Circulating HIV-1 Subtypes Research Articles

Characterization of Two Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Among Men Who Have Sex with Men and Mother-to-Child Transmission Cases in Baoding City, China.

CRF01_AE and CRF07_BC are predominant circulating HIV-1 subtypes in China. In this study, we report two novel HIV-1 CRF01_AE/CRF07_BC recombinant forms isolated from one man who has sex with men (MSM) (BDD027) and one mother-to-child transmission (MTCT) case (BDL123) in Baoding City, Hebei Province, China. The recombination breakpoint analysis showed that the recombination pattern of the near-full-length genome of BDD027 consisted of two CRF07_BC fragments inserted into a CRF01_AE backbone, while the recombination pattern of the near-full-length genome of BDL123 consisted of one CRF01_AE fragment inserted into a CRF07_BC backbone. This study demonstrates the importance of strengthening the monitoring of HIV-1 molecular epidemiological characteristics and emphasizes the urgent need to reduce the HIV-1 epidemic among MSM and MTCT populations in China.

Characterization of the Viral Reservoirs Among HIV-1 Non-B Vertically Infected Adolescents Receiving Antiretroviral Therapy: Protocol for an Observational and Comparative Study in Cameroon.

Antiretroviral therapy (ART) can bring HIV-1 levels in blood plasma to the undetectable level and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, ART is not curative and must be taken for life, because within a few weeks of treatment cessation, HIV viremia rebounds in most patients except for rare elite or posttreatment controllers of viremia. The primary source of this rebound is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of the resting memory cluster of differentiation 4 (CD4+) T cells. To achieve a cure for HIV, understanding the cell reservoir environment is of paramount importance. The size and nature of the viral reservoir might vary according to the timing of therapy, therapeutic response, ART duration, and immune response. The mechanisms of reservoir maintenance generally depend on the levels/type of immune recognition; in addition, the dynamics of viral persistence are different between pediatric and adult populations. This difference could become more evident as children grow toward adolescence. We aim to characterize the HIV reservoirs and their variability as per the virological and immunological profiles of HIV-1 non-B vertically infected adolescents receiving ART in Cameroon during the Adolescents' Viral Reservoirs study to provide accurate and reliable data for HIV cure research. This study will involve HIV-1 non-B vertically infected adolescents selected from an existing cohort in our institution. Blood samples will be collected for analyzing immunological/virological profiles, including CD4/CD8 count, plasma viral load, immune activation/inflammatory markers, genotyping, and quantification of HIV-1 viral reservoirs. We will equally recruit an age-matched group of HIV-negative adolescents as control for immunological profiling. This study received funding in November 2021 and was approved by the national institutional review board in December 2021. Sample collection will start in November 2022, and the study will last for 18 months. The HIV-1 sequences generated will provide information on the circulating HIV-1 subtypes to guide the selection of the most appropriate ART for the participants. The levels of immune biomarkers will help determine the immune profile and help identify factors driving persistent immune activation/inflammation in HIV-infected adolescents compared to those in HIV-uninfected adolescents. Analysis of the virological and immunological parameters in addition to the HIV-1 reservoir size will shed light on the characteristics of the viral reservoir in adolescents with HIV-1 non-B infection. Our findings will help in advancing the knowledge on HIV reservoirs, in terms of size and genetic variability in adolescents living with HIV. Such evidence will also help in understanding the effects of ART timing and duration on the size of the reservoirs among adolescents living with HIV-a unique population from whom the findings generated will largely contribute to designing functional cure strategies. PRR1-10.2196/41473.

Geospatial HIV-1 subtype C gp120 sequence diversity and its predicted impact on broadly neutralizing antibody sensitivity.

Evolving diversity in globally circulating HIV-1 subtypes presents a formidable challenge in defining and developing neutralizing antibodies for prevention and treatment. HIV-1 subtype C is responsible for majority of global HIV-1 infections. In the present study, we examined the diversity in genetic signatures and attributes that differentiate region-specific HIV-1 subtype C gp120 sequences associated with virus neutralization outcomes to key bnAbs having distinct epitope specificities. A total of 1814 full length HIV-1 subtype C gp120 sequence from 37 countries were retrieved from Los Alamos National Laboratory HIV database (www.hiv.lanl.gov). The amino acid sequences were assessed for their phylogenetic association, variable loop lengths and prevalence of potential N-linked glycosylation sites (pNLGS). Responses of these sequences to bnAbs were predicted with a machine learning algorithm ‘bNAb-ReP’ and compared with those reported in the CATNAP database. Subtype C sequences from Asian countries including India differed phylogenetically when compared with that from African countries. Variable loop lengths and charges within Indian and African clusters were also found to be distinct from each other, specifically for V1, V2 and V4 loops. Pairwise analyses at each of the 25 pNLG sites indicated distinct country specific profiles. Highly significant differences (p<0.001***) were observed in prevalence of four pNLGS (N130, N295, N392 and N448) between South Africa and India, having most disease burden associated with subtype C. Our findings highlight that distinctly evolving clusters within global intra-subtype C gp120 sequences are likely to influence the disparate region-specific sensitivity of circulating HIV-1 subtype C to bnAbs.

New infections and HIV-1 subtypes among febrile persons and blood donors in Oyo State, Nigeria.

There were approximately 37.9 million persons infected with HIV in 2018 globally, resulting in 770,000 deaths annually. Over 50% of this infection and deaths occur in sub-Saharan Africa, with countries like Nigeria being seriously affected. Nigeria has one of the highest rates of new infections globally. To control HIV infection in Nigeria, there is a need to continually screen high-risk groups for early HIV infection and subtypes using very sensitive methods. In this study, new HIV-1 infection and circulating HIV-1 subtypes among febrile persons and blood donors were determined. Performance characteristics of three commercial EIA kits were also evaluated. In total, 1028 participants were recruited for the study. New HIV-1 infection and subtypes were determined using enzyme immunoassays and molecular techniques, respectively. Sensitivity, specificity, predictive values, and agreements were compared among the EIA kits using PCR-confirmed HIV-positive and negative samples. The overall prevalence of HIV infection in this study was 5.35%. The rate of new HIV infection was significantly different (p < .03674) among 1028 febrile persons (Ibadan: 2.22%; Saki: 1.36%) and blood donors (5.07%) studied. Three subtypes, CRF02_AG, A, and G, were found among those with new HIV infection. Whereas the commercial ELISA kits had very high specificities (94.12%,100%, and 100%) for HIV-1 detection, Alere Determine HIV-1 antibody rapid kit had the lowest sensitivity score (50%). Genetic diversity of HIV-1 strains among infected individuals in Oyo State, Nigeria, is still relatively high. This high level of diversity of HIV-1 strains may impactthe reliability of diagnosis of the virus in Nigeria and other African countries where many of the virus strains co-circulate.

Prevalence of integrase strand transfer inhibitor resistance mutations in antiretroviral-naive HIV-1-infected individuals in Cameroon.

In Cameroon, the integrase (IN) strand transfer inhibitor (INSTI) dolutegravir was recently introduced for the treatment of HIV-1 infection. Since pretreatment HIV-1 drug resistance can jeopardize the success of ART, and considering the high heterogeneity of circulating HIV-1 subtypes in Cameroon, we investigated the prevalence of pretreatment HIV-1 resistance to INSTIs. Fingerprick dried blood spot samples were collected from 339 newly diagnosed HIV-1-infected individuals between 2015 and 2016 in four hospitals in Cameroon. Universal primers were designed to amplify the HIV-1 IN region from amino acid 1 to 276. Amplicons were sequenced with Illumina next-generation sequencing and analysed with the Polymorphism Analysis Sequencing (PASeq) platform, using the Stanford HIV Drug Resistance Database to interpret HIV-1 drug resistance mutations (DRMs). The amplification/sequencing success rate was 75.2% with 255/339 sequences obtained. Applying a cut-off of 1%, major DRMs to INSTIs were detected in 13 (5.1%) individuals, but only 1 individual harboured an INSTI DRM (E92G) at a nucleotide frequency ≥15%. However, 140/255 (54.9%) individuals harboured polymorphic accessory INSTI DRMs, mainly at high frequencies. In line with that observation, HIV-1 subtype diversity among individuals was high. Pretreatment HIV-1 resistance to INSTIs was low in the study sites, which supports the use of INSTIs in Cameroon. Nevertheless, further studies are necessary to assess the impact of polymorphic accessory INSTI DRMs on INSTI-based ART regimens.

HIV-1 Subtypes Circulating in Constanta

Abstract The HIV epidemic in Constanta describes a unique pattern in the world. It has outbreak in 1986, in the pediatric population and it is of a monoclonal aspect, being determined by the F1 subtype. The evolution of the epidemic has known different stages in time: it spreads to the adult population, the transmission pathway becomes predominantly sexual and the circulating viral strains become diversified. The study proposes the characterization of the circulating HIV-1 subtypes in Constanta from the beginning of the epidemic to the present. The results indicate that subtype F1 remains dominant in patients from Constanta, mainly due to cases coming from the pediatric cohort that have now reached adulthood and are generating secondary cases through sexual transmission. As subtype B strains appeared sporadically before 1999, the strains C and B appear systematically after that moment in time. In 2004 the first subtype A strains were isolated. The year 2007 is the one with the highest biodiversity: along with the dominant subtype F1, subtypes C, A, B, G were isolated and also the circulating recombinant forms CRF02_02, CRF06_cpx and CRF01_AE. Since 2008, the viral population has remained polymorphic, with a dynamic evolution.

Prevalence of HIV-1 transmitted drug resistance in recently infected, treatment-naïve persons in the Southwest of Iran, 2014-2015.

The emergence and transmission of drug resistant HIV mutants is a major concern, especially in resource-limited countries with expanding antiretroviral therapy. Studies have recently reported the prevalence of HIV-1 transmitted drug resistance (TDR) mutations in certain Iranian cities; however, no information is currently available about the level of TDR, as well as the nature of the circulating HIV-1 subtypes, in the Southwestern bordering province of Iran, Khuzestan. Herein, we used a WHO-recommended TDR survey method to classify the prevalence of TDR in indigenous people of Khuzestan province. For this purpose, between March 2014 and February 2015, blood samples were collected from 52 newly diagnosed, antiretroviral treatment-naïve, HIV-1 infected persons aged from 18 to 30 years. TDR mutations were determined by sequencing the protease (PR) and reverse transcriptase (RT) genes and interpreted using the WHO drug resistance mutations surveillance list. HIV-1 subtypes were characterized by sequencing the PR-RT, C2-V5, and p17 regions of the pol, env and gag genes, respectively. Two participants had non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations, specifically K103N in one individual and K101EK/K103KN/G190AG in the other. No nucleoside reverse transcriptase inhibitor (NRTI) or major protease inhibitor (PI) mutations were identified. HIV-1 subtyping revealed that all participants were infected with HIV-1 CRF35_AD. According to the WHO sequential sampling method, the prevalence of HIV-1 TDR in the sampling area (Khuzestan province) was classified as moderate for NNRTIs and low for NRTIs and PIs. This is the first HIV-1 drug resistance threshold survey in the Khuzestan province of Iran and shows a predominance of NNRTI TDR mutations in this area.

Phylodynamic analysis reveals CRF01_AE dissemination between Japan and neighboring Asian countries and the role of intravenous drug use in transmission.

BackgroundOne major circulating HIV-1 subtype in Southeast Asian countries is CRF01_AE, but little is known about its epidemiology in Japan. We conducted a molecular phylodynamic study of patients newly diagnosed with CRF01_AE from 2003 to 2010.MethodsPlasma samples from patients registered in Japanese Drug Resistance HIV-1 Surveillance Network were analyzed for protease-reverse transcriptase sequences; all sequences undergo subtyping and phylogenetic analysis using distance-matrix-based, maximum likelihood and Bayesian coalescent Markov Chain Monte Carlo (MCMC) phylogenetic inferences. Transmission clusters were identified using interior branch test and depth-first searches for sub-tree partitions. Times of most recent common ancestor (tMRCAs) of significant clusters were estimated using Bayesian MCMC analysis.ResultsAmong 3618 patient registered in our network, 243 were infected with CRF01_AE. The majority of individuals with CRF01_AE were Japanese, predominantly male, and reported heterosexual contact as their risk factor. We found 5 large clusters with ≥5 members and 25 small clusters consisting of pairs of individuals with highly related CRF01_AE strains. The earliest cluster showed a tMRCA of 1996, and consisted of individuals with their known risk as heterosexual contacts. The other four large clusters showed later tMRCAs between 2000 and 2002 with members including intravenous drug users (IVDU) and non-Japanese, but not men who have sex with men (MSM). In contrast, small clusters included a high frequency of individuals reporting MSM risk factors. Phylogenetic analysis also showed that some individuals infected with HIV strains spread in East and South-eastern Asian countries.ConclusionsIntroduction of CRF01_AE viruses into Japan is estimated to have occurred in the 1990s. CFR01_AE spread via heterosexual behavior, then among persons connected with non-Japanese, IVDU, and MSM. Phylogenetic analysis demonstrated that some viral variants are largely restricted to Japan, while others have a broad geographic distribution.

Epitope Specificity of Cross‐Clade Neutralizing Sera from Chinese HIV‐1‐Positive Individuals

Induction of broadly neutralizing antibody is considered important for an effective HIV-1 vaccine. Identification and characterization of broadly neutralizing antibodies in HIV-1-infected patients will facilitate our understanding of the immune correlates to protection and the design of an effective prophylactic vaccine. A number of studies to probe the specificity of antibodies in broadly neutralizing sera in the United States and Europe have been reported. However, little is known about and would be interesting to investigate the immunological characteristics of HIV-1-positive sera in China where non-clade B viruses are prevalent and the circulating viral subtypes are distinct and more complex than both the United States and Europe. Here, we screened 80 Chinese HIV-1-positive sera against a minipanel of pseudoviruses representing various circulating HIV-1 subtypes in China and identified 8 cross-clade neutralizing sera (CNsera). Immunological characterization of the sera showed that gp120-targeting antibodies with multiple epitope specificities contributed to the cross-clade neutralizing activity of these CNsera. V3-directed antibodies were prevalent in these CNsera, but did not mainly contribute to their neutralization breath and potency while CD4bs-specific, 2F5- and 4E10-like antibodies were rarely detected. 2G12-like neutralizing antibodies were more frequently detected in HIV-1 patients from China where recombinant subtype viruses are prevalent than in United States and Europe. One broadly neutralizing serum (Serum 45) was identified to contain antibodies with unknown epitope specificities that were sensitive to terminal glycan modifications on virus Env and insensitive to N160K mutagenesis, and correlated with the cross-clade neutralization activity of Serum 45.

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.

Circulation of HIV‐1 subtype A within the subtype C HIV‐1 epidemic in Tamil Nadu, India

The HIV-1 epidemic in India is caused mainly by subtype C viruses that are transmitted sexually and by injecting drug use. The state of Tamil Nadu in Southern India has an HIV-1 median prevalence of 16.8% among injecting drug users, 6.6% in men who have sex with men, and 4.6% in female sex workers. In the rural district of Namakkal, a prevalence >3% was detected among antenatal women. The goal of this study was to determine the HIV-1 molecular epidemiology in Tamil Nadu. Blood samples were collected from 40 high-risk HIV-seropositive individuals from Chennai and Namakkal. HIV-1 subtype was determined by envelope nucleotide sequencing. Among the samples studied, 85% were subtype C, however, a cluster of subtype A samples (12.5%) and one subtype E recombinant form CRF01_AE (close to the Thailand strains) were detected. The average genetic distance of subtype C samples from Chennai and Namakkal were 9.44 ± 0.77% and 11.8 ± 0.7%, respectively indicating an evolved epidemic. This pilot study confirmed that subtype C was predominant in these regions but an outbreak of subtype A was detected in Namakkal. These results stress the importance of periodic monitoring of circulating HIV-1 subtypes in South India.

Rapid Detection and Differentiation of Antibodies to HIV-1 and HIV-2 Using Multivalent Antigens and Magnetic Immunochromatography Testing

A simplified lateral-flow assay for the detection of antibodies to HIV using magnetic-bead conjugates and multibranched peptides from both HIV-1 and HIV-2 was developed. Magnetic immunochromatography testing (MICT) uses a standard lateral-flow platform that incorporates magnetic-bead conjugates for quantitative measurement of the magnetic field distortion associated with the bound magnetic conjugate (reported as adjusted relative magnetic units [MAR]). The results of the optimized MICT assay were compared to standard enzyme immunoassay (EIA) and Western blotting (WB) results using a blinded 649-member panel of specimens from the United States, Cameroon, and West Africa. The panel was comprised of samples from individuals infected with various HIV-1 subtypes (n = 234) or HIV-2 (n = 65) and HIV-seronegative specimens (n = 350). Additionally, 13 HIV-1 seroconversion panels (total specimens = 85), a worldwide panel containing seven of the major circulating HIV-1 subtypes (n = 18), an HIV-2 panel, an HIV-1/HIV-2 mixed panel, and 100 prospective specimens were tested with completely concordant results. Assay reproducibility (observed MAR) for both intra- and interrun testing was excellent, with coefficients of variation of <12%. MICT can provide a rapid, low-cost method of determining HIV antibody status requiring no subjective interpretations.

OA04-06 LB. Post-infection cellular immune responses in recipients following ALVAC-HIV® + AIDSVAX® B/E prime-boost vaccination in the Thai Phase III Trial

Background The phase III prime-boost trial of ALVAC-HIV® (vCP1521) and AIDSVAX® B/E spanned 2003 to 2009 in Thailand. Both candidates express HIV CRF 01_AE and subtype B antigens, the predominant circulating HIV-1 subtypes in Thailand. This preliminary study assessed cellmediated immune (CMI) responses, viral load and CD4 counts in a subset (N=47) of anti-retroviral naive incident infections (< 270 days after estimated infection) that occurred during the trial.

Evolution of human immunodeficiency virus type 1 serotypes in northern Tanzania: a retrospective study

The HIV-1 epidemic in Tanzania is characterized by the circulation of heterogeneous virus subtypes. A retrospective study was conducted to determine the changing pattern of circulating HIV-1 subtypes in northern Tanzania. A peptide-binding enzyme immunoassay (PEIA) was employed to analyse 305 HIV-1 positive serum and plasma samples collected between 1985 and 2005. Samples were serotyped using synthetic peptides representing HIV-1 genotypes A-E derived from consensus gp120 V3 sequences. Plasma samples collected in 2005 were V3 genotyped for comparison with PEIA results. In 1985, serotypes A and D were co-circulating while serotype C was first detected in 1990. In 2001 and 2005, serotype C was the most prevalent, serotype A was stable, and serotype D was declining. PEIA is relatively rapid and simple to perform compared to molecular approaches, and is a valuable epidemiological tool in regions with limited resources. HIV-1 classification into serotypes based on antigenic V3 diversity may be a useful screening tool for the identification of HIV-1 variants with regard to diagnosis, treatment, disease progression and candidate vaccine development.

Genotypic Characterization and Comparison of Full-Length Envelope Glycoproteins from South African HIV Type 1 Subtype C Primary Isolates That Utilize CCR5 and/or CXCR4

CCR5 has preferentially been used by all circulating HIV-1 subtype C viruses for cell entry. Recently, we reported the highest proportion of CXCR4-utilizing primary isolates among a cohort of 20 South African AIDS patients. This study describes and compares the Env genotypic characteristics from these 20 HIV-1 subtype C (and unique CD recombinant) primary isolates. Fourteen primary isolates utilized CCR5, four (including the CD recombinant) used CXCR4, and two were dual tropic. Extensive analysis and comparison of important structural motifs such as the N-linked glycosylation sites, signal sequences, CD4-binding sites, variable loops, cleavage sites, known neutralizing antibody and small molecule inhibitor binding sites confirmed that other than the expected differences in the V3 loop, no sequence motifs distinguished between R5 and X4 tropism. Further correlation of the env genotype to functionally relevant motifs is necessary to elucidate the relationship between biologically and immunologically relevant sites and aid vaccine and novel drug design.

Molecular Epidemiology of Human Immunodeficiency Virus Type 1 and Hepatitis C Virus in Former Blood Donors in Central China

The prevalence of hepatitis C virus (HCV) among human immunodeficiency virus (HIV-1)-positive former blood donors (FBDs) in Hubei province, central China, and the subtypes of these two viruses are identified. HIV-1-positive specimens were collected from FBDs, transfusion recipients, and their sexual partners in Hubei province, central China. The prevalence of HCV in HIV-1-positive FBDs was 78.6%. The dominant circulating HIV-1 subtype of FBDs was subtype B' (Thai-B); one belonged to U.S.-European subtype B. HCV genotypes 2a (78.6%) and 1b (21.4%) were detected. No recombinant form of HIV-1 was identified. Non-B' subtypes occurring among FBDs indicate the complexity of the HIV-1 prevalence in central China, where HIV is beginning to spread into the general population.

Genotypic Analysis of the Protease and Reverse Transcriptase of HIV Type 1 Isolates from Recently Infected Injecting Drug Users in Western China

The partial pol gene was analyzed to determine circulating HIV-1 subtypes and the prevalence of drug resistance among recently infected injecting drug users in the west of China. Phylogenetic and bootscanning analyses showed that all 25 sequences belonged to CRF07_BC. No major drug resistance mutations were found, while the CRF07_BC sequences harbored a few highly prevalent polymorphic positions in both the protease and reverse transcriptase regions. It is notable that D60E, L63P and I93L substitutions, which were more common in HIV-1 isolates from PI-treated than untreated patients, were present in most of the isolates. Compared with subtype B, the CRF07_BC strains had a decreased genetic barrier for the V106M mutation, which is selected by efavirenz and leads to high-level resistance to all present nonnucleoside RT inhibitors. Further studies are needed to determine the impact of genetic features of CRF07-BC on antitretroviral susceptibility and evolution of drug resistance mutations.

Extensive cross-reactive neutralizing antibody response in Indian patients with limited genetic diversity of HIV-1

Genome sequence analysis of HIV-1 subtype C viruses from India shows monophyletic lineage and relatively limited genetic diversity. To understand its immunological implication, cross-reactivity of neutralizing antibody response was investigated. In primary screening, neutralizing antibody response to single heterologous primary HIV-1 subtype C isolate was assessed in plasma samples from 235 HIV-1 infected, anti-retroviral treatment naive individuals from Pune, India. Plasma samples that showed ≥ 90% neutralization and two randomly selected plasma samples that showed 50–60% neutralization were tested against a panel of primary HIV-1 subtype C isolates obtained from epidemiologically unlinked individuals from India. The neutralizing antibody response showed extensive cross-neutralization, suggesting presence of shared neutralization determinants among circulating HIV-1 subtype C viruses in India.

Evaluation of a synthetic vaccine construct as antigen for the detection of HIV-induced humoral responses

Synthetic V3 loop peptides hold numerous benefits for the development of HIV vaccines and in immunodiagnosis; however, their use is limited due to the extensive antigenic variability of this region. The effectiveness of a potential HIV vaccine component, which accounts for V3 loop variability, is evaluated here. A branched peptide construct representing multiple sequences and allowing 1.8 × 10 16 possible permutations was developed to mimic circulating HIV-1 subtype C, V3 loops. The construct was found to be immunogenic, able to induce neutralizing antibodies and sensitive to HIV-1 subtype B/C and HIV-2. This alternative antigen format also incorporates conformational epitopes.

Emergence of HIV-1 CRF01_AE/B unique recombinant forms in Kuala Lumpur, Malaysia

To investigate the molecular epidemiology of HIV-1 and to screen for the emergence of intersubtype recombinants in Kuala Lumpur, Malaysia. A molecular epidemiology study was conducted among HIV-1 seropositive patients attending the University Malaya Medical Center (UMMC) from July 2003 to June 2004. Protease (PR) and reverse transcriptase (RT) gene sequences were derived from drug resistance genotyping assay of 100 newly diagnosed or antiretroviral-naive patients. These were phylogenetically analysed to determine the subtypes and recombination breakpoint analyses were performed on intersubtype recombinants to estimate the recombination breakpoint(s). CRF01_AE predominated in Kuala Lumpur with 65% in both PR and RT genes. B subtype was detected at 14% and 12% in PR and RT genes, respectively. C subtype was present at 1% in both genes. Overall, the concordance of PR and RT genes in discriminating subtypes/circulating recombinant forms (CRF) was high at 96%. In this study, novel CRF01_AE/B intersubtype recombinants were detected at high prevalence (22%), including those isolates with subtype discordance. Thai variants of CRF01_AE and B subtype were involved in the genesis of these unique recombinant forms (URF). Interestingly, 19 CRF01_AE/B intersubtype recombinant isolates shared similar recombination breakpoints in both PR and RT genes. Several distinct URF were also identified. PR and RT genes can be utilized for subtype/CRF assessment with high degree of agreement, allowing concurrent surveillance of circulating HIV-1 subtypes with antiretroviral drug resistance genotyping tests. The emergence of highly identical CRF01_AE/B intersubtype recombinants suggests the possibility of the appearance of a new circulating recombinant form in Kuala Lumpur.