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Appah A, Beelen CJ, Kirkby D, Dong W, Shahid A, Foley B, Mensah M, Ganu V, Puplampu P, Amoah LE, Nii-Trebi NI, Brumme CJ, Brumme ZL. Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage. Viruses 2022; 15:128. [PMID: 36680168 PMCID: PMC9865111 DOI: 10.3390/v15010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.
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Affiliation(s)
- Anna Appah
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Brian Foley
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA
| | - Miriam Mensah
- Fevers Unit, Department of Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Vincent Ganu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Peter Puplampu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Linda E. Amoah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box LG 25, Ghana
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
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Singh J, Ronsard L, Pandey M, Kapoor R, Ramachandran VG, Banerjea AC. Molecular and Genetic Characterization of Natural Variants of HIV-1 Nef Gene from North India and its Functional Implication in Down-Regulation of MHC-I and CD-4. Curr HIV Res 2021; 19:172-187. [PMID: 32981506 DOI: 10.2174/1570162x18666200925160755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND HIV-1 Nef is an important accessory protein with multiple effector functions. Genetic studies of the HIV-1 Nef gene show extensive genetic diversity and the functional studies have been carried out mostly with Nef derived from regions dominated by subtype B (North America & Europe). OBJECTIVE This study was carried out to characterize genetic variations of the Nef gene from HIV-1 infected individuals from North India and to find out their functional implications. METHODS The unique representative variants were sub-cloned in a eukaryotic expression vector and further characterized with respect to their ability to downregulate cell surface expression of CD4 and MHC-1 molecules. RESULTS The phylogenetic analysis of Nef variants revealed sequence similarity with either consensus subtype B or B/C recombinants. Boot scan analysis of some of our variants showed homology to B/C recombinant and some to wild type Nef B. Extensive variations were observed in most of the variants. The dN/dS ratio revealed 80% purifying selection and 20% diversifying selection implying the importance of mutations in Nef variants. Intracellular stability of Nef variants differed greatly when compared with wild type Nef B and C. There were some variants that possessed mutations in the functional domains of Nef and responsible for its differential CD4 and MHC-1 downregulation activity. CONCLUSION We observed enhanced biological activities in some of the variants, perhaps arising from amino acid substitutions in their functional domains. The CD4 and MHC-1 down-regulation activity of Nef is likely to confer immense survival advantage allowing the most rare genotype in a population to become the most abundant after a single selection event.
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Affiliation(s)
- J Singh
- National Institute of Immunology, New Delhi, India
| | - L Ronsard
- National Institute of Immunology, New Delhi, India
| | - M Pandey
- King George`s Medical University, India
| | - R Kapoor
- National Institute of Immunology, New Delhi, India
| | - V G Ramachandran
- Department of Virology, National Institute of Immunology, New Delhi-110067, India
| | - A C Banerjea
- Department of Virology, National Institute of Immunology, New Delhi-110067, India
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3
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Kalu AW, Telele NF, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Prediction of coreceptor usage by five bioinformatics tools in a large Ethiopian HIV-1 subtype C cohort. PLoS One 2017; 12:e0182384. [PMID: 28841646 PMCID: PMC5571954 DOI: 10.1371/journal.pone.0182384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022] Open
Abstract
Background Genotypic tropism testing (GTT) has been developed largely on HIV-1 subtype B. Although a few reports have analysed the utility of GTT in other subtypes, more studies using HIV-1 subtype C (HIV-1C) are needed, considering the huge contribution of HIV-1C to the global epidemic. Methods Plasma was obtained from 420 treatment-naïve HIV-1C infected Ethiopians recruited 2009–2011. The V3 region was sequenced and the coreceptor usage was predicted by five tools: Geno2Pheno clinical–and clonal–models, PhenoSeq-C, C-PSSM and Raymond’s algorithm. The impact of baseline tropism on antiretroviral treatment (ART) outcome was evaluated. Results Of 352 patients with successful baseline V3 sequences, the proportion of predicted R5 virus varied between the methods by 12.5% (78.1%-90.6%). However, only 58.2% of the predictions were concordant and only 1.7% were predicted to be X4-tropic across the five methods. Compared pairwise, the highest concordance was between C-PSSM and Geno2Pheno clonal (86.4%). In bivariate intention to treat (ITT) analysis, R5 infected patients achieved treatment success more frequently than X4 infected at month six as predicted by Geno2Pheno clinical (77.8% vs 58.7%, P = 0.004) and at month 12 by C-PSSM (61.9% vs 46.6%, P = 0.038). However, in the multivariable analysis adjusted for age, gender, baseline CD4 and viral load, only tropism as predicted by C-PSSM showed an impact on month 12 (P = 0.04, OR 2.47, 95% CI 1.06–5.79). Conclusion Each of the bioinformatics models predicted R5 tropism with comparable frequency but there was a large discordance between the methods. Baseline tropism had an impact on outcome of first line ART at month 12 in multivariable ITT analysis but only based on prediction by C-PSSM which thus possibly could be used for predicting outcome of ART in HIV-1C infected Ethiopians.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail: ,
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebreselasie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of Internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Gaetano Marrone
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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Kalu AW, Telele NF, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses-an analysis of a prospective country-wide cohort. BMC Infect Dis 2017; 17:37. [PMID: 28061826 PMCID: PMC5219668 DOI: 10.1186/s12879-016-2163-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
Background CCR5 coreceptor using HIV-1 subtype C (HIV-1C) has been reported to dominate the Ethiopian epidemic. However, almost all data have been obtained from two large cities in the central and north-west regions and recent data is lacking. Methods Plasma were obtained from 420 treatment-naïve patients recruited 2009–2011 to a large country-wide Ethiopian cohort. The V3 region was sequenced and the co-receptor tropism was predicted by the clinical and clonal models of the geno2pheno tool at different false positive rates (fpr) and for subtype. In an intention to treat analysis the impact of baseline tropism on outcome of antiretroviral therapy was evaluated. Results V3 loop sequencing was successful in 352 (84%) patients. HIV-1C was found in 350 (99.4%) and HIV-1A in two (0.6%) patients. When comparing the geno2pheno fpr10% clonal and clinical models, 24.4% predictions were discordant. X4-virus was predicted in 17.0 and 19.0%, respectively, but the predictions were concordant in only 6%. At fpr5%, concordant X4-virus predictions were obtained in 3.1%. The proportion of X4-tropic virus (clonal fpr10%) increased from 5.6 to 17.3% (p < 0.001) when 387 Ethiopian V3 loop sequences dated from 1984 to 2003 were compared with ours. In an intention to treat analysis, 67.9% reached treatment success at month 6 and only 50% at month 12. Only age and not tropism predicted therapy outcome and no difference was found in CD4+ cell gain between R5-tropic and X4-tropic infected patients. At viral failure, R5 to X4 switch was rare while X4 to R5 switch occurred more frequently (month 6: p = 0.006; month 12: p = 0.078). Conclusion The HIV-1C epidemic is monophylogenetic in all regions of Ethiopia and R5-tropic virus dominates, even in patients with advanced immunodeficiency, although the proportion of X4-tropic virus seems to have increased over the last two decades. Geno2pheno clinical and clonal prediction models show a large discrepancy at fpr10%, but not at fpr5%. Hence further studies are needed to assess the utility of genotypic tropism testing in HIV-1C. In ITT analysis only age and not tropism influenced the outcome.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden. .,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebreselasie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Samir Abdurahman
- Public Health Agency of Sweden, Solna, Sweden.,Department of Science and Technology, Örebro University, Örebro, Sweden
| | - Gaetano Marrone
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden.,Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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5
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Pandey SS, Cherian S, Thakar M, Paranjape RS. Short Communication: Phylogenetic and Molecular Characterization of Six Full-Length HIV-1 Genomes from India Reveals a Monophyletic Lineage of Indian Sub-Subtype A1. AIDS Res Hum Retroviruses 2016; 32:489-502. [PMID: 26756665 DOI: 10.1089/aid.2015.0207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although HIV-1 epidemic in India is mainly driven by subtype C, subtype A has been reported for over two decades. This is the first comprehensive analysis of sequences of HIV-1 subtype A from India, based on the near full-length genome sequences of six different HIV-1 subtype A Indian isolates along with available partial gene sequences from India and global sequences. The phylogenetic analyses revealed the convergence of all Indian whole-genome sequences and majority of the partial gene sequences to a single node with the sequences most closely related to African sub-subtype A1. The presence of the signature motifs consistent with those observed in subtype A and CTL epitopes characterized specifically for subtype A1 were observed among the study sequences. Deletion of LY amino acid of LYPXnL motif of p6gag and one amino acid in V3 loop have been observed among the study isolates, which have also been observed in a few sequences from East Africa. Overall, the results are indicative of a monophyletic lineage or founder effect of the Indian epidemic due to sub-subtype A1 and supportive of a possible migration of subtype A1 into India from East Africa.
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Affiliation(s)
| | - Sarah Cherian
- Bioinformatics Group, National Institute of Virology (ICMR), Pune, India
| | - Madhuri Thakar
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
| | - Ramesh S. Paranjape
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
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6
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Cashin K, Gray LR, Harvey KL, Perez-Bercoff D, Lee GQ, Sterjovski J, Roche M, Demarest JF, Drummond F, Harrigan PR, Churchill MJ, Gorry PR. Reliable genotypic tropism tests for the major HIV-1 subtypes. Sci Rep 2015; 5:8543. [PMID: 25712827 PMCID: PMC4894445 DOI: 10.1038/srep08543] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/23/2015] [Indexed: 01/21/2023] Open
Abstract
Over the past decade antiretroviral drugs have dramatically improved the prognosis for HIV-1 infected individuals, yet achieving better access to vulnerable populations remains a challenge. The principal obstacle to the CCR5-antagonist, maraviroc, from being more widely used in anti-HIV-1 therapy regimens is that the pre-treatment genotypic "tropism tests" to determine virus susceptibility to maraviroc have been developed primarily for HIV-1 subtype B strains, which account for only 10% of infections worldwide. We therefore developed PhenoSeq, a suite of HIV-1 genotypic tropism assays that are highly sensitive and specific for establishing the tropism of HIV-1 subtypes A, B, C, D and circulating recombinant forms of subtypes AE and AG, which together account for 95% of HIV-1 infections worldwide. The PhenoSeq platform will inform the appropriate use of maraviroc and future CCR5 blocking drugs in regions of the world where non-B HIV-1 predominates, which are burdened the most by the HIV-1 pandemic.
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Affiliation(s)
- Kieran Cashin
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010
| | - Lachlan R Gray
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - Katherine L Harvey
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010
| | | | - Guinevere Q Lee
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada Y6Z 1Y6
| | - Jasminka Sterjovski
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - Michael Roche
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - James F Demarest
- ViiV Healthcare, Research Triangle Park, North Carolina, USA 27709-3398
| | | | | | - Melissa J Churchill
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Medicine, Monash University, Melbourne, Australia 3800 [3] Department of Microbiology, Monash University, Melbourne, Australia 3800
| | - Paul R Gorry
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010 [3] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800 [4] School of Applied Sciences, College of Science, Engineering and Health, RMIT University, Melbourne, Australia 3001
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7
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Lata S, Ronsard L, Sood V, Dar SA, Ramachandran VG, Das S, Banerjea AC. Effect on HIV-1 gene expression, Tat-Vpr interaction and cell apoptosis by natural variants of HIV-1 Tat exon 1 and Vpr from Northern India. PLoS One 2013; 8:e82128. [PMID: 24367500 PMCID: PMC3868622 DOI: 10.1371/journal.pone.0082128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/18/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Since HIV-1 Tat and Vpr genes are involved in promoter transactivation, apoptosis, etc, we carried out studies to find out nature and extent of natural variation in the two genes from seropositive patients from Northern India and determined their functional implications. METHODS HIV-1 tat exon 1 and vpr were amplified from the genomic DNA isolated from the blood of HIV-1 infected individuals using specific primers by Polymerase Chain reaction (PCR) and subjected to extensive genetic analysis (CLUSTAL W, Simplot etc). Their expression was monitored by generating myc fusion clones. Tat exon 1 and Vpr variants were co-transfected with the reporter gene construct (LTR-luc) and their transactivation potential was monitored by measuring luciferase activity. Apoptosis and cell cycle analysis was done by Propidium Iodide (PI) staining followed by FACS. RESULTS Exon 1 of tat was amplified from 21 samples and vpr was amplified from 16 samples. One of the Tat exon 1 variants showed phylogenetic relatedness to subtype B & C and turned out to be a unique recombinant. Two of the Vpr variants were B/C/D recombinants. These natural variations were found to have no impact on the stability of Tat and Vpr. These variants differed in their ability to transactivate B LTR and C LTR promoters. B/C recombinant Tat showed better co-operative interaction with Vpr. B/C/D recombination in Vpr was found to have no effect on its co-operativity with Tat. Recombinant Tat (B/C) induced more apoptosis than wild type B and C Tat. The B/C/D recombination in Vpr did not affect its G2 arrest induction potential but reduced its apoptosis induction ability. CONCLUSIONS Extensive sequence and region-specific variations were observed in Tat and Vpr genes from HIV-1 infected individuals from Northern India. These variations have functional implications & therefore important for the pathogenicity of virus.
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Affiliation(s)
- Sneh Lata
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Larance Ronsard
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Vikas Sood
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Sajad A. Dar
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Vishnampettai G. Ramachandran
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- * E-mail: (VGR); (ACB)
| | - Shukla Das
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Akhil C. Banerjea
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
- * E-mail: (VGR); (ACB)
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Pandey S, Tripathy S, Paranjape R. Molecular characterization of unique intersubtype HIV type 1 A1/C recombinant strain circulating in Pune, India. AIDS Res Hum Retroviruses 2013; 29:1245-53. [PMID: 23742670 DOI: 10.1089/aid.2013.0150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
An increasing number of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) all over the world has necessitated being vigilant about new recombinants. Since the first report of a recombinant virus with an A1/C mosaic in 1998 more and more B/C and A/C recombinant viruses are being reported from India. Here we report the identification and characterization of a unique HIV-1 A1/C recombinant circulating in Western India. Analysis of the full-length genome using RIP, SimPlot, and jpHMM@Gobics has confirmed its mosaic structure with insertion of subtype A1 in the backbone of subtype C at three positions: gag-pol (1973±15-2617±47), pol-vif (4879±37-5582±32), and gp41 (8437±106-8811±8); however, RIP and SimPlot showed one more small insertion in integrase (4343-4519). Phylogenetic analysis confirmed that the recombinant virus has an insertion of clade A1 in the backbone of subtype C, which has come from Indian subtype C.
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Affiliation(s)
- Sudhanshu Pandey
- Division of Immunology, National AIDS Research Institute (ICMR), Pune, India
| | - Srikanth Tripathy
- Central JALMA Institute for Leprosy and other Mycobacterial Diseases, Agra, India
| | - Ramesh Paranjape
- Division of Immunology, National AIDS Research Institute (ICMR), Pune, India
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9
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Andrabi R, Kumar R, Bala M, Nair A, Ss P, Kushwaha V, Luthra K. Envelope diversity, characteristics of V3 region and predicted co-receptor usage of human immunodeficiency viruses infecting north Indians. J Microbiol 2012; 50:869-73. [PMID: 23124759 DOI: 10.1007/s12275-012-2136-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/12/2012] [Indexed: 11/27/2022]
Abstract
Subtypes of human immunodeficiency virus type 1 circulating in 21 north Indian patients were characterized based on the partial sequence of the gp120 envelope protein. A majority of viruses (85.7%, 18/21) were subtype C, while 14.3% (3/21) were subtype A. Sequence analysis revealed that the V3 region was highly conserved compared with V4 and V5. The predicted use of co-receptors indicated exclusive usage of R5, except for two subtype A viruses (AIIMS279 and AIIMS281). Our results demonstrate conservation within the V3 loop of subtype C viruses, and suggest the emergence of non-clade C viruses in the north Indian population.
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Affiliation(s)
- Raiees Andrabi
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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10
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Neogi U, Sood V, Ronsard L, Singh J, Lata S, Ramachandran VG, Das S, Wanchu A, Banerjea AC. Genetic architecture of HIV-1 genes circulating in north India & their functional implications. Indian J Med Res 2012; 134:769-78. [PMID: 22310812 PMCID: PMC3284088 DOI: 10.4103/0971-5916.92624] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
This review presents data on genetic and functional analysis of some of the HIV-1 genes derived from HIV-1 infected individuals from north India (Delhi, Punjab and Chandigarh). We found evidence of novel B/C recombinants in HIV-1 LTR region showing relatedness to China/Myanmar with 3 copies of Nfκb sites; B/C/D mosaic genomes for HIV-1 Vpr and novel B/C Tat. We reported appearance of a complex recombinant form CRF_02AG of HIV-1 envelope sequences which is predominantly found in Central/Western Africa. Also one Indian HIV-1 envelope subtype C sequence suggested exclusive CXCR4 co-receptor usage. This extensive recombination, which is observed in about 10 per cent HIV-1 infected individuals in the Vpr genes, resulted in remarkably altered functions when compared with prototype subtype B Vpr. The Vpu C was found to be more potent in causing apoptosis when compared with Vpu B when analyzed for subG1 DNA content. The functional implications of these changes as well as in other genes of HIV-1 are discussed in detail with possible implications for subtype-specific pathogenesis highlighted.
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Affiliation(s)
- Ujjwal Neogi
- Department of Virology, National Institute of Immunology, New Delhi, India
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11
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Prakash SS, Kalra R, Lodha R, Kabra SK, Luthra K. Diversity of HIV type 1 envelope (V3-V5) sequence in HIV type 1-infected Indian children. AIDS Res Hum Retroviruses 2012; 28:505-9. [PMID: 21902590 DOI: 10.1089/aid.2011.0206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Abstract We assessed the viral envelope (V3-V5 region) sequence diversity from 13 HIV-1-infected Indian children from north India. All of the 13 children were found to be infected with subtype C viruses. One of the viral sequences exhibited usage of the CXCR4 coreceptor predicted by Web PSSM and Geno2pheno tools. This virus also had a longer V3 sequence with 37 amino acids, a GRGQ motif, and a methionine residue before it (AIIMS_307). A unique finding was the complete deletion of the V4 region of another virus (AIIMS_363). High sequence diversity was observed in the envelope of the HIV-1-infected Indian children.
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Affiliation(s)
- Somi Sankaran Prakash
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Kalra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sushil K. Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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Neogi U, Prarthana SB, D'Souza G, DeCosta A, Kuttiatt VS, Ranga U, Shet A. Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India. AIDS Res Ther 2010; 7:24. [PMID: 20646329 PMCID: PMC2918521 DOI: 10.1186/1742-6405-7-24] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/21/2010] [Indexed: 05/26/2023] Open
Abstract
Background Understanding co-receptor tropism of HIV-1 strains circulating in India will provide key analytical leverage for assessing the potential usefulness of newer antiretroviral drugs such as chemokine co-receptor antagonists among Indian HIV-infected populations. The objective of this study was to determine using in silico methods, HIV-1 tropism among a large number of Indian isolates both from primary clinical isolates as well as from database-derived sequences. Results R5-tropism was seen in 96.8% of a total of 1045 HIV-1 subtype C Indian sequences. Co-receptor prediction of 15 primary clinical isolates detected two X4-tropic strains using the C-PSSM matrix. R5-tropic HIV-1 subtype C V3 sequences were conserved to a greater extent than X4-tropic strains. X4-tropic strains were obtained from subjects who had a significantly longer time since HIV diagnosis (96.5 months) compared to R5-tropic strains (20.5 months). Conclusions High prevalence of R5 tropism and greater homogeneity of the V3 sequence among HIV-1 subtype C strains in India suggests the potential benefit of CCR5 antagonists as a therapeutic option in India.
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