Allelic frequencies of host genetic variants influencing susceptibility to HIV-1 infection and disease in South African populations

TRIM5α 136Q, CCR5 Promoter 59029G And CCR264I Alleles Impact The Progression Of HIV In Children And Adolescents

BACKGROUND

Children show various degrees of vulnerability regarding HIV infection and disease progression. This disparity presents challenges for the follow-up of infected children. Here we investigated reasons behind this variability focusing on some host-related HIV genes.

METHODS

We screened 570 Cameroonian children and adolescents, aged 1 to 19 years old. Among them, 137 were followed over 4 years, from 2010 to 2015. Upon signing a proxy consent, children and adolescents were classified according to their age, CD4 count, viral load and clinical symptoms as long-term non-progressors (LTNP), slow progressors (SP) and rapid progressors (RP). Their blood was collected every 6 months and used for biological and host genetic polymorphism analyses. Five genes were genotyped: Trim5α (R136Q), CCR5 promoter 59029G, CCR2-64I, SDF 3'A and CCR5-Δ32. Exposed non-infected (HEU) and unexposed HIV negative children (HNEU) were recruited as control groups.

RESULTS

Among the 5 genes studied, the protective allele of Trim5α (R136Q) was present in all LTNP and in 72.34% and 2.56% of SP and RP, respectively (p<0.0001). The CCR5 promoter 59029G/G was also more present in LTNP and SP than in RP (p=0.02; p=0.04). The protective CCR2-64I homozygous genotype was almost absent in all groups, only the heterozygous genotype was present with a significant difference between RP vs SP (p=0.0001), and SP vs LTNP (p=0.0002). The CCR2-∆32 was completely absent either as homozygous or heterozygous genotype. It was a monomorphic allele. SDF 3'A was almost present as homozygous wild-type genotype in our study population and was associated neither to disease acquisition nor to disease progression.

CONCLUSION

Among the 5 genes described in the study, Trim 5α (R136Q), CCR5 promoter 59029G and CCR2V64I alleles were associated to the progression of HIV infection in children and adolescents.

KIR Gene Content Diversity in a Zimbabwean Population: Does KIR2DL2 Have a Role in Protection Against Human Immunodeficiency Virus Infection?

Killer cell immunoglobulin-like receptors (KIRs) mediate natural killer cell function through interaction with their cognate human leukocyte antigen ligands. Thus, KIR gene variants have been implicated in resistance or susceptibility to viral infections. However, research on the role of these variants remains contradictory and inconclusive. In the present study, we investigated KIR gene content diversity and its association with human immunodeficiency virus (HIV) infection in an adult Black Zimbabwean population. Presence or absence of 15 KIR genes was determined in 189 HIV-infected adults and 97 HIV-uninfected blood donors using sequence specific primer polymerase chain reaction. Frequencies of KIR genes, genotypes, and haplotypes were compared between the cases and controls to identify putative associations between KIR gene variants and HIV status. We report in this study the frequencies of 15 KIR genes and 43 KIR genotypes (40 known and 3 novel) among Zimbabweans. Importantly, the frequency of the inhibitory KIR2DL2 gene was significantly higher in the uninfected group (62%) compared to the HIV-infected group (47%) (OR = 0.55, 95% CI: 0.33-0.90, p = 0.019). KIR2DL2/2DL2 homozygosity was also significantly higher in the uninfected group (35%) compared to HIV-infected group (53%) (OR = 0.33, 95% CI: 0.16-0.72, p = 0.005) under a recessive model. We conclude that the KIR2DL2 gene may be involved in protection against HIV infection. It may be possible that inhibitory KIR genes may have an important role to play in HIV acquisition among populations of African origin in whom the activating KIR genes are less frequent compared to among Caucasians.

C-C chemokine receptor type five (CCR5): An emerging target for the control of HIV infection

When HIV was initially discovered as the causative agent of AIDS, many expected to find a vaccine within a few years. This has however proven to be elusive; it has been approximately 30 years since HIV was first discovered, and a suitable vaccine is still not in effect. In 2009, a paper published by Hutter et al. reported on a bone marrow transplant performed on an HIV positive individual using stem cells that were derived from a donor who was homozygous for a mutation in the CCR5 gene known as CCR5 delta-32 (Δ32) (Hütter et al., 2009). The HIV positive individual became HIV negative and remained free of viral detection after transplantation despite having halted anti-retroviral (ARV) treatment. This review will focus on CCR5 as a key component in HIV immunity and will discuss the role of CCR5 in the control of HIV infection.

Genetic diversity and linkage disequilibrium in the chemokine receptor CCR2-CCR5 region among individuals and populations

BACKGROUND

Chemokine receptors CCR2 and CCR5 play a key role in immune and inflammatory responses and have been associated with several diseases, including AIDS. In order to comprehend health disparities it is important to understand the nature of genetic variation in specific genes of interest in different populations. Current studies of the CCR2 and CCR5 receptor genes are primarily focused on the CCR5-Δ32, and CCR2-V64I SNPs.

METHODS

Sanger sequencing was used to sequence the regions containing 16 SNPs in the adjacent CCR2 and CCR5 genes (including CCR5-Δ32, and CCR2-V64I) in 249 subjects of African, European and Hispanic ancestry. Linkage disequilibrium (LD) and haplotypes were determined using Haploview.

RESULTS

The data revealed large differences in allele frequencies of several SNPs and LD patterns among the ethnic groups, including SNPs that were restricted to Africans or Europeans. Seven known CCR5 haplotypes and six novel CCR2 haplotypes were identified. A rare case of an HIV+ subject with the CCR5-Δ32/Δ32 was identified.

CONCLUSIONS

These data demonstrate a LD between CCR2 and CCR5 at several loci and provide new information about CCR2 that contributes to our understanding of its population-specific genetic variability. The data indicate that in addition to CCR5-Δ32 and CCR2-V64I, other SNPs and haplotypes may be important genetic determinants of disease and should be investigated.

Mutations in C-C chemokine receptor type 5 (CCR5) in South African individuals

BACKGROUND

The importance of the C-C chemokine receptor type 5 (CCR5) in HIV infection and disease progression was recognized with the discovery of the Δ32 allele. Individuals homozygous for this mutation lack functional CCR5, and are almost completely resistant to HIV infection. Heterozygous individuals display decreased cell surface CCR5, which slows disease progression. Phenotypic expression of CCR5 is heterogeneous and its relation to genetic mutations in the CCR5 gene is not currently known for the South African population. This provided the rationale for investigating genetic variation in low CCR5 expressers in South Africa.

METHODS

Flow cytometry was used to measure the phenotypic distribution of CCR5 in 245 individuals by assessing both the percentage of CD4+CCR5+ T-cells and CCR5 density.

RESULTS

Genotypic data revealed 70 single nucleotide polymorphisms (SNPs), four insertions, and the Δ32 deletion within the 65 individuals selected for sequencing. The Δ32 mutation was detected only in the Caucasian group and included a single homozygous individual with an absence of CCR5 expression. A total of eight previously described open reading frame (ORF) mutations were found in this study, as well as 12 novel mutations with two in the ORF. Greater genetic diversity was present in the black South African group, with 39 mutations being exclusive to this group.

CONCLUSIONS

Using a unique approach to genotype in individuals with lower CCR5 expression we have identified novel SNPs which could affect HIV infection.

Distribution of CCR5-Delta32, CCR5 promoter 59029 A/G, CCR2-64I and SDF1-3'A genetic polymorphisms in HIV-1 infected and uninfected patients in the west region of Cameroon

Background

Genetic variants of the genes encoding Human Immunodeficiency Virus-1 (HIV-1) co-receptors and their ligands, like CC-Chemokine Receptor 5 delta 32 mutation (CCR5-Delta32), CCR5 promoter A/G (Adenine/Guanine), CC-Chemokine Receptor 2 mutation 64 isoleucine (CCR2-64I) and the Stromal cell-derived Factor 3’A mutation (SDF1-3’A), are involved in the susceptibility to HIV-1 infection and progression. The prevalence of these mutations varies by Region. However, little is known about their distribution in the population of Dschang, located in the West Region of Cameroon. The prevalence of HIV in the West Region of Cameroon is lower than elsewhere in Cameroon. The objectives of this study were to determine the distribution of four AIDS Related Gene (ARG) variants in HIV-infected and non-infected population of Cameroon especially in the West Region and to estimate the contribution of these variants to the susceptibility or resistance to HIV infection. We also aimed to evaluate the effectiveness of genotyping using dried blood spot (DBS) samples.

Methods

A total of 179 participants were recruited from two hospitals in Dschang in the West Region of Cameroon. Their genotypes for CCR5-Delta32, CCR5 promoter 59029A/G, CCR2-64I and SDF1-3’A were analyzed using polymerase chain reaction (PCR) and restriction fragment length polymorphisms.

Results

A total of 179 participants were enrolled in the study. Among them, 32 (17.9%) were HIV positive and 147 (82.1%) were HIV negative. The allelic frequencies of these genes were: 0%, 49.72%, 17.6% and 100% respectively for CCR5-Delta32, CCR5 promoter 59029A/G, CCR2-64I and SDF1-3’A. No individual was found to carry the CCR5-Delta 32 mutation. All participants recruited were heterozygous for the SDF1-3’A allele.

Conclusion

Our data suggest that the CCR5-Delta32 cannot account for the protection as it was completely absent in our population. SDF1-3’A variants, may be in association with other polymorphisms, may account for the overall protection from HIV-1 infection in participants recruited as everyone carries this allele. The CCR5 promoter 59029 G/G genotype may be associated with the risk for HIV-1 infection in this population, while the CCR2-64I (A/A genotype) may account for the protection against HIV infection. The results of genotyping from fresh blood and DBS were comparable.

Comprehensive evaluation of imputation performance in African Americans

Imputation of genome-wide single-nucleotide polymorphism (SNP) arrays to a larger known reference panel of SNPs has become a standard and an essential part of genome-wide association studies. However, little is known about the behavior of imputation in African Americans with respect to the different imputation algorithms, the reference population(s) and the reference SNP panels used. Genome-wide SNP data (Affymetrix 6.0) from 3207 African American samples in the Atherosclerosis Risk in Communities Study (ARIC) was used to systematically evaluate imputation quality and yield. Imputation was performed with the imputation algorithms MACH, IMPUTE and BEAGLE using several combinations of three reference panels of HapMap III (ASW, YRI and CEU) and 1000 Genomes Project (pilot 1 YRI June 2010 release, EUR and AFR August 2010 and June 2011 releases) panels with SNP data on chromosomes 18, 20 and 22. About 10% of the directly genotyped SNPs from each chromosome were masked, and SNPs common between the reference panels were used for evaluating the imputation quality using two statistical metrics-concordance accuracy and Cohen's kappa (κ) coefficient. The dependencies of these metrics on the minor allele frequencies (MAF) and specific genotype categories (minor allele homozygotes, heterozygotes and major allele homozygotes) were thoroughly investigated to determine the best panel and method for imputation in African Americans. In addition, the power to detect imputed SNPs associated with simulated phenotypes was studied using the mean genotype of each masked SNP in the imputed data. Our results indicate that the genotype concordances after stratification into each genotype category and Cohen's κ coefficient are considerably better equipped to differentiate imputation performance compared with the traditionally used total concordance statistic, and both statistics improved with increasing MAF irrespective of the imputation method. We also find that both MACH and IMPUTE performed equally well and consistently better than BEAGLE irrespective of the reference panel used. Of the various combinations of reference panels, for both HapMap III and 1000 Genomes Project reference panels, the multi-ethnic panels had better imputation accuracy than those containing only single ethnic samples. The most recent 1000 Genomes Project release June 2011 had substantially higher number of imputed SNPs than HapMap III and performed as well or better than the best combined HapMap III reference panels and previous releases of the 1000 Genomes Project.

The effect of combined polymorphisms in chemokines and chemokine receptors on the clinical course of HIV-1 infection in a Brazilian population

Polymorphisms in genes that encode chemokines or their receptors can modulate susceptibility to human immunodeficiency virus (HIV) infection and disease progression. The objective of this study was to assess the frequency of polymorphisms CCR5-Δ32, CCR2-64I, CCR5-59029A and SDF1-3'A and their role in the course of HIV infection in a Southern Brazilian population. Clinical data were obtained from 249 patients for an average period of 6.4 years and genotypes were determined by standard polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism. Survival analyses were conducted for three outcomes: CD4+ T-cell counts below 200 cells/µL, acquired immune deficiency syndrome (AIDS) or death. The frequency of the polymorphisms CCR5-Δ32, CCR2-64I, CCR5-59029A and SDF1-3'A were 0.024, 0.113, 0.487 and 0.207, respectively. CCR5-Δ32 was associated with a reduction in the risk for CD4+ T-cell depletion and with an increased risk for death after AIDS diagnosis. CCR2-64I was associated with a reduction in the risk for developing AIDS. SDF1-3'A was also associated with decreased risk for AIDS, but its effect was only evident when CCR2-64I was present as well. These results highlight the possibility of using these markers as indicators for the prognosis of disease progression and provide evidence for the importance of analysing the effects of gene polymorphisms in a combined fashion.

Distribution of CCR5-{delta}32, CCR2-64I, and SDF1-3'A in Guangxi Zhuang population

BACKGROUND

To investigate the distribution of CCR5-Delta32, CCR2-64I, and SDF1-3'A alleles in Guangxi province Zhuang population.

METHOD

A total of 180 healthy individuals and 150 HIV-positive patients were recruited. All individuals were genotyped for CCR5 polymorphism using polymerase chain reaction (PCR), and CCR2 and SDF1 polymorphism using PCR restriction fragment length polymorphisms (PCR-RFLPs).

RESULTS

No CCR5-Delta32 mutation was found. CCR2-64I frequency was 24.7% in the healthy group and 20.3% in the HIV-positive group, and SDF1-3'A was 30.6% and 29.3% in the 2 groups, respectively. There were no significances in the frequencies of CCR2-64I (chi(2) = 1.795, P = .180) and SDF1-3'A (chi(2) = 0.116, P = .733) between the 2 groups.

CONCLUSIONS

The protective CCR5-Delta32 mutation is absent in the Zhuang population, but CCR2-64I and SDF1-3'A are relatively common and seem not to confer protection against HIV-1 infection. The results suggest that the Zhuang people may have a similar genetic susceptibility to HIV-1 infection with most other Chinese ethnic groups.

Genetic variation within the gene encoding the HIV-1 CCR5 coreceptor in two South African populations

Polymorphisms within the open reading frame as well as the promoter and regulatory regions can influence the amount of CCR5 expressed on the cell surface and hence an individual's susceptibility to HIV-1. In this study we characterize CCR5 genes within the South African African (SAA) and Caucasian (SAC) populations by sequencing a 9.2kb continuous region encompassing the CCR5 open reading frame (ORF), its two promoters and the 3' untranslated region. Full length CCR5 sequences were obtained for 70 individuals (35 SAA and 35 SAC) and sequences were analyzed for the presence of single-nucleotide polymorphisms (SNPs), indels and intragenic haplotypes. A novel SNP (+258G/C) within the ORF leading to a non-synonomous amino acid (Trp-->Cys) change was detected in one Caucasian individual. Results demonstrate a high degree of genetic variation: 68 SNP positions, four indels, as well as the Delta32 deletion mutant, were detected. Seven complex putative haplotypes spanning the length of the sequenced region have been identified. These haplotypes appear to be extensions of haplotypes previously described within CCR5. Two haplotypes, SAA-HHE and SAC-HHE were found in high frequency in the SAA and SAC population groups studied (20.0% and 18.6%, respectively) and share four SNP positions suggesting an evolutionary link between the two haplotypes. Only one of the identified haplotypes, SAA/C-HHC, is common to both study populations but the haplotype frequency differs markedly between the two groups (8.6% in SAA and 52.9% in SAC). The two population groups show differences in both haplotype arrangement as well as SNP profile.

A whole genome association study of mother-to-child transmission of HIV in Malawi

BACKGROUND

More than 300,000 children are newly infected with HIV each year, predominantly through mother-to-child transmission (HIV MTCT). Identification of host genetic traits associated with transmission may more clearly explain the mechanisms of HIV MTCT and further the development of a vaccine to protect infants from infection. Associations between transmission and a selection of genes or single nucleotide polymorphisms (SNP)s may give an incomplete picture of HIV MTCT etiology. Thus, this study employed a genome-wide association approach to identify novel variants associated with HIV MTCT.

METHODS

We conducted a nested case-control study of HIV MTCT using infants of HIV(+) mothers, drawn from a cohort study of malaria and HIV in pregnancy in Blantyre, Malawi. Whole genome scans (650,000 SNPs genotyped using Illumina genotyping assays) were obtained for each infant. Logistic regression was used to evaluate the association between each SNP and HIV MTCT.

RESULTS

Genotype results were available for 100 HIV(+) infants (at birth, 6, or 12 weeks) and 126 HIV(-) infants (at birth, 6, and 12 weeks). We identified 9 SNPs within 6 genes with a P-value < 5 × 10(-5) associated with the risk of transmission, in either unadjusted or adjusted by maternal HIV viral load analyses. Carriers of the rs8069770 variant allele were associated with a lower risk of HIV MTCT (odds ratio = 0.27, 95% confidence interval = 0.14, 0.51), where rs8069770 is located within HS3ST3A1, a gene involved in heparan sulfate biosynthesis. Interesting associations for SNPs located within or near genes involved in pregnancy and development, innate immunological response, or HIV protein interactions were also observed.

CONCLUSIONS

This study used a genome-wide approach to identify novel variants associated with the risk of HIV MTCT in order to gain new insights into HIV MTCT etiology. Replication of this work using a larger sample size will help us to differentiate true positive findings.

Genome-wide patterns of population structure and admixture in West Africans and African Americans

Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th-75th percentiles: 11.6-27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

Distribution of CCR5-Delta32, CCR5m303A, CCR2-64I and SDF1-3'A in HIV-1 infected and uninfected high-risk Uighurs in Xinjiang, China

BACKGROUND

Genetic variants of the genes encoding HIV-1 co-receptors and their ligands, CCR5-Delta32, CCR5m303A, CCR2-64I and SDF1-3'A, are implicated in the susceptibility to HIV-1 infection, and the prevalence of these mutations varies by ethnicity. However, little is known about their distribution in Uighurs.

OBJECTIVES

This study aimed at characterizing the frequency of these HIV-related gene variants in a high-risk Uighur population.

STUDY DESIGNS

A total of 251 HIV-1 seropositive and 238 seronegative high-risk Uighurs were recruited and their genotypes of CCR5-Delta32, CCR5m303A, CCR2-64I and SDF1-3'A were analyzed by PCR and PCR-ligase detection reaction (PCR-LDR).

RESULTS

The allelic frequency of CCR5-Delta32, CCR5m303A, CCR2-64I and SDF1-3'A was 4.40%, 2.66%, 25.66% and 57.36%, respectively, in this population. Apparently, the Uighur population has low frequency of CCR5-Delta32 and CCR5m303A, but high frequency of CCR2-64I and SDF1-3'A. While there was no significant difference in the frequency of CCR5-Delta32, CCR2-64I and SDF1-3' A between HIV-1 seropositive and seronegative groups the frequency of CCR5m303A in HIV-1 seropositive group was significantly higher than that in seronegative group (P=0.006, OR=3.982 and 95%CI 1.514-10.476).

CONCLUSIONS

Our data suggest that the CCR5-Delta32, CCR2-64I and SDF1-3'A variants may have limited effect on protecting from HIV-1 infection in Uighurs. Rather, the CCR5m303A may be associated with the risk for HIV-1 infection in high-risk Uighurs.

African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping

Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility.

Bisexually active Black men in the United States and HIV: acknowledging more than the "Down Low"

HIV is disproportionately impacting Black men who have sex with men and heterosexual women in the United States. Current speculation posits a "bisexual bridge" of HIV transmission connecting these two subpopulations of the Black community. Specifically, bisexually active Black men who identify as heterosexual but do not disclose their same-sex behavior, or "down low" (DL) men, have received the most attention and blame as the primary group fueling this epidemic. This essay explores the current knowledge and limitations of public health research on bisexually active Black men. Implications for future research initiatives are discussed.

CCR2b-64I allelic polymorphisms in advanced HIV-infected Koreans accelerate disease progression

Genetic polymorphisms of chemokine genes and chemokine-receptor genes in HIV-infected patients have been associated with delayed progression of this disease. The allelic frequencies of these genetic variants also differ between ethnic groups. To investigate the effects of the SDF1 and CCR2b genotypes on disease progression, survival of 200 HIV-infected persons for whom at least four subsequent immunologic data items had been collected was analyzed. A genotyping assay of SDF1 and CCR2b genes was carried out using polymerase chain reaction-restriction fragment length polymorphism analyses. HIV-infected persons heterozygous for the SDF1-3'A or CCR2b-64I alleles were included in the survival analysis, but homozygotes were excluded because of a very small sample number. Neither the CCR2b-+/64I allele nor the SDF1-+/3'A allele, separately or in combination, had a significant impact on survival during the asymptomatic period of HIV infection. However, CCR2b-+/64I alleles were associated with accelerated disease progression during the advanced period of HIV infection. The survival time of HIV-infected people with CCR2b-+/64I and SDF1-+/+ genotypes was significantly shorter than those of the other groups (p < 0.01), but this effect was not apparent in persons with CCR2b-+/64I alleles and SDF1-+/3'A genotypes. These results suggest that the effect of CCR2b-64I polymorphisms on disease progression may differ according to the stage of HIV infection and interactions with other gene variants.

Greater risk for HIV infection of black men who have sex with men: a critical literature review

HIV rates are disproportionately higher for Black men who have sex with men (MSM) than for other MSM. We reviewed the literature to examine 12 hypotheses that might explain this disparity. We found that high rates of HIV infection for Black MSM were partly attributable to a high prevalence of sexually transmitted diseases that facilitate HIV transmission and to undetected or late diagnosis of HIV infection; they were not attributable to a higher frequency of risky sexual behavior, nongay identity, or sexual nondisclosure, or to reported use of alcohol or illicit substances. Evidence was insufficient to evaluate the remaining hypotheses.Future studies must address these hypotheses to provide additional explanations for the greater prevalence of HIV infection among Black MSM.

Risk for HIV-1 infection associated with a common CXCL12 (SDF1) polymorphism and CXCR4 variation in an African population

CXC chemokine ligand 12 (CXCL12), or stromal cell-derived factor 1 (SDF1), is the only known natural ligand for the HIV-1 coreceptor, CXC chemokine receptor 4 (CXCR4). A single nucleotide polymorphism (SNP) in the CXCL12 gene (SDF1-3'A) has been associated with disease progression to AIDS in some studies, but not others. Mutations in the CXCR4 gene are generally rare and have not been implicated in HIV-1/AIDS pathogenesis. This study analyzed the SDF1-3'A SNP and performed mutation screening for polymorphic markers in the CXCR4 gene to determine the presence or absence of significant associations with susceptibility to HIV-1 infection. The study consisted of 257 HIV-1-seropositive patients and 113 HIV-1-seronegative controls representing a sub-Saharan African population belonging to the Xhosa ethnic group of South Africa. The SDF1-3'A SNP was associated with an increased risk for HIV-1 infection (P = 0.0319) whereas no significant association was observed between the occurrence of the SDF1-3'A SNP and increased or decreased plasma levels of CXCL12. Comprehensive mutation analysis of the CXCR4 gene confirmed a high degree of genetic conservation within the coding region of this ancient population.

Distribution of CCR2-64I and SDF1-3'A alleles and HIV status in 7 ethnic populations of Cameroon

Limited information is available on the prevalence among rural Africans of host genetic polymorphisms conferring resistance to HIV-1 infection or slowing HIV disease progression. We report the allelic frequencies of the AIDS-related polymorphisms CCR2-64I, SDF1-3'A, and CCR5-Delta32 in 321 volunteers from 7 ethnic groups in Cameroon. Allelic frequencies differed among the 7 ethnic groups, ranging from 10.8% to 31.3% for CCR2-64I and 0.0% to 7.1% for SDF1-3'A. No CCR5-Delta32 alleles were found. HIV seroprevalence was 6.9% in the total population and peaked at younger ages in girls and women than in boys and men. Among 15- to 54-year-olds, HIV seroprevalence varied from 2.0% to 11.1% among the village populations. Conditional logistic regression analysis using data from boys and men aged 15 to 54 years showed the number of CCR2-64I alleles to be a significant risk factor for HIV seropositivity (odds ratio per allele adjusted for age and matched on ethnic group = 6.3, 95% confidence interval: 1.3-30.3); this association was not found in women. The findings are consistent with the hypothesis that CCR2-64I alleles may delay HIV disease progression without affecting susceptibility to infection among men. We did not observe this relation among women, and other factors, such as multiple pregnancies or maternal stressors (eg, breastfeeding), may have masked any protective effect of CCR2-64I alleles. Further study of this issue among women is warranted. SDF1-3'A did not differ between HIV-seropositive and HIV-seronegative individuals but was associated with increasing age among HIV-seronegative women, suggesting a protective effect against HIV-1 infection.

Supplementation of CXCL12 (CXCL12) induces homing of CD11c+ dendritic cells to the spleen and enhances control of Plasmodium berghei malaria in BALB/c mice

In malaria, parasitaemia is controlled in the spleen, a multicomponent organ that undergoes changes in its cellular constituents to control the parasite. During this process, dendritic cells (DCs) orchestrate the positioning of effector cells in a timely manner for optimal parasite clearance. We have recently demonstrated that CXCL12 [stromal cell-derived factor-1 (CXCL12)] supplementation partially restores the ability to control parasitaemia in Plasmodium berghei-infected mice. In the present study, we investigated the nature of the DCs involved by flow cytometry and immunohistochemistry of CD11c(+) cells. Flow cytometry of bone marrow cells showed that infection with P. berghei did not alter the proportion of CD11c(+) cells present in this haematopoietic compartment, while CXCL12 supplementation of naïve uninfected mice induced only minor increases in the population of CD11c(+) cells. In the spleen, P. berghei infection alone resulted in an increase in CD11c(+) cells as compared with naïve animals. Exogenously administered CXCL12 in the absence of infection resulted in a significant expansion of the splenic CD11c(+) population, and this effect was even more pronounced in infected and supplemented mice. Immunohistochemistry revealed that CD11c(+) cells infiltrated the perivascular areas and marginal zone of the spleen in infected animals treated with CXCL12, suggesting that this chemokine induces homing of CD11c(+) dendritic cells to the splenic compartment. Our results show that small amounts of CXCL12 supplementation are effective in recruiting DCs to the spleens of both uninfected and infected mice, suggesting the participation of CXCL12 and CD11c(+) cells in the establishment of an adequate environment in the spleen for malaria control.

HIV and the CCR5-Δ32 resistance allele

The combination of molecular biology, epidemiology, virology, evolutionary and population genetics has enabled us to understand the delicate interplay between HIV and the CCR5-Delta32 HIV resistance allele. We here review and collect from the different approaches to show how they can be combined to elucidate the interaction between host and pathogen genetics in this system. We will present an overview of the normal role of CCR5, its involvement in HIV, the molecular biology of the CCR5-Delta32 allele and its probable origins. By focusing on this well-documented and important system we hope to demonstrate the power that such a "holistic" approach might offer in the study of infectious diseases.

Prevalence of chemokine and chemokine receptor polymorphisms in seroprevalent children with symptomatic HIV-1 infection in the United States

Several chemokines and chemokine receptors are involved in HIV-1 infection, disease progression, and transmission. We studied the prevalence of genetic variations in CCR2, SDF1, and the CCR5 gene and its promoter region at positions 59029, 59353, and 59356 in a seroprevalent cohort of 1057 children with symptomatic HIV-1 infection in the United States. The percentage of children with the CCR5-wt/Delta32 genotype was significantly higher for white, non-Hispanic children (15%) than for Hispanic (6%) or black, non-Hispanic children (4%). For the CCR5-59029-G/A, CCR5-59353-T/C, and CCR5-59356-C/T polymorphisms, there were significant or marginally significant differences in genotype frequencies across race/ethnicity groups. For the CCR2-wt/64I polymorphism, both black, non-Hispanic and Hispanic children had a higher frequency of the CCR2-wt/64I genotype (24% and 21%, respectively) and CCR2-64I/64I genotype (4% and 3%, respectively) than white, non-Hispanic children (14% and 2%, respectively). For the SDF1-3'-G/A polymorphism, black, non-Hispanic children had a lower combined frequency of the SDF1-3'-G/A and SDF1-3'-A/A genotypes (15%) than did Hispanic children (33%) and white, non-Hispanic children (37%). These analyses show that the distribution of chemokine receptor and chemokine genetic polymorphisms varies significantly across race/ethnicity subgroups of HIV-1-infected children in the United States.

The CCR5 and CXCR4 coreceptors are both used by human immunodeficiency virus type 1 primary isolates from subtype C

Human immunodeficiency virus type 1 (HIV-1) subtype C viruses with different coreceptor usage profiles were isolated from 29 South African patients with advanced AIDS. All 24 R5 isolates were inhibited by the CCR5-specific agents, PRO 140 and RANTES, while the two X4 viruses and the three R5X4 viruses were sensitive to the CXCR4-specific inhibitor, AMD3100. The five X4 or R5X4 viruses were all able to replicate in peripheral blood mononuclear cells that did not express CCR5. When tested using coreceptor-transfected cell lines, one R5 virus was also able to use CXCR6, and another R5X4 virus could use CCR3, BOB/GPR15, and CXCR6. The R5X4 and X4 viruses contained more-diverse V3 loop sequences, with a higher overall positive charge, than the R5 viruses. Hence, some HIV-1 subtype C viruses are able to use CCR5, CXCR4, or both CXCR4 and CCR5 for entry, and they are sensitive to specific inhibitors of entry via these coreceptors. These observations are relevant to understanding the rapid spread of HIV-1 subtype C in the developing world and to the design of intervention and treatment strategies.

Population survey of CCR5 delta32, CCR5 m303, CCR2b 64I, and SDF1 3'A allele frequencies in indigenous Chinese healthy individuals, and in HIV-1-infected and HIV-1-uninfected individuals in HIV-1 risk groups

The aim of this study is to determine in indigenous Chinese ethnic groups the frequencies of the chemokine (SDF1 3'A) and chemokine receptors (CCR5 delta32, CCR5 m303, and CCR2b 64I) HIV-1/AIDS restriction alleles. The study includes two cohorts; the first comprised 3165 indigenous healthy subjects representing eight ethnic groups: Han (n = 1406), Uygur (n = 316), Mongolia (n = 134), Hui (n = 386), Tibetan (n = 330), Zhuang (n = 378), Dai (n = 101), and Jingbo (n =114). The second cohort consisted of 330 HIV-1-infected (86 subjects infected by sexual transmission and 198 subjects infected by HIV-1-contaminated blood or by sharing injection equipment; the remaining 46 subjects said nothing about HIV-1 transmission) and 474 HIV-1-uninfected Han Chinese belonging to one of two HIV-1 high-risk groups: intravenous drug users (n = 215) and individuals with sexually transmitted diseases (n = 259). Genotypes for the four genes were obtained using PCR (CCR5 delta32) or PCR-restriction fragment length polymorphism. Randomly selected amplified PCR products were further confirmed by direct DNA sequencing. The variant allele frequencies were determined to be 0% to 3.48% for CCR5 delta32, 0% for CCR5 m303, 16.23% to 28.79% for CCR2b 64I, and 17.70% to 27.76% for SDF1 3'A in Chinese healthy individuals from eight ethnic groups. These findings show that allele frequencies differ among the eight Chinese ethnic groups for CCR5 delta32, CCR2b 64I, and SDF1 3'A and that the CCR5 m303 and CCR5 delta32 mutant alleles were absent or infrequent in Chinese, which may be helpful for studies of specific anti-HIV-1 vaccine trials and coreceptor inhibitor drug targets in Chinese populations. Furthermore, we observed no significant differences in allele or genotypic frequencies between HIV-1-infected and HIV-1-uninfected groups from the Han ethnic group. Our finding is the first reporting that there is likely no effect of the examined polymorphisms in our study on HIV-1 transmission in the Chinese Han population, However, the genetic effects of these and other AIDS-modifying polymorphisms on the pathogenesis and clinical outcome of HIV-1/AIDS diseases is under investigation in Chinese populations.

Coreceptor usage and biological phenotypes of HIV-1 isolates

The discovery of chemokine receptors as HIV-1 entry molecules or "coreceptors" has lead to a greater understanding of how HIV-1 infects human cells. This has provided insight into the biological properties of HIV-1 isolates and unravelled the meaning of the syncytium-inducing and non-syncytium-inducing phenotypes. Understanding how HIV-1 exploits these coreceptors has given way to novel approaches to controlling HIV. As a result a new class of drugs has emerged that are being tested to prevent virus infection and to act as an alternative, or adjunct, to existing anti-retroviral drugs for HIV-infected individuals.

Fluorescence resonance energy transfer analysis of CCR-V64I and SDF1-3'a polymorphisms: prevalence in southern Spain hiv type 1+ cohort and noninfected population

The relationship between host genotype and AIDS, as well as the different genotype frequencies observed in different populations, have become important topics in HIV research. Therefore, the development of methods that provide faster and reliable results may contribute to further development and knowledge of those topics. We present the results of genotyping SDF1-3'A and CCR2-V64I in 440 HIV-1-infected people and 100 noninfected controls from southern Spain, using a novel method based on real-time PCR with LightCycler technology and fluorescence resonance energy transfer. Frequencies obtained were 23.8% for SDF1-3'A and 9.5% for CCR2-V64I for both HIV+ cohort and general population. Both polymorphisms are in accordance with the Hardy-Weinberg equilibrium law and no differences between patients and controls have been observed.