of Genotypic Algorithms for Predicting HIV-1 Tropism Measured against the Enhanced-Sensitivity Trofile Coreceptor Tropism Assay

The objectives of this study were to assess the performance of genotypic algorithms for predicting CXCR4-using virus, with enhanced sensitivity Trofile HIV coreceptor tropism assay (ES Trofile) as the reference, and to compare the concordance/accuracy of genotypic tests with ES Trofile and with the original Trofile assay. Paired phenotypic and genotypic determinations of HIV-1 coreceptor usage were compared in plasma samples from HIV-1-infected patients. Sequencing of the third hypervariable (V3) loop of the viral gene and phenotypic assays were performed for each sample. Genotypic rules used to predict tropism were Geno2pheno (false-positive rate at 1 to 20%), position-specific scoring matrix X4R5 (PSSM(X4R5)) and PSSM(sinsi) (where "sinsi" stands for syncytium inducing and non-syncytium inducing), and the 11/25, 11/24/25, and net charge rules. Two hundred forty-four phenotypic and genotypic samples were tested. Coreceptor usage was obtained from ES Trofile for 145 (59%) samples and from Trofile for 99 (41%) samples. The highest concordance (82.6%) was obtained with PSSM(X4R5) when ES Trofile was used as the reference. Geno2pheno at a 20% false-positive rate showed the highest sensitivity (76.7%) for CXCR4-using virus detection with ES Trofile. Samples from naïve subjects and those with CD4 cell counts between 200 and 500 cells/mm(3) showed the best predictive performance. Overall, the accuracy of the bioinformatics tools to detect CXCR4-using virus was similar for ES Trofile and Trofile; however, the negative predictive values for genotypic tools with ES Trofile were slightly higher than they were with Trofile. The accuracy of genotypic algorithms for detecting CXCR4-using viruses is high when using ES Trofile as the reference. Results are similar to those obtained with Trofile. The concordance with ES Trofile is better with higher CD4 cell counts and nonexposure to antiretroviral therapy.

Complete Genome Sequencing of a Non-syncytium-Inducing HIV Type 1 Subtype D Strain from Cape Town, South Africa

The fast growing HIV-1 epidemic in South Africa is mainly caused by HIV-1 group M subtype C, spreading via heterosexual transmission. In South Africa HIV-1 subtype B and D viruses were responsible for the initial epidemic during the 1980s, primarily in the homosexual population. This study describes the full-length PCR amplification and sequencing of an HIV-1 subtype D strain recovered from plasma from a sample taken during 1990. This is only the second full-length non-syncytium-inducing (NSI) subtype D strain described. Although restricted, the subtype D strain is still being detected in the South African population.

Role of HIV-1 subtype C envelope V3 to V5 regions in viral entry, coreceptor utilization and replication efficiency in primary T-lymphocytes and monocyte-derived macrophages

BackgroundSeveral subtypes of HIV-1 circulate in infected people worldwide, including subtype B in the United States and subtype C in Africa and India. To understand the biological properties of HIV-1 subtype C, including cellular tropism, virus entry, replication efficiency and cytopathic effects, we reciprocally inserted our previously characterized envelope V3–V5 regions derived from 9 subtype C infected patients from India into a subtype B molecular clone, pNL4-3. Equal amounts of the chimeric viruses were used to infect T-lymphocyte cell lines (A3.01 and MT-2), coreceptor cell lines (U373-MAGI-CCR5/CXCR4), primary blood T-lymphocytes (PBL) and monocyte-derived macrophages (MDM).ResultsWe found that subtype C envelope V3–V5 region chimeras failed to replicate in T-lymphocyte cell lines but replicated in PBL and MDM. In addition, these chimeras were able to infect U373MAGI-CD4+-CCR5+ but not U373MAGI-CD4+-CXCR4+ cell line, suggesting CCR5 coreceptor utilization and R5 phenotypes. These subtype C chimeras were unable to induce syncytia in MT-2 cells, indicative of non-syncytium inducing (NSI) phenotypes. More importantly, the subtype C envelope chimeras replicated at higher levels in PBL and MDM compared with subtype B chimeras and isolates. Furthermore, the higher levels subtype C chimeras replication in PBL and MDM correlated with increased virus entry in U373MAGI-CD4+-CCR5+.ConclusionTaken together, these results suggest that the envelope V3 to V5 regions of subtype C contributed to higher levels of HIV-1 replication compared with subtype B chimeras, which may contribute to higher viral loads and faster disease progression in subtype C infected individuals than other subtypes as well as rapid HIV-1 subtype C spread in India.

R5 to X4 coreceptor switch of human immunodeficiency virus type 1 B’ and Bʼ/C recombinant subtype isolates in China

he chemokine receptors CCR5 and CXCR4 play an important role as coreceptors for human immunodeficiency virus type 1 (HIV-1) entring into cells. HIV-1 isolates can be distinguished by the chemokine coreceptors. Nonsyncytium inducing (NSI), macrophage tropic viruses utilizing CCR5, are called R5 viruses; syncytium inducing (SI) isolates use CXCR4 and known as X4 viruses. R5 viruses generally are associated with latent stage of infection and X4 viruses with later, more severe stages of infection. This phenotypic switch from R5 to X4 correlated with the decreased CD4

Sequence analysis of the full-length glycoprotein 120 gene of HIV-1 CRF01_AE in Fujian, China

To characterize full length glycoprotein 120 gene variations of 21 HIV-1 CRF01_AE isolated in Fujian, China, so as to help in the immunogenic research and vaccine design. Twenty-one peripheral blood samples were randomly collected form 100 HIV-1CRF01_AE infected persons in Fujian 2004 approximately 2005. DNA was extracted, Nested-PCR was used to amplify the envelop protein full length gp120 gene. The PVR products underwent Sepharose electrophoresis. Genotype identification was done by BLAST program. Sequence analysis was conducted with Megalign and CLUSTAL1.83. Phylogenetic tree and genetic distance were analyzed by Neighbor-joining method and Distance program of MEGA software. The amino acid similarity analysis was done with DNASIS, and N-glycosylation site analysis was done with N-GLYCOSIDE program. Phylogenetic tree analysis showed that these 21 HIV-1 subtype CRF01_AE strains clustered with the AE reference strain, with an overall genetic distance of 9.5% +/- 2.5%. There were four types of V3 loop central motif: GPGQ (71.43%), GPGR (19.05%), GPGH (4.76%), and GQGQ (4.76%). Prediction of the potential use of co-receptors on the basis of the critical amino acids within V3 loop disclosed potential use of CCR4/CCR5 in 16 of the 21 sequences (76.19%), potential use of CCR4/CCR5 in 1 sequence (4.76%), and 4 samples (19.05%) failed to be predicted. Amino acid sequence analysis showed that V3 region was relatively conservative, whereas V1, V2, V4, and V5 wee more variable. N-linked glycosylation site analysis showed that most of the 21 sequences were relatively conservative. Sequences analysis show Most of the CRF01_AE virus strains in Fujian have a complicated source, and most of them are closely related to those of Southeast Asia and belong to the non-syncytium inducing (NSI) type.

High specificity of V3 serotyping among human immunodeficiency virus type‐1 subtype C infected patients with varying disease status and viral phenotype

V3 serotyping is a technique for determining HIV-1 genetic subtype based on the binding of antibodies from patient sera or plasma to synthetic V3 peptides derived from subtype consensus sequences. Variation in the performance of this assay has been attributed to V3 sequence heterogeneity, the degree of which varies with patient disease progression, virus co-receptor usage, and genetic subtype. This study assessed the performance of a competitive peptide enzyme immunoassay (cPEIA) in samples from HIV-1 subtype C infected patients with varying disease profiles, including those with syncytium (SI) and non-syncytium-inducing (NSI) viruses. Out of 90 sera tested, 94.4% reacted strongly against the subtype C peptide. There was no significant difference in assay sensitivity among samples from advanced AIDS patients in which humoral immune response may be lower, nor among SI viruses which carry changes in the V3 sequence. Four samples were found to be cross-reactive with other subtypes and one acutely infected patient sample was non-reactive due to low anti-gp120 antibody titers. A significantly higher number of samples showed secondary reactivity to subtype A, compared to other subtypes (P < 0.005). In conclusion, the assay was able to identify HIV-1 subtype C infection with a high level of sensitivity (94%) irrespective of the stage of disease and therefore provides a valuable resource for the large-scale epidemiological monitoring of the spread of HIV-1 subtypes in South Africa.

Single-Round HIV Type 1 Neutralization Measured by ELISPOT Technique in Primary Human Cells

To accurately quantify HIV-1 neutralizing antibody titers in primary human cells, we developed a single round, focus-forming unit (FFU) reduction assay in human peripheral blood mononuclear cells (PBMC). Infected PBMC were enumerated by a reverse ELISPOT technique in which they were incubated under agarose in the presence of a protease inhibitor in anti-p24 antibody-coated microtiter plates. Viral p24, secreted in the immediate vicinity of infected cells and captured by immobilized antibodies, was subsequently stained using gold-labeled anti-p24-antibody and a precipitating silver substrate. The resulting spots were counted visually, without the aid of a microscope, and percent neutralization titers were determined using curve-fitting software. Results of this ELISPOT neutralization assay (ENA) for 15 HIV-positive human specimens were compared with results from a standard PBMC neutralization assay (standard assay) that measured neutralization as a function of p24 concentration by enzyme immunoassay (EIA). The ENA measures FFU reduction of both syncytium-inducing (SI) and non-syncytium-inducing (NSI) primary isolates. Completed assay plates may be retained as a physical record of results or saved as an image using a flat-bed computer scanner.

Differential effects of R5 and X4 human immunodeficiency virus type 1 infection on CD4+ cell proliferation and activation

Human immunodeficiency virus type 1 (HIV-1) isolates can be distinguished by their chemokine coreceptor usage. Non-syncytium-inducing (NSI), macrophage-tropic viruses utilize CCR5 and are called R5 viruses; syncytium-inducing (SI) isolates use CXCR4 and are known as X4 viruses. R5 and X4 HIV isolates are both transmitted but, in most cases, R5 viruses predominate in the blood prior to the development of AIDS-related pathogenesis. The reason for the selective growth of the R5 strain is not known, but could reflect a replication advantage of R5 viruses over X4 viruses in CD4+ cells. To explore this possibility, eight phenotypically distinct viruses were used to infect CD4+ cells and cellular proliferation and activation were evaluated. In unstimulated CD4+ cells, R5 virus isolates increased the level of cell activation compared with X4 virus isolates and uninfected control cells. In CD4+ cells that were stimulated with interleukin 2, both R5 and X4 viruses were found to decrease the level of cell proliferation and reduce the majority of the activation markers studied when compared with uninfected control CD4+ cells from the same donors. However, although equal amounts of CD4+ cells were infected, R5 virus-infected CD4+ cells showed a two- to fourfold increase in cellular proliferation over X4 viruses, as measured by [3H]thymidine incorporation (P=0.001) and nuclear expression of Ki67 (P=0.001). In addition, a larger proportion of CD4+ T cells infected with R5 viruses had significantly higher levels of activation-marker expression (e.g. CD25, CD71 and HLA-DR) than CD4+ T lymphocytes infected with X4 viruses (P<0.02). Taken together, these results indicate that CD4+ cells infected with R5 virus isolates may have a selective advantage over X4 virus-infected CD4+ T cells for survival and, hence, virus spread.

Homeostatic role of IL‐7 in HIV‐1 infected children on HAART: Association with immunological and virological parameters

To investigate the role of IL-7 in HIV-infected children on highly active antiretroviral therapy (HAART) and its association with laboratory parameters related to disease progression. A cross-sectional study in 31 vertically HIV-infected children (median age 8.4 y) treated with HAART, and a longitudinal study in four of those same children was carried out. In both studies, viral load, CD4+ T-cell counts, thymic production of T cells by TCR rearrangement excision circles (TRECs), IL-7 plasma levels and viral phenotype were determined. IL-7 levels were higher in HIV-infected children than in age-matched, uninfected controls. In addition, HIV children with CD4+ T cells between 200 and 500 T cells/mm3 had higher IL-7 levels and lower TREC values than HIV-infected children with CD4+ T cells >500 T cells/mm3. IL-7 levels were higher in children with syncytium-inducing (SI) phenotype than in those with non-syncytium-inducing (NSI) variants. During the follow-up of four HIV children, the decrease in viral load after HAART was always associated with a recovery of CD4+ T cells and TRECs, which was followed by a decrease in IL-7 returning to the levels present prior to the drop in CD4+ T cells. The four HIV-infected children had SI/X4 isolates in PBMC before HAART, and the viral phenotype switched to NSI/R5 after HAART. Our data suggest that IL-7 plays a key role in the maintenance of T-cell homeostasis in HIV-infected children on HAART, both through peripheral expansion and through a thymus-dependent mechanism.

High IL-7 plasma levels may induce and predict the emergence of HIV-1 virulent strains in pediatric infection

HIV-1 infection results in severe immunodeficiency when T-cell loss cannot be compensated. IL-7 is one of the main cytokines involved in the maintenance of T-cell homeostasis. However, IL-7 can also enhance HIV-1 replication in vivo and lead to an accelerated progression of AIDS. The aim of our study was to evaluate if the increase of IL-7 levels in response to CD4+ T cell depletion could favor the emergence of HIV-1 strains with more aggressive phenotypes in pediatric infection. Plasma IL-7 levels were measured in 42 HIV-1 vertically infected infants at different times of infection, and HIV-1 isolates were obtained from primary cell cultures to determine replication rate and syncytium-inducing (SI) capability on MT-2 cell line. IL-7 levels were significantly higher in infants harboring HIV-1 SI strains compared to those with non-syncytium-inducing (NSI) viruses (p<0.0001). Likewise, IL-7 levels were higher in infants with rapid replicating viral strains versus those with slow replicating viruses (p=0.0006). Despite the strong negative correlation between IL-7 levels and CD4+ T lymphocyte counts (r=-0.55, p=0.0001), covariance analysis demonstrated that the high levels of IL-7 were associated with more virulent phenotype features (SI and rapid replicating strains) independently of CD4+ T cell depletion. In 19 of the 42 infants, longitudinal follow-up studies showed that SI to NSI phenotype switch can occur after HAART administration, with a reduction in IL-7 levels and an increase in CD4+ T cell counts. IL-7 response to T-cell depletion may enhance T-cell production, but at the same time may foster HIV-1 disease progression favoring the emergence of more virulent HIV-1 strains characterized by SI capability and rapid replication rate.

Longitudinal Assessment of Immune Response and Viral Characteristics in HIV-Infected Patients with Prolonged CD4+/Viral Load Discordance

Although suppression of HIV-1 RNA below the limit of detection is associated with optimal outcomes, many patients can maintain or increase their CD4(+) count for prolonged time periods in the presence of persistent low-level viremia. We followed seven patients with prolonged (>5 years) discordant CD4(+)/viral load (VL) responses on protease inhibitor (PI)-based highly active antiretroviral therapy (HAART) prospectively for 1 year to assess evolution of immune function, viral phenotype, replication capacity (RC), and resistance profile. Immune function was assessed by qualitative and quantitative measurement of cellular activation (CD38(+)HLA-DR(+) and CD38 antibodies bound per cell), and the interferon (IFN)-() ELISpot assay. Presence of syncytium-inducing (SI) or nonsyncytium-inducing (NSI) viral strains was determined by MT-2 cell culture. RC was measured by a modified rapid recombinant virus assay. The resistance profile was characterized by both genotypic and phenotypic analysis. Over the year of follow-up, IFN-() production to gag persisted, responses to other HIV antigens increased, and markers of cellular activation did not change. NSI virus predominated. The genotypic (GSS) and phenotypic (PSS) susceptibility scores remained stable. Evolution of RC was variable over the year of follow-up, but the RC of viruses remained well below that of wild-type clinical isolates. Thus, CD4(+)/VL discordance can be maintained for periods exceeding 5 years in some patients receiving PI-based HAART without significant evolution of HIV resistance.

Expansion of CCR5+ CD4+ T-lymphocytes in the course of active pulmonary tuberculosis.

Nonsyncytium inducing, macrophage tropic HIV strains predominate in the course of active tuberculosis (TB). The present study assesses the expression of CCR5 in CD4+ T-lymphocytes from blood and bronchoalveolar lavage (BAL) of TB patients, non-TB lung disease controls and healthy controls. Memory (CD45RO+), recently activated (CD69+), proliferating (Ki67+) CCR5+ or CCR3+ CD4+ T-lymphocytes were determined by multiparametric flow cytometry analysis. Results show that BAL CD4+ T-lymphocytes expressing CCR5 or CCR3 were significantly increased when compared to peripheral blood both in patients and in healthy controls. However, the data show that the proportions of peripheral blood CCR5+ CD4+ and CCR3+ CD4+ T-lymphocytes and BAL CCR5+ CD4+ T-lymphocytes, but not BAL CCR3+ CD4+ T-lymphocytes, were significantly increased in TB patients. Furthermore, the observation that BAL CCR5+ CD4+ T-lymphocytes from TB patients expressed early activation markers, were not proliferating and showed down-regulation of CCR5 expression suggests recruitment and trapping at the site of disease. Altogether, these results suggest that the lower respiratory tract mucosa may provide cellular targets accessible for efficient transmission of macrophage tropic HIV-1 variants and that tuberculosis may enhance this phenomenon.

Relationships between infectious titer, capsid protein levels, and reverse transcriptase activities of diverse human immunodeficiency virus type 1 isolates.

Most studies on human immunodeficiency virus type 1 (HIV-1) replication kinetics or fitness must rely on a particular assay to initially standardize inocula from virus stocks. The most accurate measure of infectious HIV-1 titers involves a limiting dilution-infection assay and a calculation of the dose required for 50% infectivity of susceptible cells in tissue culture (TCID(50)). Surrogate assays are now commonly used to measure the amount of p24 capsid, the endogenous reverse transcriptase (RT) activity, or the amount of viral genomic RNA in virus particles. However, a direct comparison of these surrogate assays and actual infectious HIV-1 titers from TCID(50) assays has not been performed with even the most conserved laboratory strains, let alone the highly divergent primary HIV-1 isolates of different subtypes. This study indicates that endogenous RT activity, not p24 content or viral RNA load, is the best surrogate measure of infectious HIV-1 titer in both cell-free supernatants and viruses purified on sucrose cushions. Sequence variation between HIV-1 subtypes did not appear to affect the function or activity of the RT enzyme in this endogenous assay but did affect the detection of p24 capsid by both enzyme immunoassays and Western blots. Clear groupings of non-syncytium-inducing (NSI), CCR5-tropic (R5), and SI/CXCR4-tropic (X4) HIV-1 isolates were observed when we compared the slopes derived from correlations of RT activity with infectious titers. Finally, the replication efficiency or fitness of both the NSI/R5 and SI/X4 HIV-1 isolates was not linked to the titers of the virus stocks.

Selection in ContextSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AF016760, AF016761, AF016762, AF016763, AF016764, AF016765, AF016766, AF016767, AF016768, AF016769, AF016770, AF016771, AF016772, AF016773, AF016774, AF016775, AF016776, AF016777, AF016778, AF016779, AF016780, AF016781, AF016782, AF016783, AF016784, AF016785, AF016786, AF016787, AF016788, AF016789, AF016790, AF016791, AF016792, AF016793, AF016794, AF016795, AF016796, AF016797, AF016798, AF016799, AF016800, AF016801,

Evolution of the HIV-1 V3 loop was monitored in 15 subjects over a period of 5 years at approximately 6-month intervals. Putative recombination was detected in many of the sequences. Evolutionary trees were estimated from the nonrecombinant viral sequences found in each individual. Selection and altered demographic regimes were detected with logit and other contingency analyses in a highly context-dependent fashion. Mutations leading to amino acid substitutions are subject to positive selection over a broad range of clinical conditions in the nonsyncytium-inducing (NSI) form, and the growth rates of the NSI strains and their level of genetic subdivision change little in going from a healthy immune system to a severely compromised immune system. In contrast, the SI form has a significant increase in growth rate as the immune system goes from healthy to compromised, particularly in those subjects who did not receive any antiviral drug therapy. This increase in SI growth rate results in a significant growth advantage of SI over NSI when the immune system is compromised. The SI strains also show more demographic subdivision when the immune system is healthy than when the immune system is compromised, and the SI form has greater demographic subdivision than NSI in subjects with healthy immune systems who also are not receiving antiviral drug therapy. Positive selection on amino-acid-changing mutations weakens and then intensifies again in the SI strains in going from healthy to compromised immune systems. These patterns are consistent with other studies that suggest that NSI strains inhibit replication of SI strains, that the V3 loop is more hidden from the immune system in the NSI form, that evolution in the V3 loop influences cell tropism and coreceptor usage, that substrate for replication of SI forms increases as the disease progresses, and that death of CD8 cells is influenced by the type of coreceptor usage typically found in SI but not in NSI strains. Finally, the transition between NSI and SI forms is associated with a burst of evolutionary change due to strong positive selection at sites other than those that define the NSI/SI phenotypes.

Human immunodeficiency virus type 1 primary isolate neutralization resistance is associated with the syncytium-inducing phenotype and lower CD4 cell counts in subtype CRF01_AE-infected patients.

A number of human immunodeficiency virus type 1 (HIV-1) non-B-subtype products have been developed for present or future vaccine trials; in Thailand, several studies using subtype B and/or CRF01_AE vaccines have been conducted. To better characterize the biologic properties of these subtypes, 70 HIV-1 subtype B and E isolates were phenotyped as syncytium-inducing (SI) or non-syncytium-inducing (NSI) isolates and assessed for sensitivity to neutralizing antibody (NAb). A significantly higher number of NSI subtype E viruses were neutralization sensitive than SI subtype E viruses (P = 0.009), while no association between viral phenotype and sensitivity to NAb was observed for subtype B (P = 0.856), suggesting a difference in the neutralization patterns of subtypes B and E. Strikingly, concurrent CD4 T-cell numbers were significantly lower for subtype E-infected patients whose isolates were more resistant to NAb, both for the overall study group (P < 0.001) as well as for the 22 patients with NSI isolates (P = 0.013). Characterization of the evolution of biologic properties of both B and non-B HIV-1 subtypes will provide a clearer understanding of the repertoire of antibodies that must be elicited for a vaccine to be effective against all phenotypes and subtypes.

An Unusual Syncytia-Inducing Human Immunodeficiency Virus Type 1 Primary Isolate from the Central Nervous System that is Restricted to CXCR4, Replicates Efficiently in Macrophages, and Induces Neuronal Apoptosis

Macrophage/microglia cells are the principal targets for human immunodeficiency virus type 1 (HIV-1) in the central nervous system (CNS). Prototype HIV-1 isolates from the CNS are macrophage (M)-tropic, non-syncytia-inducing (NSI), and use CCR5 for entry (R5 strains), but whether syncytia-inducing (SI) CXCR4-using X4 strains might play a role in macrophage/microglia infection and neuronal injury is unknown. To explore the range of features among HIV-1 primary isolates from the CNS, the authors analyzed an HIV-1 strain (TYBE) from cerebrospinal fluid of an individual with acquired immunodeficiency syndrome (AIDS) that was unusual because it was SI. Like other CNS isolates, HIV-1/TYBE replicated to high level in primary human macrophages, but, in contrast to CNS prototypes, TYBE used CXCR4 exclusively to infect macrophages. A functional TYBE env clone confirmed the X4 phenotype and displayed a highly charged V3 sequence typical of X4 strains. Supernatant from TYBE-infected primary human macrophages induced apoptosis of neurons. Thus, TYBE represents a novel type of CNS-derived HIV-1 isolate that is CXCR4-restricted yet replicates efficiently in macrophages and induce neuronal injury. These results demonstrate that HIV-1 variants in the CNS may possess a broader range of biological characteristics than generally appreciated, raise the possibility that X4 strains may participate in AIDS neuropathogenesis, and provide a prototype clade B HIV-1 strain that replicates efficiently in primary macrophages through the exclusive use of CXCR4 as a coreceptor.