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Mokgethi PT, Choga WT, Maruapula D, Moraka NO, Seatla KK, Bareng OT, Ditshwanelo DD, Mulenga G, Mohammed T, Kaumba PM, Chihungwa M, Marukutira T, Moyo S, Koofhethile CK, Dickinson D, Mpoloka SW, Gaseitsiwe S. High prevalence of pre-treatment and acquired HIV-1 drug resistance mutations among non-citizens living with HIV in Botswana. Front Microbiol 2024; 15:1338191. [PMID: 38476948 PMCID: PMC10929613 DOI: 10.3389/fmicb.2024.1338191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Background Approximately 30,000 non-citizens are living with HIV in Botswana, all of whom as of 2020 are eligible to receive free antiretroviral treatment (ART) within the country. We assessed the prevalence of HIV-1 mutational profiles [pre-treatment drug resistance (PDR) and acquired drug resistance (ADR)] among treatment-experienced (TE) and treatment-naïve (TN) non-citizens living with HIV in Botswana. Methods A total of 152 non-citizens living with HIV were enrolled from a migrant HIV clinic at Independence Surgery, a private practice in Botswana from 2019-2021. Viral RNA isolated from plasma samples were genotyped for HIV drug resistance (HIVDR) using Sanger sequencing. Major known HIV drug resistance mutations (DRMs) in the pol region were determined using the Stanford HIV Drug Resistance Database. The proportions of HIV DRMs amongst TE and TN non-citizens were estimated with 95% confidence intervals (95% CI) and compared between the two groups. Results A total of 60/152 (39.5%) participants had a detectable viral load (VL) >40 copies/mL and these were included in the subsequent analyses. The median age at enrollment was 43 years (Q1, Q3: 38-48). Among individuals with VL > 40 copies/mL, 60% (36/60) were treatment-experienced with 53% (19/36) of them on Atripla. Genotyping had a 62% (37/60) success rate - 24 were TE, and 13 were TN. A total of 29 participants (78.4, 95% CI: 0.12-0.35) had major HIV DRMs, including at least one non-nucleoside reverse transcriptase inhibitor (NNRTI) associated DRM. In TE individuals, ADR to any antiretroviral drug was 83.3% (20/24), while for PDR was 69.2% (9/13). The most frequent DRMs were nucleoside reverse transcriptase inhibitors (NRTIs) M184V (62.1%, 18/29), NNRTIs V106M (41.4%, 12/29), and K103N (34.4%, 10/29). No integrase strand transfer inhibitor-associated DRMs were reported. Conclusion We report high rates of PDR and ADR in ART-experienced and ART-naïve non-citizens, respectively, in Botswana. Given the uncertainty of time of HIV acquisition and treatment adherence levels in this population, routine HIV-1C VL monitoring coupled with HIVDR genotyping is crucial for long-term ART success.
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Affiliation(s)
- Patrick T. Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Center of Epidemic Response and Innovation, Faculty of Data Sciences, Stellenbosch University, Cape Town, South Africa
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Natasha O. Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ontlametse T. Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | | | | | - Pearl M. Kaumba
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | | | - Tafireyi Marukutira
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Public Health, Burnet Institute, Melbourne, VIC, Australia
- Department of Epidemiology, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Catherine K. Koofhethile
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | | | | | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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de Almeida SM, Beltrame MP, Tang B, Rotta I, Justus JLP, Schluga Y, da Rocha MT, Martins E, Liao A, Abramson I, Vaida F, Schrier R, Ellis RJ. CD3 +CD56 + and CD3 -CD56 + lymphocytes in the cerebrospinal fluid of persons with HIV-1 subtypes B and C. J Neuroimmunol 2023; 377:578067. [PMID: 36965365 PMCID: PMC10817703 DOI: 10.1016/j.jneuroim.2023.578067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 03/19/2023]
Abstract
The transactivator of transcription (Tat) is a HIV regulatory protein which promotes viral replication and chemotaxis. HIV-1 shows extensive genetic diversity, HIV-1 subtype C being the most dominant subtype in the world. Our hypothesis is the frequency of CSF CD3+CD56+ and CD3-CD56dim is reduced in HIV-1C compared to HIV-1B due to the Tat C30S31 substitution in HIV-1C. 34 CSF and paired blood samples (PWH, n = 20; PWoH, n = 14) were studied. In PWH, the percentage of CD3+CD56+ was higher in CSF than in blood (p < 0.001), comparable in both compartments in PWoH (p = 0.20). The proportion of CD3-CD56dim in CSF in PWH was higher than PWoH (p = 0.008). There was no subtype differences. These results showed CNS compartmentalization of NKT cell response in PWH.
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Affiliation(s)
- Sergio M de Almeida
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil.
| | | | - Bin Tang
- HIV Neurobehavioral Research Center (HNRC), UCSD, San Diego, CA, USA
| | - Indianara Rotta
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Julie Lilian P Justus
- Immunophenotyping Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Yara Schluga
- Immunophenotyping Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Maria Tadeu da Rocha
- Immunophenotyping Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Edna Martins
- Immunophenotyping Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Antony Liao
- HIV Neurobehavioral Research Center (HNRC), UCSD, San Diego, CA, USA
| | - Ian Abramson
- HIV Neurobehavioral Research Center (HNRC), UCSD, San Diego, CA, USA
| | - Florin Vaida
- HIV Neurobehavioral Research Center (HNRC), UCSD, San Diego, CA, USA
| | - Rachel Schrier
- HIV Neurobehavioral Research Center (HNRC), UCSD, San Diego, CA, USA
| | - Ronald J Ellis
- HIV Neurobehavioral Research Center (HNRC), UCSD, San Diego, CA, USA
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Mbhele N, Gordon M. Structural effects of HIV-1 subtype C integrase mutations on the activity of integrase strand transfer inhibitors in South African patients. J Biomol Struct Dyn 2022; 40:12546-12556. [PMID: 34488561 DOI: 10.1080/07391102.2021.1972840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
HIV-1 integrase enzyme is responsible for the integration of viral DNA into the host genomic DNA. Integrase strand transfer inhibitors (INSTIs) are highly potent antiretroviral agents that inhibit this process, and are internationally approved for the treatment of both naïve and treated HIV-1 patients. However, their long-term efficacy is threatened by development of drug resistance strains resulting in resistance mutations. This work aimed to examine the effect of INSTI resistance-associated mutations (RAMs) and polymorphisms on the structure of HIV-1 subtype C (HIV-1C) integrase. Genetic analysis was performed on seven HIV-1C infected individuals with virologic failure after at least 6 months of INSTI-based antiretroviral therapy, presenting at the King Edward VIII hospital in Durban, South Africa. These were compared with sequences from 41 INSTI-naïve isolates. Integrase structures of selected isolates were modeled on the SWISS model online server. Molecular docking and dynamics simulations were also conducted using AutoDock-Vina and AMBER 18 force fields, respectively. Only one INSTI-treated isolate (14.28%) harboured major mutations (G140A + Q148R) as well as the E157Q minor mutation. Interestingly, S119T and V151I were only found in patients failing raltegravir (an INSTI drug). Molecular modeling and docking showed that RAMs and polymorphisms associated with INSTI-based therapy affect protein stability and this is supported by their weakened hydrogen-bond interactions compared to the wild-type. To the best of our knowledge, this is the first study to identify a double mutant in the 140's loop region from South African HIV-1C isolates and study its effects on Raltegravir, Elvitegravir, and Dolutegravir binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nokuzola Mbhele
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Michelle Gordon
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
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Bareng OT, Seselamarumo S, Seatla KK, Choga WT, Bakae B, Maruapula D, Kelentse N, Moraka NO, Mokaleng B, Mokgethi PT, Ditlhako TR, Pretorius-Holme M, Mbulawa MB, Lebelonyane R, Bile EC, Gaolathe T, Shapiro R, Makhema JM, Lockman S, Essex M, Novitsky V, Mpoloka SW, Moyo S, Gaseitsiwe S. Doravirine-associated resistance mutations in antiretroviral therapy naïve and experienced adults with HIV-1 subtype C infection in Botswana. J Glob Antimicrob Resist 2022; 31:128-134. [PMID: 35973671 PMCID: PMC9750894 DOI: 10.1016/j.jgar.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/25/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES There are limited data on the prevalence of doravirine (DOR)-associated drug resistance mutations in people with HIV (PWH) in Botswana. This cross-sectional, retrospective study aimed to explore the prevalence of DOR-associated resistance mutations among ART-naïve and -experienced PWH in Botswana enrolled in the population-based Botswana Combination Prevention Project (BCPP). METHODS A total of 6078 HIV-1C pol sequences were analysed for DOR-associated resistance mutations using the Stanford HIV drug resistance database, and their levels were predicted according to the Stanford DRM penalty scores and resistance interpretation. Virologic failure was defined as HIV-1 RNA load (VL) >400 copies/mL. RESULTS Among 6078 PWH, 5999 (99%) had known ART status, and 4529/5999 (79%) were on ART at time of sampling. The suppression rate among ART-experienced was 4517/4729 (96%). The overall prevalence of any DOR-associated resistance mutations was 181/1473 (12.3% [95% confidence interval {CI}: 10.7-14.1]); by ART status: 42/212 (19.8% [95% CI: 14.7-25.4]) among ART-failing individuals (VL ≥400 copies/mL) and 139/1261 (11.0% [95% CI: 9.3-12.9]) among ART-naïve individuals (P < 0.01). Intermediate DOR-associated resistance mutations were observed in 106/1261 (7.8% [95% CI: 6.9-10.1]) in ART-naïve individuals and 29/212 (13.7% [95% CI: 9.4-8.5]) among ART-experienced participants (P < 0.01). High-level DOR-associated resistance mutations were observed in 33/1261 (2.6% [95% CI: 1.8-3.7]) among ART-naïve and 13/212 (6.1% [95% CI: 3.6-10.8]) among ART-failing PWH (P < 0.01). PWH failing ART with at least one EFV/NVP-associated resistance mutation had high prevalence 13/67 (19.4%) of high-level DOR-associated resistance mutations. CONCLUSION DOR-associated mutations were rare (11.0%) among ART-naive PWH but present in 62.7% of Botswana individuals who failed NNRTI-based ART with at least one EFV/NVP-associated resistance mutation. Testing for HIV drug resistance should underpin the use of DOR in PWH who have taken first-generation NNRTIs.
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Affiliation(s)
- Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Sekgabo Seselamarumo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Kaelo K Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Blessing Bakae
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Natasha O Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Medical Sciences, Faculty of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | - Patrick T Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | | | - Molly Pretorius-Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Ebi Celestin Bile
- FHI 360, Department of Clinical Sciences, Durham, North Carolina, USA
| | | | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
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de Almeida SM, Beltrame MP, Tang B, Rotta I, Schluga Y, Justus JLP, da Rocha MT, Abramson I, Vaida F, Schrier R, Ellis RJ. Main lymphocyte subpopulations in cerebrospinal fluid and peripheral blood in HIV-1 subtypes C and B. J Neurovirol 2022; 28:291-304. [PMID: 35190973 DOI: 10.1007/s13365-022-01054-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
Abstract
HIV-1 subtype C (HIV-1C) shows reduced Tat protein chemoattractant activity compared with HIV-1B. The impact of HIV-1C Tat on the chemotaxis of the main lymphocyte subpopulations in the cerebrospinal fluid (CSF) and the peripheral blood (PB) is unclear. We hypothesized that there would be a lower frequency of specific lymphocyte subpopulations CD3+ or CD19+ in CSF in HIV-1C than in HIV-1B. The objectives were to detect the differences in the proportions of main lymphocyte subpopulations in CSF and PB, between people with HIV (PWH) and HIV-1-uninfected volunteers (PWoH) and in HIV-1B and HIV-1C. Lymphocyte immunophenotyping was studied in CSF and paired PB samples of PWH (n = 22) and PWoH (n = 14). Lymphocytes were analyzed within the CD45+ gated region. The proportions of CSF CD3+CD4+, CD3+CD8+, and CD3-CD19+ lymphocytes in CSF were comparable in HIV-1B and C. There was an increase in the proportion of CD3+CD8+ cells and a decrease in CD3+CD4+ T cells (ps = 0.016) in the CSF samples of the PWH compared with the PWoH group. In the PWH group, both CD3+CD4+ and CD3+CD8+ lymphocytes were significantly higher in the CSF than in the PB (p = 0.047 and 0.005). The proportion of CD3+CD4+ was lower and that of CD3+CD8+ was higher in the CSF samples of the aviremic group than that of HIV-negative control (p = 0.0008 and < 0.0001, respectively). HIV-1C Tat substitution (C30S) did not interfere with the CNS migration of the main lymphocyte subpopulations. This is the first study to evaluate these lymphocytes in CSF and PB of HIV-1C compared with HIV-1B.
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Affiliation(s)
- Sergio M de Almeida
- Laboratório de Virologia, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil.
| | - Miriam Perlingeiro Beltrame
- Laboratório de Citometria de Fluxo, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Bin Tang
- HNRC- HIV Neurobehavioral Research Center, UCSD, San Diego, CA, USA
| | - Indianara Rotta
- Laboratório de Virologia, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Yara Schluga
- Laboratório de Citometria de Fluxo, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Julie Lilian P Justus
- Laboratório de Citometria de Fluxo, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Maria Tadeu da Rocha
- Laboratório de Citometria de Fluxo, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Ian Abramson
- HNRC- HIV Neurobehavioral Research Center, UCSD, San Diego, CA, USA
| | - Florin Vaida
- HNRC- HIV Neurobehavioral Research Center, UCSD, San Diego, CA, USA
| | - Rachel Schrier
- HNRC- HIV Neurobehavioral Research Center, UCSD, San Diego, CA, USA
| | - Ronald J Ellis
- HNRC- HIV Neurobehavioral Research Center, UCSD, San Diego, CA, USA
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6
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Seatla KK, Maruapula D, Choga WT, Ntsipe T, Mathiba N, Mogwele M, Kapanda M, Nkomo B, Ramaabya D, Makhema J, Mmalane M, Mine M, Kasvosve I, Lockman S, Moyo S, Gaseitsiwe S. HIV-1 Subtype C Drug Resistance Mutations in Heavily Treated Patients Failing Integrase Strand Transfer Inhibitor-Based Regimens in Botswana. Viruses 2021; 13:v13040594. [PMID: 33807382 PMCID: PMC8066386 DOI: 10.3390/v13040594] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022] Open
Abstract
There are limited real-world mutational and virological outcomes data of treatment-experienced persons diagnosed with HIV-1 subtype C (HIV-1 C) who are failing Integrase Strand Transfer Inhibitor-based regimens. Requisition forms sent for HIV-1 genotypic resistance testing (GRT) between May 2015 and September 2019 were reviewed and participants experiencing virologic failure while on dolutegravir (DTG) or raltegravir (RAL) cART at sampling recruited. Sanger sequencing of the HIV-1 Pol gene was performed from residual plasma samples and drug resistance mutational (DRM) analysis performed using the Stanford University HIV drug resistance database. 40 HIV-1C integrase sequences were generated from 34 individuals, 24 of whom were on DTG cART, three on RAL cART and seven on an unknown (DTG or RAL)-anchored cART at time of GRT. 11/34 (32%) individuals had DRMs to DTG and other integrase inhibitors. 7/11 (64%) patients had exposure to a RAL-based cART at the time of sampling. Out of the 11 individuals with DRMs, one (9%) had 2-class, 6 (55%) had 3-class, and 4 (36%) had 4-class multidrug-resistant HIV-1C. 7/11 individuals (64%) are currently virologically suppressed. Of the four individuals not virologically suppressed, three had extensive DRMs involving 4-classes of ARV drugs and one individual has demised. Resistance to DTG occurs more often in patients exposed to RAL cART. Individuals with 4-class DRMs plus integrase T97 and E157Q mutations appear to have worse outcomes. There is a need for frequent VL monitoring and GRT amongst treatment-experienced HIV-1C diagnosed individuals.
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Affiliation(s)
- Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 0000, Botswana;
- Correspondence: ; Tel.: +267-390-2671; Fax: +267-390-1284
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 0000, Botswana;
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Tshenolo Ntsipe
- National Health Laboratory, Ministry of Health & Wellness, Gaborone 0000, Botswana; (T.N.); (M.M.)
| | - Nametso Mathiba
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
| | - Mompati Mogwele
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
| | - Max Kapanda
- Botswana Ministry of Health and Wellness, Gaborone 0000, Botswana; (M.K.); (B.N.); (D.R.)
| | - Bornapate Nkomo
- Botswana Ministry of Health and Wellness, Gaborone 0000, Botswana; (M.K.); (B.N.); (D.R.)
| | - Dinah Ramaabya
- Botswana Ministry of Health and Wellness, Gaborone 0000, Botswana; (M.K.); (B.N.); (D.R.)
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
| | - Mompati Mmalane
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
| | - Madisa Mine
- National Health Laboratory, Ministry of Health & Wellness, Gaborone 0000, Botswana; (T.N.); (M.M.)
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 0000, Botswana;
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (D.M.); (W.T.C.); (N.M.); (M.M.); (J.M.); (M.M.); (S.L.); (S.M.); (S.G.)
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Menon M, Budhwar R, Shukla RN, Bankar K, Vasudevan M, Ranga U. The Signature Amino Acid Residue Serine 31 of HIV-1C Tat Potentiates an Activated Phenotype in Endothelial Cells. Front Immunol 2020; 11:529614. [PMID: 33101270 PMCID: PMC7546421 DOI: 10.3389/fimmu.2020.529614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
The natural cysteine to serine variation at position 31 of Tat in HIV-1C disrupts the dicysteine motif attenuating the chemokine function of Tat. We ask if there exists a trade-off in terms of a gain of function for HIV-1C Tat due to this natural variation. We constructed two Tat-expression vectors encoding Tat proteins discordant for the serine 31 residue (CS-Tat vs. CC-Tat), expressed the proteins in Jurkat cells under doxycycline control, and performed the whole transcriptome analysis to compare the early events of Tat-induced host gene expression. Our analysis delineated a significant enrichment of pathways and gene ontologies associated with the angiogenic signaling events in CS-Tat stable cells. Subsequently, we validated and compared angiogenic signaling events induced by CS- vs. CC-Tat using human umbilical vein endothelial cells (HUVEC) and the human cerebral microvascular endothelial cell line (hCMEC/D3). CS-Tat significantly enhanced the production of CCL2 from HUVEC and induced an activated phenotype in endothelial cells conferring on them enhanced migration, invasion, and in vitro morphogenesis potential. The ability of CS-Tat to induce the activated phenotype in endothelial cells could be of significance, especially in the context of HIV-associated cardiovascular and neuronal disorders. The findings from the present study are likely to help appreciate the functional significance of the SAR (signature amino acid residues) influencing the unique biological properties.
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Affiliation(s)
- Malini Menon
- Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| | | | | | | | | | - Udaykumar Ranga
- Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
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Chakraborty S, Kabi M, Ranga U. A Stronger Transcription Regulatory Circuit of HIV-1C Drives the Rapid Establishment of Latency with Implications for the Direct Involvement of Tat. J Virol 2020; 94:e00503-20. [PMID: 32669338 DOI: 10.1128/JVI.00503-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
The magnitude of transcription factor binding site variation emerging in HIV-1 subtype C (HIV-1C), especially the addition of NF-κB motifs by sequence duplication, makes the examination of transcriptional silence challenging. How can HIV-1 establish and maintain latency despite having a strong long terminal repeat (LTR)? We constructed panels of subgenomic reporter viral vectors with varying copy numbers of NF-κB motifs (0 to 4 copies) and examined the profile of latency establishment in Jurkat cells. Surprisingly, we found that the stronger the viral promoter, the faster the latency establishment. Importantly, at the time of commitment to latency and subsequent points, Tat levels in the cell were not limiting. Using highly sensitive strategies, we demonstrate the presence of Tat in the latent cell, recruited to the latent LTR. Our data allude, for the first time, to Tat establishing a negative feedback loop during the late phases of viral infection, leading to the rapid silencing of the viral promoter.IMPORTANCE Over the past 10 to 15 years, HIV-1 subtype C (HIV-1C) has been evolving rapidly toward gaining stronger transcriptional activity by sequence duplication of major transcription factor binding sites. The duplication of NF-κB motifs is unique and exclusive to HIV-1C, a property not shared with any of the other eight HIV-1 genetic families. What mechanism(s) does HIV-1C employ to establish and maintain transcriptional silence despite the presence of a strong promoter and concomitant strong, positive transcriptional feedback is the primary question that we attempted to address in the present manuscript. The role that Tat plays in latency reversal is well established. Our work with the most common HIV-1 subtype, HIV-1C, offers crucial leads toward Tat possessing a dual role in serving as both a transcriptional activator and repressor at different phases of viral infection of the cell. The leads that we offer through the present work have significant implications for HIV-1 cure research.
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Sutar J, Padwal V, Nagar V, Patil P, Patel V, Bandivdekar A. Analysis of sequence diversity and selection pressure in HIV-1 clade C gp41 from India. Virusdisease 2020; 31:277-291. [PMID: 32904888 DOI: 10.1007/s13337-020-00595-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/28/2020] [Indexed: 01/31/2023] Open
Abstract
Evaluation of viral diversity is critical for the rational design of treatment modalities against Human immunodeficiency virus (HIV). Predominated by HIV-1 clade C (HIV-1C), the epidemic in India represents the third largest population infected with HIV-1 globally. Glycoprotein 41 (gp41) is critical for viral replication and is a target for the design of therapeutic strategies. However, documentation of viral diversity of gp41 gene in infected individuals from India remains limited. Present study employed high throughput sequencing to examine variation in gp41 amplicons generated from blood derived viruses in 24 HIV-1C infected individuals from Mumbai, India. Sequence diversity profiles were documented in different functional domains of gp41. Furthermore, through a meta-analysis approach, all reported gp41 sequences from India (N = 70) were compared with those from South Africa (N = 126), country with the largest HIV epidemic globally, also predominated by HIV-1C. A total of 44 positions displayed statistically significant differential (p < 0.05) Shannon entropy in the two regions. This comparison also identified 11 codon sites undergoing distinct selection, 8 of which remained differentially selected in an extended comparison of data from Asia (N = 137) and Africa(N = 383). Assessment of correlated mutation networks associated with differentially selected residues revealed common as well as distinct interaction networks. Furthermore, codon usage analysis revealed 17 differentially selected codons (Mann-Whitney test, p < 0.001) in Asia and Africa. Dissimilar trends in GC content across codon positions were also observed. In depth understanding of these divergent evolutionary signatures through extended analysis with larger data-sets would assist development of effective interventions being considered for HIV-1C.
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Affiliation(s)
- Jyoti Sutar
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Varsha Padwal
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Vidya Nagar
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Priya Patil
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Vainav Patel
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Atmaram Bandivdekar
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
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Dave RS, Ali H, Sil S, Knight LA, Pandey K, Madduri LSV, Qiu F, Ranga U, Buch S, Byrareddy SN. NF-κB Duplications in the Promoter-Variant HIV-1C LTR Impact Inflammation Without Altering Viral Replication in the Context of Simian Human Immunodeficiency Viruses and Opioid-Exposure. Front Immunol 2020; 11:95. [PMID: 32076422 PMCID: PMC7006833 DOI: 10.3389/fimmu.2020.00095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Recent spread of the promoter variant (4-κB) Human immunodeficiency virus-1 clade C (HIV-1C) strain is attributed to duplication of the Nuclear Factor Kappa B (NF-κB) binding sites and potential increased heroin consumption in India. To study the underlying biology of 4-κB HIV-1C in rhesus macaques, we engineered a promoter-chimera variant (4NF-κB) Simian Human Immunodeficiency Virus (SHIV) by substituting the HIV-1C Long Terminal Repeat (LTR) region consisting of 4 NF-κB and 3 Sp-1 sites with the corresponding segment in the LTR of SHIV AD8EO. The wild-type (3NF-κB) promoter-chimera SHIV was generated by inactivating the 5' proximal NF-κB binding site in SHIV 4NF-κB. CD8-depleted rhesus macaque PBMCs (RM-PBMCs) were infected with the promoter-chimera and AD8EO SHIVs to determine the effects of opioid-exposure on inflammation, NF-κB activation, neurotoxicity in neuronal cells and viral replication. Morphine-exposure of RM-PBMCs infected with SHIVs 4NF-κB, 3NF-κB, and AD8EO altered cellular transcript levels of monocyte chemoattractant protein 1, interleukin 6, interleukin 1β, and Tumor Necrosis Factor α. Of note, divergent alteration of the cytokine transcript levels was observed with these promoter-chimera wild-type and variant SHIVs. NF-κB activation was observed during infection of all three SHIVs with morphine-exposure. Finally, we observed that SHIV AD8EO infection and exposure to both morphine and naloxone had the greatest impact on the neurotoxicity. The promoter-chimera SHIV 4NF-κB and SHIV 3NF-κB did not have a similar effect on neurotoxicity as compared to SHIV AD8EO. All SHIVs replicated efficiently at comparable levels in RM-PBMCs and morphine-exposure did not alter viral replication kinetics. Future in vivo studies in rhesus macaques will provide greater understanding of 4-κB HIV-1C viral immunopathogenesis and onset of disease in the central nervous system during morphine-exposure.
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Affiliation(s)
- Rajnish S. Dave
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Haider Ali
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| | - Susmita Sil
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Lindsey A. Knight
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Lepakshe S. V. Madduri
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Fang Qiu
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
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Sharma S, Arunachalam PS, Menon M, Ragupathy V, Satya RV, Jebaraj J, Aralaguppe SG, Rao C, Pal S, Saravanan S, Murugavel KG, Balakrishnan P, Solomon S, Hewlett I, Ranga U. PTAP motif duplication in the p6 Gag protein confers a replication advantage on HIV-1 subtype C. J Biol Chem 2018; 293:11687-11708. [PMID: 29773649 DOI: 10.1074/jbc.m117.815829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 04/30/2018] [Indexed: 11/06/2022] Open
Abstract
HIV-1 subtype C (HIV-1C) may duplicate longer amino acid stretches in the p6 Gag protein, leading to the creation of an additional Pro-Thr/Ser-Ala-Pro (PTAP) motif necessary for viral packaging. However, the biological significance of a duplication of the PTAP motif for HIV-1 replication and pathogenesis has not been experimentally validated. In a longitudinal study of two different clinical cohorts of select HIV-1 seropositive, drug-naive individuals from India, we found that 8 of 50 of these individuals harbored a mixed infection of viral strains discordant for the PTAP duplication. Conventional and next-generation sequencing of six primary viral quasispecies at multiple time points disclosed that in a mixed infection, the viral strains containing the PTAP duplication dominated the infection. The dominance of the double-PTAP viral strains over a genetically similar single-PTAP viral clone was confirmed in viral proliferation and pairwise competition assays. Of note, in the proximity ligation assay, double-PTAP Gag proteins exhibited a significantly enhanced interaction with the host protein tumor susceptibility gene 101 (Tsg101). Moreover, Tsg101 overexpression resulted in a biphasic effect on HIV-1C proliferation, an enhanced effect at low concentration and an inhibitory effect only at higher concentrations, unlike a uniformly inhibitory effect on subtype B strains. In summary, our results indicate that the duplication of the PTAP motif in the p6 Gag protein enhances the replication fitness of HIV-1C by engaging the Tsg101 host protein with a higher affinity. Our results have implications for HIV-1 pathogenesis, especially of HIV-1C.
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Affiliation(s)
- Shilpee Sharma
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Prabhu S Arunachalam
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Malini Menon
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Viswanath Ragupathy
- the Laboratory of Molecular Virology, Division of Emerging and Transmission Transmitted Diseases, Office of Blood Review and Research, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | | | - Joshua Jebaraj
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | | | - Chaitra Rao
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Sreshtha Pal
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Shanmugam Saravanan
- the Y. R. Gaitonde Centre for AIDS Research and Education, Chennai 600113, India
| | | | | | - Suniti Solomon
- the Y. R. Gaitonde Centre for AIDS Research and Education, Chennai 600113, India
| | - Indira Hewlett
- the Laboratory of Molecular Virology, Division of Emerging and Transmission Transmitted Diseases, Office of Blood Review and Research, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Udaykumar Ranga
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India,
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Kulkarni AG, Paranjape RS, Thakar MR. Higher Expression of Activating Receptors on Cytotoxic NK Cells is Associated with Early Control on HIV-1C Multiplication. Front Immunol 2014; 5:222. [PMID: 24904577 PMCID: PMC4032894 DOI: 10.3389/fimmu.2014.00222] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 05/01/2014] [Indexed: 12/02/2022] Open
Abstract
Natural killer (NK) cells may be important in modulating HIV replication in early course of HIV infection. The effector function of NK cells is finely tuned by a balance between signals delivered by activating and inhibitory receptors. However, the influence of expression of these receptors on the early course of HIV replication and subsequent disease progression is not explored in the context of HIV-1C infection. The expression pattern of activating (NKp46, NKp44, NKp30, NKG2D, and NKG2C) and inhibitory (CD158b, NKG2A, and ILT2) receptors was determined in 20 patients with recent HIV-1C infection within 3–7 months of acquiring HIV infection and was compared with the expression pattern in individuals with progressive (N = 12), non-progressive HIV-1C infection (LTNPs, N = 12) and healthy seronegative individuals (N = 20). The association of the expression of these receptors on the rate of disease progression was assessed using viral load set point of recently infected individuals as a marker of disease progression. The study showed that higher cytotoxic potency of NK cells was associated with low viral load set point in recent HIV infection (r = −0.701; p = 0.0006) and higher CD4 counts (r = 0.720; p = 0.001). The expression of activating receptors (NKp46, NKp30, and NKG2D) on cytotoxic NK cells but not on regulatory NK cells was also significantly associated with low viral set point (p < 0.01) and viral load in LTNPs and progressors (p < 0.01). The study also indicated that cytotoxic NK cells might show the ability to specifically lyse HIV infected CD4 cells. This data collectively showed that early and sustained higher expression of activating receptors on cytotoxic NK cells could be responsible for increased cytotoxicity, reduced viral burden, and thus delaying the disease progression. The study to identify the molecular mechanism of the expression of these receptors in HIV infection will be helpful in further understanding of NK cell mediated control in early HIV infection.
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