Distribution of HIV-1 resistance-conferring polymorphic alleles SDF-1-3'A, CCR2-64I and CCR5-Delta32 in diverse populations of Andhra Pradesh, South India

Mutation in AIDS restriction gene affecting HIV infection and disease progression in a high risk group from Northeastern India

BACKGROUND

HIV estimates for 2009 released by National AIDS Control Organization (NACO) reveals that 2.4 million people in India were living with HIV, 39% being female, 4.4% children and 82.4% adult males between the age group of 15 and 49 years. Persons with host genetic polymorphism CCR5Δ32 mutation are known to be partially or fully resistant to HIV infection. Persons with mutation affecting both the alleles (homozygous) are resistant to HIV infection whereas single allele (heterozygous) polymorphism leads to slower progression to AIDS. CCR5Δ32 mutation is commoner in Caucasians but less prevalent amongst Africans and Asians thereby rendering them susceptible to HIV infection.

METHOD

571 HIV serologically naive subjects from a young and homogenous male population hailing from the seven northeastern states; West Bengal and Gorkha people were selected. All the subjects belonged to a special high risk group, sexually active and typically working in difficult and uncongenial terrain involved in frequent moves including overseas missions. Their family lives are severely disrupted. 181 HIV seropositive cases of which 92 cases that were admitted in a large tertiary care hospital were also included. The distribution of CCR5Δ32 polymorphism amongst both HIV seronegative (HSN) and HIV seropositive study cohorts (HSP) using molecular methods was studied.

RESULTS AND CONCLUSION

There was failure to detect any CCR5Δ32 amongst this study group suggesting that this population from the northeastern India, West Bengal and Gorkha people are not protected by this specific host polymorphism in respect of acquisition of HIV infection as well as progression to AIDS.

Genetic Markers of the Host in Persons Living with HTLV-1, HIV and HCV Infections

Human T-cell leukemia virus type 1 (HTLV-1), hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) are prevalent worldwide, and share similar means of transmission. These infections may influence each other in evolution and outcome, including cancer or immunodeficiency. Many studies have reported the influence of genetic markers on the host immune response against different persistent viral infections, such as HTLV-1 infection, pointing to the importance of the individual genetic background on their outcomes. However, despite recent advances on the knowledge of the pathogenesis of HTLV-1 infection, gaps in the understanding of the role of the individual genetic background on the progress to disease clinically manifested still remain. In this scenario, much less is known regarding the influence of genetic factors in the context of dual or triple infections or their influence on the underlying mechanisms that lead to outcomes that differ from those observed in monoinfection. This review describes the main factors involved in the virus–host balance, especially for some particular human leukocyte antigen (HLA) haplotypes, and other important genetic markers in the development of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and other persistent viruses, such as HIV and HCV.

Low prevalence of CCR5-Δ32, CCR2-64I and SDF1-3'A alleles in the Baiga and Gond tribes of Central India

Human immunodeficiency virus-1 (HIV-1) which causes acquired immune deficiency syndrome (AIDS), by infecting CD4⁺ immune cells and hence weakening the host defense mechanism till death, is one of the major factor responsible for human demises worldwide. Both innate (monocytes and macrophages) and adaptive (T cells) immune cells expresses chemokines receptors (2 and 5) and stromal cell derived factor-1 (SDF-1) which play crucial role in HIV-1 virus entry and progression. Allele variants of genes CCR5 (CCR5-Δ32), CCR2 (CCR2-64I) and SDF1 (SDFA-3′A; the ligand of CXCR4) are known to slow down the HIV-1 progression in infected individual. In the present study, the frequency of CCR5-Δ32, CCR2-64I and SDF1-3′A alleles in primitive tribe (Baiga) and a non-primitive tribe (Gond) of central India were investigated. A total 200 seronegative samples for HIV from healthy individuals of tribes were analyzed and observed allele frequencies of CCR5-Δ32, CCR2-64I and SDF1-3′A were (0, 0.035, 0.080) and (0, 0.110, 0.100) in Baiga and Gond respectively. Minor allele frequency of these alleles of Gond and Baiga tribes were compared with different populations of the world for relative hazard (RH), which indicate the risk of progression after infection of HIV1. The RH values were calculated based on genotypic frequency, showed the high RH value (RH1-AIDS1993-0.98, RH2-AIDS1987-0.98 and death/RH3-0.97) in Baiga tribe, indicates the low level of resistance against HIV-1 progression after infection.

Analysis of CCR5 and SDF-1 genetic variants and HIV infection in Indian population

HIV-1 infection and progression exhibits interindividual variation. The polymorphism in the chemokine receptors CCR5 and CXCR4, the principal coreceptors for HIV-1 and their ligands like SDF-1 have a profound effect in altering the HIV-1 disease progression rate. A single nucleotide polymorphism designated SDF1-3'UTR-801G-A has been associated with resistance to HIV-1 infection or delayed progression to AIDS. In this study, the SDF1-3'A polymorphism, CCR5∆32 polymorphism and CCR5 promoter polymorphism at positions 58934 G/T, 59029 G/A, 59353 T/C, 59356 C/T, 59402 A/G and 59653 C/T were analysed in Indian population. The polymorphisms in HIV-1 patients and healthy individuals were evaluated by conventional PCR, RFLP-PCR and direct sequencing techniques. The CCR5∆32 mutant allele was found to be almost absent in Indian population. The analysis of the CCR5-59356C/T polymorphism revealed a trend towards an association of the C allele with an increased risk of HIV-1 infection. The frequency of allele CCR5-59356C was higher in HIV-1 patients (100%) as compared to healthy control subjects (89%, P = 0.003). The correlation of SDF1-3'A and CCR5 promoter CCR5-58934G/T, CCR5-59029G/A, CCR5-59353T/C, CCR5-59402 A/G and CCR5-59653C/T polymorphisms and protection to HIV-1 infection and progression to AIDS was found to be nonsignificant. Nine haplotypes with more than 1% frequency were detected but were not significant in their protective role against HIV. Comparative analysis with global populations showed a noteworthy difference in CCR5 and SDF-1 polymorphisms' frequency distribution, indicating the ethnic variability of Indians. Although susceptibility to infections cannot be completely dependent on one or few genetic variants, it is important to remember that SDF-1 and CCR5 variants have been correlated globally with HIV-1 infection and disease progression. In the light of that, higher frequency of SDF-1 variants in the Indian population is noteworthy.

The Distribution of CCR2-64I, SDF1-3'A and MCP1-2518 G/A Genes Polymorphism in a Specific High Risk Group from the Northeastern States West Bengal, and Gorkha Population in India

We studied the prevalence and effects of host genetic polymorphisms for the three AIDS restriction genes (ARGs) namely CCR2-64I, SDF1-3'A and MCP1-2518 G/A for HIV infection and progression to AIDS using PCR-RFLP analysis on a total of 568 HIV seronegative serum samples collected from a specific high risk and young population hailing from the seven Northeastern states of India (n = 346), West Bengal (n = 96) and Gorkha population (n = 101). In addition, 181 HIV seropositive cases of which 92 inpatient cases in a large tertiary care hospital located at Kolkata were included in the study. HIV prevalence in our study group was 0.52 %. Four cases seroconverted, 25 cases progressed to AIDS and 05 died during the follow up period of 41 months. The genotype percentage of CCR2-64I, SDF1-3'A and MCP1-2518 G/A in the Northeastern states were 18.5, 40.3 and 54 % respectively in the seronegative population. Allele frequencies for SDF1-3'A in Northeastern states were significantly higher as compared to the Gorkha (21 %) and the North Indian population (24 %). Relative Hazard values were more than 0.9 for progression to AIDS and death. Kaplan-Meier survival analysis using Cox proportional regression model did not reveal any significant survival benefit (p value <0.05) for any of the 3 ARGs individually or in combination either to seroconversion or disease progression. This is the first study on host genetic polymorphism amongst the Eastern, Northeastern and Gorkha regions in India. We are also the first to report the MCP1-2518 G/A polymorphism in India that is known to increase the rate of neuropsychological impairment (NPI) in AIDS patients.

Distribution of CC-chemokine receptor-5-∆32 allele among the tribal and caste population of Vidarbha region of Maharashtra state

BACKGROUND:

Genetic relationships among the ethnic groups are not uniform across the geographical region. Considering this assumption, we analyzed the frequency of the CC-chemokine receptor-5 (CCR5)-∆32 allele of the CCR5 chemokine receptor, which is considered a Caucasian marker, in Bhil tribal and Brahmin caste sample sets from the population.

MATERIALS AND METHODS:

108 blood samples were collected from 6 tribe's populations and a caste population from the district of Vidarbha region.

RESULTS AND DISCUSSION:

The presence of low frequencies of CCR5-Δ32 in an individual of Bhil tribe (0.034, χ² value 0.017) in the present study implies that these communities may have a better resistance toward human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) than the other studied tribe sample, as non-show such mutation.

CONCLUSION:

The marginal presence of the allele seen in the studied tribal population could be due to gene flow from the people of European descent. However, lack of the homozygous CCR5-Δ32 mutation and the low prevalence of heterozygous CCR5-Δ32 mutations suggest that the Indians are highly susceptible to HIV/AIDS, and this correlates with the highest number of HIV/AIDS infected individuals in India.

Association of human mannose receptor in sexual transmission of human immunodeficiency virus in serodiscordant couples

HIV binds specifically to the human mannose receptor (hMR) on vaginal epithelial cells that are devoid of a conventional CD4 receptor. HIV binding to hMR on vaginal epithelial cells induces the production of matrix metalloproteinase 9 (MMP9) leading to degradation of the extracellular matrix, which may increase the risk of HIV entry into vaginal epithelial cells and further transmission into distal cells. Immunofluorescent localization of hMR on vaginal epithelial cells of seronegative females from the general population included the control group (n=52) and seronegative females from serodiscordant couples. There was PCR amplification of DNA from peripheral blood mononuclear cells (PBMCs) of the serodiscordant females for the CCR5 gene flanking the CCR5-Δ32 region; PCR amplification and sequencing of the C2-V3 region of HIV variants in PBMCs and sperm of the infected male partners of the serodiscordant couples; and the presence of hMR on 0-11% of the vaginal epithelial cells of seronegative females (n=39) from serodiscordant couples and 90-95% that of a control group of females (n=52). Nine of these serodiscordant females did not show a CCR5-Δ32 deletion. The translated amino acid sequence of the C2-V3 region of the env gene of HIV-1C in PBMCs (n=9) and sperm (n=5) of the male partners showed the presence of distinct variants and the variation in PBMCs and sperm of serodiscordant males was almost similar to that of infected males from concordant couples. The presence of hMR in a smaller number of vaginal epithelial cells of serodiscordant females prevented binding and HIV entry into these cells and therefore prevented sexual transmission of HIV.

Genetic correlates influencing immunopathogenesis of HIV infection

Variability to HIV infection, its progression as well as responsiveness to antiretroviral therapy (ART) is observed among individuals including viraemia controllers or exposed uninfected, rapid versus slow progressors and ART responders compared to non responders. This differential responsiveness/vulnerability to HIV-1 is governed by multiple host genetic factors that include HLA, cytokines, chemokines, their receptors and others. This review highlights the influence of these genetic factors on HIV/AIDS outcome; however, in India, the information in this area is very limited and most of these genetic studies have been conducted in Caucasian and South African populations. Considering, the population specific differences in the frequencies of protective or susceptibility favouring alleles and their influence on the disease outcome, it is of utmost importance to strengthen ongoing efforts towards defining largely unknown genetic propensity in Indian population, particularly by recruitment of large cohorts of well categorized exposed uninfected individuals, rapid, long term non progressors and elite viraemic controllers. Multi-parametric analysis of these potentially interactive immunogenetic variables in these cohorts may help to define potential targets for diagnostics and therapy in a population specific manner.

The Consequence of a Founder Effect: CCR5-∆32, CCR2-64I and SDF1-3'A Polymorphism in Vlach Gypsy Population in Hungary

Frequencies of genetic polymorphisms of the three most frequent HIV-1 resistance-conferring alleles playing an important role in HIV-1 pathogenesis were analysed in Vlach Gypsy populations living in Hungary, as the largest minority. Mutations in the encoding genes, such as CCR5-∆32, CCR2-64I and SDF1-3'A are shown to result in protective effects against HIV-1 infection and disease progression. 560 samples collected from Vlach Gypsy individuals living in 6 North-East Hungarian settlements were genotyped by PCR-RFLP method. Overall allele frequencies of CCR5-∆32, CCR2-64I and SDF1-3'A were found as 0.122, 0.186 and 0.115 respectively. All the observed genotype frequencies were in accordance with Hardy-Weinberg equilibrium . In regions, however, Vlach Gypsies live in majority and in ethnically homogenous communities, a higher CCR5-∆32 mutations were found, with allele frequencies of 0.148 and 0.140 respectively, which are remarkably higher than those in general Hungarian people, and ten times higher than in regions of North-Western India from where present day Hungarian Gypsies originated in the Middle Ages. In the background of this higher CCR5-∆32 allele frequency in the population analysed in our study a genetic founder effect could be assumed. Allele frequency of CCR2-64I was found to be among the highest in Europe. SDF1-3'A allele frequency in Vlach Gypsies was significantly lower than in ethnic Hungarians. 63% of the total 560 individuals tested carried at least one of the mutations studied. These results could partially explain the low incidence of HIV/AIDS among Vlach Gypsies in Hungary.

Genetic determinants of HIV-1 infection and progression to AIDS: susceptibility to HIV infection

Interindividual variability in susceptibility to HIV-1 infection, its transmission, disease progression, and response to antiviral therapy has been attributed to host determinants and variability in multiple genes. Although most people exposed to the virus go on to develop full-blown disease at variable intervals, a proportion of them, labeled as long-term nonprogressors or exposed uninfected, possess 'natural resistance' to infection. A better understanding of genetic and immunologic basis of such a natural resistance to infection would bear important implications in designing therapeutic vaccine designs. The genetic variants that could influence susceptibility to HIV-1 and limit AIDS vary in different populations and among individuals. Meta-analyses of large cohort studies have identified numerous 'AIDS restriction genes' that regulate HIV cell entry (particularly chemokine coreceptors and their ligands), acquired and innate immunity (major histocompatibility complex, killer cell immunoglobulin-like receptor, and cytokines), and others [tripartite interaction motif 5 alpha (TRIM5alpha) and apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G] that influence outcome of HIV infection. Studies carried out in the Indian population with regard to genetic polymorphisms in chemokine receptors have shown that (i) the protective CCR5 Delta32 variant is rare, (ii) CCR5HHE carrying *59402A is associated with increased likelihood of infection and development of AIDS, and (iii) the Indian population generally has low CCL3L1 copy numbers (approximately 2.3). These data have implications in developing screening tests that could identify people at higher or lower risk of infection and rate of disease progression, predict vaccine responsiveness in clinical trials and understand the pathogenic mechanisms.

The Latitude Wise Prevalence of the CCR5-Δ32-HIV Resistance Allele in India

The chemokine receptor CCR5 plays a crucial role during CD4-mediated entry of HIV-1 in macrophages and a 32 bp deletion in the CCR5 gene (CCR5-Δ32) confers protection against HIV infection and AIDS progression. To evaluate the contribution of this host genetic factor in aggravating India's HIV/AIDS problem, we exclusively examined the frequency of CCR5-Δ32 in 43 different ethnic endogamous Indian populations comprising 1,882 individuals and its latitude-wise distribution in India. This is the first report of prevalence and latitude-wise distribution of CCR5-Δ32 in such large scale in India, which indicates that most of the Indian populations lack the CCR5-Δ32 mutation. This mutation was exhibited in only 13 out of the 43 ethnic populations of India studied with allelic frequency 0.62 - 5%. Southward decreasing cline was observed for frequencies of CCR5-Δ32 (0.79% to 5.0% in North vs. 0.62% to 1.4% South). These results are in accordance with HIV/AIDS prevalence in India, and suggest that absence of CCR5-Δ32 mutation may be one of the important factors for HIV/AIDS incidence in India.

Association of chemokines receptor (CCR5 Delta32) in idiopathic recurrent miscarriages among north Indians

PURPOSE

Human reproduction is a complex process involving multiple factors for the success of pregnancy. Chemokines are one of the immunomodulators which may determine pregnancy outcome. In the present study, we have tested genetic association between CCR5 Delta32 polymorphism and idiopathic recurrent miscarriages (IRM) among north Indians.

METHODS

Two hundred patients and 300 age, sex and ethnically matched controls were genotyped for CCR5 Delta32 polymorphism, genotype and allele frequencies were compared in both the groups.

RESULTS

IRM patients had a three times higher (5.5 vs. 1.7%) frequency of heterozygote genotype (P = 0.0335, OR = 3.43; 95% CI = 1.17-10.04). Allele frequency in IRM patients was 3.7 and 0.83% among controls and the differences were statistically significant (P = 0.0349, OR = 3.37; 95% CI = 1.16-9.76).

CONCLUSIONS

Our results demonstrated that it had a higher frequency of CCR5 Delta32 at allelic level suggesting a possible susceptibility trend (OR = 3.43) and CCR5 Delta32 may be a potential genetic risk factor for IRM.

Polymorphic variants in DC-SIGN, DC-SIGNR and SDF-1 in high risk seronegative and HIV-1 patients in Northern Asian Indians

A single nucleotide polymorphism (SNP) in SDF-1, the natural ligand for the HIV-1 coreceptor CXCR4, is implicated to have protective effects against HIV-1 infection. Dendritic cells are the first to encounter HIV-1 at mucosal sites and virus binding occurs via receptors known as DC-SIGN. Variations in the number of repeats in the neck region of DC-SIGN and DC-SIGNR are reported to possibly influence host susceptibility to HIV-1 infection. We examined the SNP of SDF1-3'A by PCR-restriction fragment length polymorphism (RFLP) and repeat region polymorphisms in DC-SIGN and DC SIGNR by PCR in healthy HIV seronegative individuals, high risk STD patients seronegative for HIV, and HIV-1 seropositive patients from northern India. The detected polymorphisms were confirmed by cloning and sequencing. The genotypic frequency of SDF1-3'A/SDF1-3'A in the 100 HIV-seronegative healthy individuals, 150 HIV seronegative STD patients, and 100 HIV-1 seropositive patients were 4%, 18% and 7%, respectively. A significantly higher frequency of SDF1-3'A/SDF1-3'A was observed in high risk STD patients as compared to HIV seropositive (p=0.014) and healthy HIV-1 seronegative tested individuals (p=0.001), suggesting a protective role of SDF1-3'A in HIV-1 infection. DC-SIGN polymorphism was rare and genotype 7/7 was predominant in all groups studied. DC-SIGNR was highly polymorphic and 11 genotypes were observed among the different study groups. The precise role of the polymorphic variants of DC-SIGNR needs to be elucidated in the population.

Immunogenetic basis of HIV-1 infection, transmission and disease progression

Susceptibility to HIV-1 infection and rate of disease progression to AIDS are complex traits modulated by environmental and genetic factors. Studies on large AIDS cohorts and their meta-analyses have identified numerous AIDS restriction genes that regulate HIV cell entry (particularly chemokine co-receptors and their ligands), acquired and innate immunity (major histocompatibility complex (MHC), killer immunoglobulin-like receptors (KIRs), and cytokines) and others that influence outcome of HIV infection. However, vast inter-individual variability is often observed and some rare individuals like 'long-term non-progressors (LTNPs) or exposed uninfected' (EUs) appear to be protected due to natural resistance. A better understanding of genetic basis of such a 'natural resistance' to infection would bear important implications in designing therapeutic vaccine designs. The genetic variants that could limit AIDS vary in different populations. We have studied genetic variations in the MHC, cytokines and CCR2-CCR5 loci in the Asian-Indian HIV-infected population and compared with other global populations.

Distribution of CCR2 polymorphism in HIV-1-infected and healthy subjects in North India

Substitution of V64I in CCR2 relates to delayed progression to AIDS and protects against HIV-1 infection. We examined the distribution of V64I in HIV-infected and healthy North Indian subjects. No significant difference in the allele or genotype distribution of CCR2 V64I polymorphism was observed, indicating that there is no association between CCR2 V64I polymorphism and susceptibility to HIV infection in North Indian population.

Chemokine receptor 5 (CCR5) deletion polymorphism in North Indian patients with coronary artery disease

BACKGROUND

Polymorphisms in genes coding for chemokine receptors, CCR2 and CCR5 have been studied as genetic markers of coronary artery disease (CAD). V64Ile polymorphism in CCR2 has been implicated in the manifestation of myocardial infarction in different populations, but data on association of the CCR5 deletion variant in etiology of CAD are conflicting. In the present study we tested genetic association between CCR5 Delta32 polymorphism and CAD among North Indians (Uttar Pradesh).

METHODS

Two hundred angiographically proven patients with coronary artery disease and two hundred age, sex and ethnically matched controls were genotyped for CCR5 Delta32 polymorphism by polymerase chain reaction. Genotype/allele frequencies were compared in patients and controls using the chi-square test.

RESULTS

The frequency of the heterozygote genotype in the population, including both patient and control group, was 3% and the frequency of the mutant allele Delta32 was 1.5%. CAD patients had a three times higher (4.6% vs. 1.5%) frequency of heterozygote genotype but the differences were statistically not significant. Association analysis did not achieve statistical significance, though odds ratio of 3.13 was observed for heterozygote genotype.

CONCLUSIONS

The allele frequency of the CCR5 Delta32 polymorphism in CAD patients is 2.25% and 0.75% among controls but the differences were not significant. Overall this fits well with the pattern of CCR5 Delta32 allele frequency in Indian subcontinent where it varies from 1 to 3%. The heterozygote (+/ Delta32) genotype does not seem to have any protective role against development of CAD in this population. In fact, North Indian CAD had a higher frequency of CCR5 Delta32 allele suggesting a possible susceptibility trend (odds ratio 3.08, CI 0.83-11.46, chi-square 2.167, NS).

Distribution of CCR5Δ32, CCR2-64I and SDF1-3′A and plasma levels of SDF-1 in HIV-1 seronegative North Indians

Host genetic factors play an important role in susceptibility to HIV-1 infection and progression to AIDS. Mutations in genes encoding chemokine receptors and their ligands, viz., CCR5delta32, CCR2-64I and SDF1-3'A are implicated to have protective effects against HIV-1 infection and/or disease progression. The distribution of these gene polymorphisms and their role in the course of the disease varies between individuals of different racial, ethnic and risk groups. We have examined the allelic frequencies of CCR5delta32, CCR2-64I and SDF1-3'A in 500 healthy North Indians tested seronegative for HIV-1, by PCR-RFLP. The plasma levels of stromal derived factor (SDF-1) protein were estimated in 75 individuals using ELISA kit. Frequencies of CCR5delta32, CCR2-64I and SDF1-3'A alleles in 500 individuals were 1.5%, 9.1% and 20.4%, respectively. The SDF1-3'A homozygosity was confirmed by PCR product cloning and sequencing. The relative hazard values calculated on the basis of the three locus genotype of each individual revealed high relative hazard values (>0.9). The plasma levels of SDF-1 ranged from 1.77 to 3.42 ng/ml and were comparable between the three genotypes of SDF-1. This is the first study to assess the plasma level of SDF-1 protein in Asian Indians. Low frequency of the protective allele CCR5delta32 observed in this study suggests high vulnerability of North Indians to HIV-1 infection. The precise role of SDF1-3'A in HIV-1 infection needs to be elucidated.

HIV/AIDS in Asia

HIV (ie, HIV-1) epidemics in Asia show great diversity, both in severity and timing. But epidemics in Asia are far from over and several countries including China, Indonesia, and Vietnam have growing epidemics. Several factors affect the rate and magnitude of growth of HIV prevalence, but two of the most important are the size of the sex worker population and the frequency with which commercial sex occurs. In view of the present state of knowledge, even countries with low prevalence of infection might still have epidemics affecting a small percentage of the population. Once HIV infection has become established, growing needs for care and treatment are unavoidable and even the so-called prevention-successful countries of Thailand and Cambodia are seeing burgeoning care needs. The manifestations of HIV disease in the region are discussed with the aim of identifying key issues in medical management and care of HIV/AIDS. In particular, issues relevant to developing appropriate highly active antiretroviral treatment programmes in the region are discussed. Although access to antiretroviral therapy is increasing globally, making it work effectively while simultaneously expanding prevention programmes to stem the flow of new infections remains a real challenge in Asia. Genuine political interest and commitment are essential foundations for success, demanding advocacy at all levels to drive policy, mobilise sufficient resources, and take effective action.