CI | Novels & Fanfic

Explore

Journal info

nature

scientific reports

articles

article

Article

Open Access

Published: 20 May 2019

Genetic Polymorphisms in the Open Reading Frame of the CCR5 gene From HIV-1 Seronegative and Seropositive Individuals From National Capital Regions of India

Larance Ronsard,

Vikas Sood,

[…]

Akhil C. Banerjea

Scientific Reports volume 9, Article number: 7594 (2019) Cite this article

1879 Accesses

2 Citations

Metricsdetails

Abstract

C-C chemokine receptor type 5 (CCR5) serves as a co-receptor for Human immunodeficiency virus (HIV), enabling the virus to enter human CD4 T cells and macrophages. In the absence of CCR5, HIV strains that require CCR5 (R5 or M-tropic HIV) fail to successfully initiate infection. Various natural mutations of the CCR5 gene have been reported to interfere with the HIV-CCR5 interaction, which influences the rate of AIDS progression. Genetic characterization of the CCR5 gene in individuals from the National Capital Regions (NCRs) of India revealed several natural point mutations in HIV seropositive/negative individuals. Furthermore, we identified novel frame-shifts mutations in the CCR5 gene in HIV seronegative individuals, as well as the well reported CCR5Δ32 mutation. Additionally, we observed a number of mutations present only in HIV seropositive individuals. This is the first report to describe the genetic variations of CCR5 in individuals from the NCRs of India and demonstrates the utility of investigating understudied populations to identify novel CCR5 polymorphisms.

Download PDF

Introduction

UNAIDS reported that India currently has the third largest Human immunodeficiency virus (HIV) epidemic globally, with 2.1 million individuals currently infected. This burgeoning epidemic of HIV in India is linked to genetic variability and dominating emergence of various subtypes, including recombinants, and subtype B and C1,2,3,4,5, which predominantly use C-C chemokine receptor 5 (CCR5) as a co-receptor to initiate infection6. CCR5 interaction with HIV is critical for HIV transmission and disease progression rate7,8. Over the past decade, several mutations of CCR5 that seem to have a significant impact on HIV acquisition and disease progression have been identified in different populations7,9,10. The nature and frequency of these mutations varies between populations. Despite the large burden of HIV on the Indian population, the majority of genetic reports has focused on Caucasian, Chinese, African, and American populations11; only a few reports from India focus on mutations in the CCR5 gene12. Therefore, the purpose of this study is to characterize the genetic variations in the ORF of CCR5.

CCR5 (C-C chemokine receptor type 5) is a G-protein coupled receptor with seven transmembrane domains, that is expressed on T cells, B cells, monocytes/macrophages and microglia13,14 and binds the β-chemokines such as RANTES (Regulated on Activation, Normal T cell Expressed and Secreted), and MIP (Macrophages Inflammatory Proteins)-1α and -1β15,16,17. Notably, CCR5 acts as the co-receptor for R5-tropic HIV strains, and thus is crucial in initiating HIV infection18,19. HIV glycoprotein120 (gp120) binds to the cluster of differentiation 4 (CD4) receptor, resulting in a conformational change in gp120, which allows it to bind to either co-receptor CCR5 (R5-tropic), C-X-C chemokine receptor type 4 (CXCR4) (X4-tropic), or both (dual tropic viruses)20,21,22,23,24,25.

Mutations in the CCR5 gene have been shown to influence the rate of HIV progression by inhibiting co-receptor activity of CCR5 include CCR5∆32, CCR5-59653T, CCR5-59029 and CCR5-m30318,26,27,28,29. The CCR5Δ32 has attracted much interest as individuals carrying this mutation showed resistance to HIV infection30,31. The CCR5Δ32 mutation causes a frame-shift with a premature stop codon and generates a truncated form of CCR5 (215 amino acids instead of 352 amino acids in wild type CCR5). The truncated protein is not expressed on the cell surface, and thus viral binding to the receptor is hindered31,32. Individuals homozygous for CCR5Δ32 were protected against HIV33,34, and heterozygous individuals experienced delayed AIDS progression11,35. In 2007, a patient from Berlin was reported to be cured of AIDS after three years of treatment with bone marrow stem cell transplantation carrying homozygous CCR5∆3236,37, highlighting the importance of this mutation for combatting HIV infection. The frequency of the CCR5∆32 mutation was found to vary regionally, approximately 15% in Northern Europeans, 10% in Caucasians, and 19% in African Americans18,38,39. Amongst Asians, the frequency varies from 1 to 12%32. In India, the first report on heterozygosity of CCR5∆32 was documented with 1% prevalence in 1998 by our group12. This observation was critical for understanding genetic characteristics of Asian populations and led to further genetic screening of various mutations in the CCR5 gene.

Varying HIV transmission rate among infected individuals can mainly be attributed to polymorphisms in the co-receptors40. Therefore, we examined the polymorphisms in the open reading frame (ORF) of CCR5 in our population. The objective of this study was to identify the prevalence of various mutations in the CCR5 gene among NCRs of India, and to determine the genetic variations in between HIV seropositive and seronegative individuals. The CCR5 gene was amplified from peripheral blood mononuclear cells (PBMCs) of seronegative (n = 70) and seropositive (n = 72) individuals. Screening of 142 individuals in total resulted in identification of various mutations. In both seronegative and seropositive individuals, we identified (1) reported point mutations from various other population; (2) reported mutations but replaced with different amino acid at the same position, (3) novel frame-shift mutations, 32-bp (base pair) deletion mutation, and (4) novel mutations. In summary, this report describes the genetic variations occurring in the CCR5 gene from NCRs of India.

Results

CCR5 mutations in HIV seronegative individuals

We identified ten mutations in the ORF of CCR5 that had previously been described in various other populations41,42, namely K26R, L55Q, F166L, CCR5Δ32, Q194H, R223Q, Δ228K, I253T, F299S, and R319H (Table 1). These mutations were present at highly conserved amino acid positions within the CCR5 gene9 and most of these mutations have already been shown to be associated with delayed progression to AIDS10,40. Previous reports have suggested that K26R and L55Q mutations reduce expression of CCR5 for the R5 viruses, and thus alter the receptor's functional activity. These mutations have been reported in 1.6% in Chinese and African-American individuals who are HIV seronegative43,44, whereas in our population, K26R and L55Q mutations were observed at 1.4% and 4.3% respectively. F166L was identified amongst Americans in the majority of HIV infected long-term non-progressive individuals45, and has been reported to attenuate HIV infection46. This mutation was observed in 1.4% of our population.

Table 1 Earlier reported mutations and we also observed in HIV-1 seronegative individuals.

Full size table

We had identified the well-known HIV protective mutation CCR5Δ32 in 1% of our population in an earlier study12,47. In the present study, we observed this deletion at a rate of 2.8%. Q194H alters expression of CCR5 and lies at 2% in Chinese HIV seropositive individuals48. In our population, this mutation was found at 5.7%. R223Q diminishes the functional activity of CCR5 but is able to bind to gp120 at lower levels18. The mutation had been identified in China at 4.4% and 4.1% in HIV seronegative and seropositive donors respectively40,49; in our population, the frequency was at 2.8%. A single lysine (K) residue deletion at the 228th position in CCR5 (Δ228 K), which does not significantly alter CCR5 expression18,40, has previously been identified in Caucasian HIV seropositive individuals at a rate of 0.2%. This deletion was observed in 1.4% of our population. I253T alters the hydrophobicity of CCR5's transmembrane domain but does not significantly affect receptor and co-receptor activity49. Both this mutation, as well as F299S, had previously been identified in 0.6% of South Chinese HIV seronegative individuals; we observed this mutation at a frequency of 1.4% in our population. R319H can alter cell surface expression of CCR518. This mutation had been found in 1% of Caucasian HIV seronegative individuals. In our population, the prevalence was around 5.7%.

In our study, we observed 13 mutations at the same positions that were, however, substituted with different amino acids, and are therefore considered novel mutations in HIV seronegative individuals. This encompasses I12V, C20R, L55P, R60K, R60G, C101Y, F118L, F118S, W153L, S215P, R225P, E330K and S336G, out of which, C20R, L55P, C101Y, W153L and E330K were found slightly more frequent (Table 2). In Caucasians, I12L and C20S have been shown to alter cell surface expression, ligand binding, and co-receptor properties18. C20S hinders disulfide bond formation between the N-terminal and the ECL-3 (Extracellular Lumen 3), resulting in the inability to respond to chemokines by in-vitro40, as was shown with MIP-1β18. Both mutations occur at the N-terminal of CCR5 in 0.3% of Caucasians. We show that the Indian equivalent, I12V and C20R, occur in 1.4% and 2.8% of our population, respectively.

Table 2 Earlier reported mutations but substituted with different amino acids at the same positions therefore considered as novel mutations in HIV-1 seronegative individuals.

Full size table

L55Q can alter receptor activity but does not change chemokine binding affinity18. In Caucasians and African-Americans, the mutation has been identified in 4.1% of HIV seronegative and 0.7% of seropositive individuals. The equivalent mutation in our population, L55P, had a prevalence of 5.7%. The R60S mutation, which can alter cell surface expression, has been observed in 1.5% of African Americans40. The equivalent R60K and R60G mutations were found in 1.4% of our population. The N-terminal domain and three extracellular lumens of CCR5 are critical for CCR5 expression and activity. Two disulfide bonds bridge the CCR5 extracellular domains between C20-C269 and C101-C178, which ensures efficient expression of CCR5 on the cell surface50. The interaction with gp120 depends on ECL-2, which acts as the principal determinant of ligand selectivity11, and on the disulfide bonds bridging the extracellular lumens, as they are required for chemokine binding50. The motifs of charged and aromatic residues in the N-terminal are also crucial for the interaction between chemokines and gp12051. Disruption of the disulfide bond linking the N-terminal to ECL-3 strongly reduces cell surface expression of the receptor18. The C101X mutation in the ECL-1 of CCR5 leads to premature termination and disrupts this critical bond structure, leading to low receptor expression and impaired responsiveness to chemokines18. The mutation had previously been observed in 1.4% of HIV-negative African-Americans. In our population, the equivalent mutation C101Y appeared in 2.8% of individuals.

A previously identified mutation, a deletion of phenylalanine (F) at the 118th amino acid position in the third transmembrane domain of CCR5, results in attenuated AIDS progression in the Nepalese population52. We observed the mutations F118L and F118S at the same locations in our population, with a frequency of 1.4%. W153C, a mutation which can alter expression of CCR5 on the cell surface53,54, had been reported in HIV seronegative individuals. We observed the location-equivalent W153L mutation in 4.3% of our population. S215L, a mutation of the fifth transmembrane of CCR5 which results in the alteration of CCR5 protein expression on the cell surface, and consequently low binding affinity towards MIP-1 β40, has been found in 1% of African American HIV seronegative individuals27. In our population, the equivalent S215P mutation was identified in 1.4%.

The R225Q mutation results in premature termination of translation and leads to the receptors inability to be expressed on the cell surface, bind chemokines, and respond to HIV infection55. This mutation has been found in 0.7% of African seronegative individuals56. The presence of R225P was observed at 1.4% in our present report. E330E has been identified in the C-terminal of CCR5 in HIV infected long-term non-progressive patients of African descent18, suggesting an inhibitory effect. In our population, E330K was observed at 4.3%. S336I has been found in the C-terminal of CCR5 in 0.4% of HIV seropositive individuals from Southern China53,54. The equivalent S336G mutation was observed at 1.4% in our population.

Sixteen novel mutations were identified in HIV seronegative individuals namely S17P, V25A, S38L, L50P, V51A, L77P, L81P, F85L, F112L, F158L, F158V, H181S, I198V, I212V, F311S and G344R. Amongst these, S38L, L50P, F85L, F158L, H181S and F311S appeared slightly more frequent than other novel mutations (Table 3). Various frame-shifts, either due to insertion or deletion of a nucleotide, were identified. Insertion of Guanidine (G) at the 467th nucleotide position results in a frame-shift at the 156th amino acid position of CCR5, which leads to a truncated form CCR5 with 226 amino acids instead of 352 (wild type CCR5). This frame-shift was observed in 5.7% of our population. Deletion of Thymine (T) at the 498th nucleotide position results in a frame-shift at the 166th amino acid position of CCR5, which leads to a truncated protein of 227 amino acids, which we found in 2.8% of our population. Deletion of Adenine (A) at the 658th nucleotide position results in a frame-shift at the 220th position of amino acid, which results in a truncated protein of 233 amino acids. This was observed in 5.7% of NCRs of India (Table 4).

Table 3 Novel mutations in HIV-1 seronegative individuals.

Full size table

Table 4 Novel frame-shifts in HIV-1 seronegative individuals.

Full size table

CCR5 mutations in HIV seropositive individuals

The single mutation F107L, previously reported in African populations9, results in normal CCR5 expression, chemokine binding and co-receptor properties by in-vitro55. In our population, this mutation was identified at a higher percentage of 8.3% (Table 5). The five mutations A29T, A73P, W86G, C101R and W153R had previously been reported in different populations (Table 6). In our population, we observed mutations at the same positions that were substituted with different amino acids and are therefore considered novel mutations. A29S results in normal expression of CCR5 on the cell surface, thus enabling HIV to cause infection40. This mutation had been found in 1.5% of African-Americans. We identified the position-equivalent A29T mutation in 2.7% of our population. The A73V mutation triggers HIV infection and has been shown to increase ligand binding affinity by 4-8-fold in-vitro18. We observed the position-equivalent A73P mutation in 5.5% of our population. W86C has been found in 1.4% of African-American HIV infected individuals9, while W86G was found at the elevated rate of 8.3% in our population.

Table 5 Earlier reported mutations and we also observed in HIV-1 seropositive individuals.

Full size table

Table 6 Earlier reported mutations but substituted with different amino acids at the same positions therefore considered as novel mutations in HIV-1 seropositive individuals.

Full size table

C101X, a mutation of the ECL-1, results in premature termination, and consequently lowered cell surface expression, as well as altered chemokine binding affinity. C101X has been identified in 1.4% of African-American HIV negative individual. The position-equivalent C101R mutation was found in the same percentage of 1.4 in our population. W153C has been observed in HIV infected patients of the southern regions of China57 while the position-equivalent W153R was observed in our population at 5.5%. Nine novel mutations namely R31G, F41L, A87V, H88R, A90P, G97E, T177I, R235W and T282A were observed in HIV infected individuals of our population. F41L, H88R, and G97E were observed in 4.5%, and A90P was present at an elevated rate of 6.9% (Table 7).

Table 7 Novel mutations in HIV-1 seropositive individuals.

Full size table

Discussion

Over the years, clinical trials have been conducted in different locations with the aim of strengthening cellular immune response to protect against HIV; however there has been no definitive cure58. This speaks for the complex nature of HIV, which is characterized by genetic diversity, high mutation rates, and issues of antiretroviral drug toxicity and viral resistance, presenting further obstacles. Following the breakthrough discovery of CCR5Δ32 as a protective mutant against HIV, research has shifted its focus towards targeting of the CCR5 co-receptor59,60. In this report, we have identified several novel mutations in seronegative and seropositive individuals from the NCRs of India and compared their presence to other populations.

In seronegative individuals, we identified several mutations that had also been reported in different populations. K26R, F166L, Δ228K, I253T and F299S were identified in 1 out of 70 individuals. CCR5Δ32 and R223Q were identified in 2 out of 70 individuals. L55Q was observed in 3 out of 70 individuals. Q194H and R319H was found in 4 out of 70 individuals. It is important note that these mutations (K26R, C178R, Q194H and R223Q) were also observed in the Chinese population52,61. In a 1998 study, CCR5Δ32 was a rare mutation in India expressed in about 1% of the population12, whereas in the present study, we observed this deletion at a percentage of 2.8. The increase in the frequency of delta 32 mutation in CCR5 among NCRs of India may be attributed to multiple factors. One relevant factor is India's rapid population growth, with this mutation increasing by natural selection, as prevalence of this mutation aids survival against HIV.

In addition to CCR5Δ32, nine other mutations namely K26R, L55Q, F166L, Q194H, R223Q, Δ228K, I253T, F299S, and R319H (Table 1) had previously been identified in African-American, Hispanic, Chinese, Israeli and Japanese populations27,57,62,63. We also observed those mutations in our population, however at different rates11,64. The differences in allelic percentage of these mutations between populations may reflect the reason for the varying risk for HIV infection.

We further identified a class of mutations at the same amino acid positions as mutations that had been identified in other populations. However, as they were substituted with different amino acids, they could be classed as novel mutations. The thirteen mutations include I12V, R60K, R60G, F118L, F118S, S215P, R225P and S336G, which only occurred in 1 out of 70 individuals; C20R and C101Y were observed in 2 out of 70 individuals, and W153L as well as E330K were found in 3 out of 70 individuals. L55P was identified in 4 out of 70 individuals. Most of these mutations were common among Caucasians, Africans and Chinese18; our study constitutes the first report of these mutations in NCRs of India.

Apart from these mutations, 16 novel mutations were observed for the first time in our chosen population such as S17P, V25A, S38L, L50P, V51A, L77P, L81P, F85L, F112L, F158L, F158V, H181S, I198V, I212V, F311S and G344R. Amongst these, L50P, F85L and F311S were found in 3 out of 70 individuals. S38L and H181S mutations were identified in 4 out of 70 individuals.

Novel frame-shifts due to singe nucleotide insertions or deletions were identified at amino acid positions 156, 166, and 220. These mutations resulted in frame-shifts at 467, 498, 658 nucleotide positions respectively, resulting in premature termination of translation. As a result, the gene product of CCR5 lacked approximately 118 to 126 amino acid residues in the C-terminal cytoplasmic tail, i.e. loss of three transmembrane domains, thus reducing its length from 352 amino acids, as found in wild-type CCR5, to a truncated form of 226–233 amino acids (Table 4). Frame-shifts at amino acid positions 156 and 220 were found at a higher percentage, in 4 out of 70 individuals. The C-terminal transmembrane domains are essential for gp120 interaction, and any changes in these regions could affect initial HIV entry31. Our results are the first report identifying these frame-shifts amongst our population; however, the functional consequences of these mutations are yet to be studied.

In seropositive individuals, F107L had been reported in Africans. In our population, we observed this mutation in 6 out of 72 individuals. Novel mutations located at earlier reported amino acid positions but substituted with different amino acids, were reported in our population. The five mutations include A29T, A73P, W86G, C101R, and W153R, out of which W86G was observed six times and W153R four times in our group of 72 participants. Nine novel mutations were identified in HIV seropositive individuals. The five mutations R31G, A87V, T177I, R235W and T282A were identified in 2 out of 72 individuals; the three mutations F41L, R88H and G97E were identified in 4 out of 72 individuals; and A90P was identified in 5 individuals out of 72.

We observed certain mutations more frequently than others, namely F41L, A73P, W86G, R88H, A90P, G97E, F107L and W153R in HIV seropositive individuals. We noticed that the number of mutations in CCR5 was fewer in individuals undergoing ART, when compared to individuals on non-ART. Interestingly, we didn't find any truncated forms of CCR5 in HIV seropositive individuals, which suggests that presence of the full frame of CCR5 is essential for successful HIV infection.

In our cohort study, genotypic frequencies of the majority of mutants did not significantly differ between HIV seropositive and seronegative individuals (see Supplemental Table S2). However, certain mutations, namely S38L, L55P, H181S, Q194H and R319H including the frame shifts at 156 and 220 were enriched in HIV seronegative individuals. At the same time, mutations such as F41L, A73P, W86G, R88H, A90P, G97E, F107L and W153R were enriched in HIV seropositive individuals (Table 8). These findings are congruent with other reports describing some of these mutations, in which the association between CCR5 genotypes and HIV progression rate was reported10,18; however, most of the identified novel mutations are yet to be characterized in relation to their functional consequences.

Table 8 Comparison of mutations between HIV-1 seronegative and seropositive individuals.

Full size table

Available methods of therapeutic interventions have failed to fully cure HIV infection due to partial restoration of the immune system and continuous progression to AIDS, which warrants the necessity to develop novel strategies. This study presents a report of genetic variations occurring in the ORF of CCR5 in HIV seronegative and seropositive individuals. As a next step, the functional implications (effects on CCR5 expression on the cell surface and the role of identified mutations in HIV progression) of these natural mutations will be studied in detail. Modification of CCR5 cell surface expression through natural mutations using novel techniques such as siRNA silencing, zinc-finger nuclease silencing, CRISPR-cas9 system, and gene therapy65,66,67,68,69,70 may presents a novel approach to the development of chemokine-based therapeutics against HIV.

Materials and Methods

Ethics statement

This study was approved by Research Project Advisory Committee, Institutional Biosafety Committee and Institutional Ethical Committee from Human Research of University College of Medical Sciences and GTB hospital, Delhi, India and from PGIMER, Chandigarh, India. Ethics committees of each of these institutes independently approved the written informed consents which were obtained from HIV seropositive individuals and from the guardians of HIV seropositive children participants involved in this study. All the experiments were performed in accordance with relevant guidelines and regulations.

Patient selection and ethics statement

HIV seronegative (n = 70) and HIV seropositive (n = 72) samples chosen for the study were collected from NCRs of India (Haryana, Punjab, Chandigarh, Delhi, Uttar Pradesh) from patients who were registered and monitored at the ART clinic of GTB hospital, Delhi and PGIMER, Chandigarh within the period from 2005 to 2013. The participants were made up of 45% males, 13% HIV mother to child pairs, and 42% other females (see Supplemental Table S1).

Genomic DNA isolation and PCR for CCR5 genes

Genomic DNA was extracted from PBMCs of HIV seropositive individuals by QIAamp DNA Blood Mini Kit (Qiagen) and sequence spanning the open reading frame (ORF) of CCR5 was PCR amplified using the following primers.

FP: 5′-GGG TGG AAC AAG ATG GAT TAT CAA GTG-3′

RP: 5′-ACC CCC AGC CCA GGC TGT GTA T-3′

PCR amplification of CCR5 genes was carried out in 15 μl reaction volumes in separate PCR tubes. The reaction mixture contained 400 ng genomic DNA (3 µl), 10X PCR Buffer (1.5 µl) 10 mM dNTP mix (0.37 µl), 25 pmol of each primer, 1.5 U Taq DNA polymerase (Takara) and DNase RNase Nuclease free water (7.93 µl). The reaction mixture was subjected to 94 °C for 5 mins as initial denaturation, followed by 40 cycles at 94 °C for 1 min, 70 °C for 30 sec and 72 °C for 1 min, and a final extension step was carried out at 72 °C for 7 mins. The PCR product was then resolved on 1.5% agarose gel after electrophoresis. The amplicons were eluted out from the gel by using Qiagen Gel extraction kit (Qiagen).

CCR5 genotyping by cloning and sequencing

The gel purified PCR products (see Supplemental Fig. S1) were cloned in pGEM-T Easy vector system (Promega). The ligation reaction was incubated at 4 °C for 10 hrs, and the ligation mix was plated on LB ampicillin plates with E.coli DH5α strain as host. The plates were then incubated overnight at 37 °C. The positive clones were selected by picking a single colony, grown in 5 ml LB Broth with ampicillin antibiotic (100 µg/ml), and incubated overnight at 37 °C. Plasmid DNA was isolated from the culture by QIAprep Spin Mini Kit (Qiagen). The positive clones were screened by restriction digestion of plasmid DNA with EcoRI in a 10 μl reaction volume at 37 °C for 2 hrs. The digested products were analyzed on a 1.5% agarose gel after electrophoresis and the amplified bands were screened for positive clones by restriction digestion of the products with EcoR1 (see Supplemental Fig. S2). Three clones from each individual were subjected to sequencing from LabIndia and SciGenom laboratories by dideoxy chain termination method. CCR5 open reading frame (ORF) was then translated to amino acids by Gene Runner and the amino acid sequences were aligned with reference sequence (NM_000579) by ClustalW to identify novel mutants.

Statistical analysis

In this study, Chi-square test was used to assess the statistical significance of the mutations between the two groups using GraphPad Prism8 and the values p < 0.05 was considered to be statistically significant. Multiple comparison was tested using the Benjamini-Hochberg test for the mutations between the two groups and the values q < 0.2 was considered to be statistically significant.

Accession numbers

CCR5 sequences (n = 110) from NCRs of India [GenBank KM355846 - KM355955].

References

Ronsard, L. et al. Genetic and functional characterization of HIV-1 Vif on APOBEC3G degradation: First report of emergence of B/C recombinants from North India. Sci Rep 5, 15438 (2015).

ADS CAS Article Google Scholar

Ronsard, L. et al. Molecular and genetic characterization of natural HIV-1 Tat Exon-1 variants from North India and their functional implications. PLoS One 9, e85452 (2014).

ADS Article Google Scholar

Verma, S., Ronsard, L., Kapoor, R. & Banerjea, A. C. Genetic characterization of natural variants of Vpu from HIV-1 infected individuals from Northern India and their impact on virus release and cell death. PLoS One 8, e59283 (2013).

ADS CAS Article Google Scholar

Ronsard, L., Rai, T., Rai, D., Ramachandran, V. G. & Banerjea, A. C. In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity. Front Microbiol 8, 1467 (2017).

Article Google Scholar

Ronsard, L. et al. Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction. Front Microbiol 8, 706 (2017).

Article Google Scholar

Connor, R. I. & Ho, D. D. Human immunodeficiency virus type 1 variants with increased replicative capacity develop during the asymptomatic stage before disease progression. Journal of virology 68, 4400–4408 (1994).

CAS PubMed PubMed Central Google Scholar

Michael, N. L. et al. The role of viral phenotype and CCR-5 gene defects in HIV-1 transmission and disease progression. Nature medicine 3, 338–340 (1997).

CAS Article Google Scholar

Berger, E. A., Murphy, P. M. & Farber, J. M. Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol 17, 657–700 (1999).

CAS Article Google Scholar

Picton, A. C., Paximadis, M. & Tiemessen, C. T. Genetic variation within the gene encoding the HIV-1 CCR5 coreceptor in two South African populations. Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 10, 487–494 (2010).

CAS Article Google Scholar

10.

Carrington, M., Dean, M., Martin, M. P. & O'Brien, S. J. Genetics of HIV-1 infection: chemokine receptor CCR5 polymorphism and its consequences. Human molecular genetics 8, 1939–1945 (1999).

CAS Article Google Scholar

11.

Samson, M. et al. Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382, 722–725 (1996).

ADS CAS Article Google Scholar

12.

Husain, S., Goila, R., Shahi, S. & Banerjea, A. First report of a healthy Indian heterozygous for delta 32 mutant of HIV-1 co-receptor-CCR5 gene. Gene 207, 141–147 (1998).

CAS Article Google Scholar

13.

Gabuzda, D. & Wang, J. Chemokine receptors and virus entry in the central nervous system. Journal of neurovirology 5, 643–658 (1999).

CAS Article Google Scholar

14.

Zaitseva, M. et al. Expression and function of CCR5 and CXCR4 on human Langerhans cells and macrophages: implications for HIV primary infection. Nature medicine 3, 1369–1375 (1997).

CAS Article Google Scholar

15.

Cocchi, F. et al. Higher macrophage inflammatory protein (MIP)-1alpha and MIP-1beta levels from CD8+ T cells are associated with asymptomatic HIV-1 infection. Proceedings of the National Academy of Sciences of the United States of America 97, 13812–13817 (2000).

ADS CAS Article Google Scholar

16.

Alkhatib, G. et al. CC CKR5: a RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science 272, 1955–1958 (1996).

ADS CAS Article Google Scholar

17.

Combadiere, C., Ahuja, S. K., Tiffany, H. L. & Murphy, P. M. Cloning and functional expression of CC CKR5, a human monocyte CC chemokine receptor selective for MIP-1(alpha), MIP-1(beta), and RANTES. Journal of leukocyte biology 60, 147–152 (1996).

CAS Article Google Scholar

18.

Carrington, M. et al. Novel alleles of the chemokine-receptor gene CCR5. American journal of human genetics 61, 1261–1267 (1997).

CAS Article Google Scholar

19.

Premack, B. A. & Schall, T. J. Chemokine receptors: gateways to inflammation and infection. Nature medicine 2, 1174–1178 (1996).

CAS Article Google Scholar

20.

Dubay, J. W., Dubay, S. R., Shin, H. J. & Hunter, E. Analysis of the cleavage site of the human immunodeficiency virus type 1 glycoprotein: requirement of precursor cleavage for glycoprotein incorporation. J Virol 69, 4675–4682 (1995).

CAS PubMed PubMed Central Google Scholar

21.

Clapham, P. R. & McKnight, A. Cell surface receptors, virus entry and tropism of primate lentiviruses. The Journal of general virology 83, 1809–1829 (2002).

CAS Article Google Scholar

22.

Dragic, T. et al. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature 381, 667–673 (1996).

ADS CAS Article Google Scholar

23.

Clapham, P. R. & McKnight, A. HIV-1 receptors and cell tropism. British medical bulletin 58, 43–59 (2001).

CAS Article Google Scholar

24.

Deng, H. et al. Identification of a major co-receptor for primary isolates of HIV-1. Nature 381, 661–666 (1996).

ADS CAS Article Google Scholar

25.

Rucker, J. et al. Regions in beta-chemokine receptors CCR5 and CCR2b that determine HIV-1 cofactor specificity. Cell 87, 437–446 (1996).

CAS Article Google Scholar

26.

An, P. et al. Influence of CCR5 promoter haplotypes on AIDS progression in African-Americans. Aids 14, 2117–2122 (2000).

CAS Article Google Scholar

27.

Ansari-Lari, M. A., Liu, X. M., Metzker, M. L., Rut, A. R. & Gibbs, R. A. The extent of genetic variation in the CCR5 gene. Nature genetics 16, 221–222 (1997).

CAS Article Google Scholar

28.

Ometto, L. et al. Analysis of the CC chemokine receptor 5 m303 mutation in infants born to HIV-1-seropositive mothers. Aids 13, 871–872 (1999).

CAS Article Google Scholar

29.

Quillent, C. et al. HIV-1-resistance phenotype conferred by combination of two separate inherited mutations of CCR5 gene. Lancet 351, 14–18 (1998).

CAS Article Google Scholar

30.

Agrawal, L. et al. Role for CCR5Delta32 protein in resistance to R5, R5X4, and X4 human immunodeficiency virus type 1 in primary CD4+ cells. Journal of virology 78, 2277–2287 (2004).

CAS Article Google Scholar

31.

Dean, M. et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273, 1856–1862 (1996).

ADS CAS Article Google Scholar

32.

Michael, N. L. et al. The role of CCR5 and CCR2 polymorphisms in HIV-1 transmission and disease progression. Nature medicine 3, 1160–1162 (1997).

CAS Article Google Scholar

33.

Biti, R. et al. HIV-1 infection in an individual homozygous for the CCR5 deletion allele. Nature medicine 3, 252–253 (1997).

CAS Article Google Scholar

34.

Murphy, P. M. Chemokine receptors: structure, function and role in microbial pathogenesis. Cytokine & growth factor reviews 7, 47–64 (1996).

CAS Article Google Scholar

35.

Liu, Y. Z., Lania, L. & Latchman, D. S. Functional interaction between the HIV-1 Tat transactivator and the inhibitory domain of the Oct-2 cellular transcription factor. Aids 10, 1323–1329 (1996).

CAS Article Google Scholar

36.

Allers, K. et al. Evidence for the cure of HIV infection by CCR5Delta32/Delta32 stem cell transplantation. Blood 117, 2791–2799 (2011).

CAS Article Google Scholar

37.

Hutter, G. et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. The New England journal of medicine 360, 692–698 (2009).

Article Google Scholar

38.

Boldt, A. B. et al. Analysis of the CCR5 gene coding region diversity in five South American populations reveals two new non-synonymous alleles in Amerindians and high CCR5*D32 frequency in Euro-Brazilians. Genetics and molecular biology 32, 12–19 (2009).

CAS Article Google Scholar

39.

Martinson, J. J., Chapman, N. H., Rees, D. C., Liu, Y. T. & Clegg, J. B. Global distribution of the CCR5 gene 32-basepair deletion. Nature genetics 16, 100–103 (1997).

CAS Article Google Scholar

40.

Blanpain, C. et al. Multiple nonfunctional alleles of CCR5 are frequent in various human populations. Blood 96, 1638–1645 (2000).

CAS PubMed Google Scholar

41.

Yang, C. et al. Polymorphisms in the CCR5 coding and noncoding regions among HIV type 1-exposed, persistently seronegative female sex-workers from Thailand. AIDS research and human retroviruses 19, 661–665 (2003).

CAS Article Google Scholar

42.

Libert, F. et al. The deltaccr5 mutation conferring protection against HIV-1 in Caucasian populations has a single and recent origin in Northeastern Europe. Human molecular genetics 7, 399–406 (1998).

CAS Article Google Scholar

43.

Rusert, P. et al. Virus isolates during acute and chronic human immunodeficiency virus type 1 infection show distinct patterns of sensitivity to entry inhibitors. Journal of virology 79, 8454–8469 (2005).

CAS Article Google Scholar

44.

Ma, L. et al. Biochemical and HIV-1 coreceptor properties of K26R, a new CCR5 Variant in China's Sichuan population. Journal of acquired immune deficiency syndromes 39, 38–43 (2005).

CAS Article Google Scholar

45.

Cohen, O. J. et al. CXCR4 and CCR5 genetic polymorphisms in long-term nonprogressive human immunodeficiency virus infection: lack of association with mutations other than CCR5-Delta32. Journal of virology 72, 6215–6217 (1998).

CAS PubMed PubMed Central Google Scholar

46.

Cohen, O. J., Kinter, A. & Fauci, A. S. Host factors in the pathogenesis of HIV disease. Immunological reviews 159, 31–48 (1997).

CAS Article Google Scholar

47.

Suresh, P., Wanchu, A., Sachdeva, R. K. & Bhatnagar, A. Gene polymorphisms in CCR5, CCR2, CX3CR1, SDF-1 and RANTES in exposed but uninfected partners of HIV-1 infected individuals in North India. Journal of clinical immunology 26, 476–484 (2006).

CAS Article Google Scholar

48.

Zheng, Y. H. et al. Human APOBEC3F is another host factor that blocks human immunodeficiency virus type 1 replication. J Virol 78, 6073–6076 (2004).

CAS Article Google Scholar

49.

Capoulade-Metay, C. et al. New CCR5 variants associated with reduced HIV coreceptor function in southeast Asia. Aids 18, 2243–2252 (2004).

CAS Article Google Scholar

50.

Blanpain, C. et al. CCR5 binds multiple CC-chemokines: MCP-3 acts as a natural antagonist. Blood 94, 1899–1905 (1999).

CAS PubMed Google Scholar

51.

Kwong, J. A. et al. A tyrosine-sulfated CCR5-mimetic peptide promotes conformational transitions in the HIV-1 envelope glycoprotein. Journal of virology 85, 7563–7571 (2011).

CAS Article Google Scholar

52.

Zhao, X. Y. et al. A novel CCR5 mutation selectively affects immunoreactivity and fusogenic property of the HIV co-receptor. Aids 18, 1729–1732 (2004).

CAS Article Google Scholar

53.

Zheng, L., Yang, Y. D., Lu, G. C. & Salvato, M. S. Extracellular HIV Tat and Tat cysteine rich peptide increase CCR5 expression in monocytes. J Zhejiang Univ Sci B 6, 668–672 (2005).

Article Google Scholar

54.

Zhao, X. Y. et al. Functional analysis of naturally occurring mutations in the open reading frame of CCR5 in HIV-infected Chinese patients and healthy controls. Journal of acquired immune deficiency syndromes 38, 509–517 (2005).

CAS Article Google Scholar

55.

Folefoc, A. T., Fromme, B. J., Katz, A. A. & Flanagan, C. A. South African mutations of the CCR5 coreceptor for HIV modify interaction with chemokines and HIV Envelope protein. Journal of acquired immune deficiency syndromes 54, 352–359 (2010).

CAS Article Google Scholar

56.

Petersen, D. C. et al. Novel mutations identified using a comprehensive CCR5-denaturing gradient gel electrophoresis assay. Aids 15, 171–177 (2001).

CAS Article Google Scholar

57.

Zheng, B. J. et al. Polymorphisms of CCR5 gene in a southern Chinese population and their effects on disease progression in HIV infections. Aids 16, 2480–2482 (2002).

Article Google Scholar

58.

Sekaly, R. P. The failed HIV Merck vaccine study: a step back or a launching point for future vaccine development? The Journal of experimental medicine 205, 7–12 (2008).

CAS Article Google Scholar

59.

Alkhatib, G. The biology of CCR5 and CXCR4. Curr Opin. HIV AIDS 4, 96–103 (2009).

PubMed Google Scholar

60.

Choi, W. T. & An, J. Biology and clinical relevance of chemokines and chemokine receptors CXCR4 and CCR5 in human diseases. Exp Biol Med (Maywood) 236, 637–647 (2011).

CAS Article Google Scholar

61.

Ma, L. Y. et al. Single nucleotide polymorphisms of HIV coreceptor CCR5 gene in Chinese Yi ethnic group and its association with HIV infection. Zhonghua yi xue za zhi 85, 3181–3185 (2005).

CAS PubMed Google Scholar

62.

Kageyama, S. et al. Polymorphism of CCR5 affecting HIV disease progression in the Japanese population. AIDS research and human retroviruses 17, 991–995 (2001).

CAS Article Google Scholar

63.

Kantor, R. & Gershoni, J. M. Distribution of the CCR5 gene 32-base pair deletion in Israeli ethnic groups. Journal of acquired immune deficiency syndromes and human retrovirology: official publication of the International Retrovirology Association 20, 81–84 (1999).

CAS Article Google Scholar

64.

Liu, R. et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86, 367–377 (1996).

CAS Article Google Scholar

65.

Anderson, J. S., Walker, J., Nolta, J. A. & Bauer, G. Specific transduction of HIV-susceptible cells for CCR5 knockdown and resistance to HIV infection: a novel method for targeted gene therapy and intracellular immunization. Journal of acquired immune deficiency syndromes 52, 152–161 (2009).

CAS Article Google Scholar

66.

Holt, N. et al. Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo. Nature biotechnology 28, 839–847 (2010).

CAS Article Google Scholar

67.

DiGiusto, D. L. et al. RNA-based gene therapy for HIV with lentiviral vector-modified CD34(+) cells in patients undergoing transplantation for AIDS-related lymphoma. Science translational medicine 2, 36ra43 (2010).

Article Google Scholar

68.

Anderson, J. & Akkina, R. Complete knockdown of CCR5 by lentiviral vector-expressed siRNAs and protection of transgenic macrophages against HIV-1 infection. Gene therapy 14, 1287–1297 (2007).

CAS Article Google Scholar

69.

Tebas, P. et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. The New England journal of medicine 370, 901–910 (2014).

CAS Article Google Scholar

70.

Lopalco, L. CCR5: From Natural Resistance to a New Anti-HIV Strategy. Viruses 2, 574–600 (2010).

CAS Article Google Scholar

Download references

Acknowledgements

We thank Dr. Ajay Wanchu, PGIMER, Chandigarh, India for providing HIV infected blood samples. We appreciate Dr. Matthew Gorman and Dr. Evan Rossignol from The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA, and Miss. Nada Jovanovic from MGH IHP for proof-reading the manuscript. This study was supported by Department of Biotechnology (BT/PR10599/Med/29/76/2008) and Indian Council of Medical Research (HIV/50/142/9/2011-ECD-II), Government of India, to Dr. Akhil C Banerjea, National Institute of Immunology, New Delhi, India and Dr. V. G Ramachandran, UCMS and GTB Hospital, Delhi, India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author information

Affiliations

Laboratory of Virology, National Institute of Immunology, New Delhi, India

Larance Ronsard, Vikas Sood, Vijay Shankar & Akhil C. Banerjea

Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India

Larance Ronsard, Vikas Sood & Vishnampettai G. Ramachandran

Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA, USA

Larance Ronsard, Ashraf S. Yousif & Jishnu Das

Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA

Janani Ramesh

Endocrinology & Toxicology Lab, Department of Zoology, University of Calicut, Kerala, India

N. Sumi

Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, Delhi, India

Tripti Rai

Veterinary Physiology and Pharmacology, Texas A&M University, Texas, USA

Kumaravel Mohankumar

Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India

Subhashree Sridharan

The University of St Andrews, St Andrews, KY16 9AJ, UK

Arianna Dorschel

Contributions

L.R., V.S., V.G.R. and A.C.B. conceived and designed the experiments. L.R., V.S., V.S.R. performed the experiments. L.R., A.S.Y., J.R., J.D., S.N., T.R., K.M., S.S., V.G.R. and A.C.B. analyzed and interpreted the data. L.R., V.S., A.S.Y., J.R., V.S.R., J.D., S.N., T.R., K.M., S.S., A.D., V.G.R. and A.C.B. contributed reagents/materials/analysis tools. L.R., A.S.Y., J.R., V.G.R. and A.C.B. wrote the manuscript. L.R., A.S.Y., J.R., S.N., T.R., K.M., S.S. and A.D. assisted in making tables and edited the manuscript. J.D., S.N. and J.R. verified all the statistics in the manuscript. A.D. performed grammar and textual edits for the revision of the manuscript.

Corresponding authors

Correspondence to Larance Ronsard or Akhil C. Banerjea.

Ethics declarations

Competing Interests

The authors declare no competing interests.

Additional information

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplemental tables and figures

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Reprints and Permissions

About this article

Cite this article

Ronsard, L., Sood, V., Yousif, A.S. et al. Genetic Polymorphisms in the Open Reading Frame of the CCR5 gene From HIV-1 Seronegative and Seropositive Individuals From National Capital Regions of India. Sci Rep 9, 7594 (2019). https://doi.org/10.1038/s41598-019-44136-z

Download citation

Received09 March 2017

Accepted10 May 2019

Published20 May 2019

DOIhttps://doi.org/10.1038/s41598-019-44136-z

Share this article

Anyone you share the following link with will be able to read this content:

Get shareable link

Provided by the Springer Nature SharedIt content-sharing initiative

Subjects

Retrovirus

Viral epidemiology

Virus–host interactions

CI

Table of contents

Volume 1

Chapter 1 - CI