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Omar S, Woodman ZL. The evolution of envelope function during coinfection with phylogenetically distinct human immunodeficiency virus. BMC Infect Dis 2024; 24:934. [PMID: 39251948 PMCID: PMC11385138 DOI: 10.1186/s12879-024-09805-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 08/23/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Coinfection with two phylogenetically distinct Human Immunodeficiency Virus-1 (HIV-1) variants might provide an opportunity for rapid viral expansion and the emergence of fit variants that drive disease progression. However, autologous neutralising immune responses are known to drive Envelope (Env) diversity which can either enhance replicative capacity, have no effect, or reduce viral fitness. This study investigated whether in vivo outgrowth of coinfecting variants was linked to pseudovirus and infectious molecular clones' infectivity to determine whether diversification resulted in more fit virus with the potential to increase disease progression. RESULTS For most participants, emergent recombinants displaced the co-transmitted variants and comprised the major population at 52 weeks postinfection with significantly higher entry efficiency than other co-circulating viruses. Our findings suggest that recombination within gp41 might have enhanced Env fusogenicity which contributed to the increase in pseudovirus entry efficiency. Finally, there was a significant correlation between pseudovirus entry efficiency and CD4 + T cell count, suggesting that the enhanced replicative capacity of recombinant variants could result in more virulent viruses. CONCLUSION Coinfection provides variants with the opportunity to undergo rapid recombination that results in more infectious virus. This highlights the importance of monitoring the replicative fitness of emergent viruses.
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Affiliation(s)
- Shatha Omar
- Department of Integrative Biomedical Sciences (IBMS), Division of Medical Biochemistry and Structural Biology, University of Cape Town, Cape Town, South Africa
- Department of Biomedical Sciences, Division of Molecular Biology and Human Genetics, TB Genomics Group, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Zenda L Woodman
- Department of Integrative Biomedical Sciences (IBMS), Division of Medical Biochemistry and Structural Biology, University of Cape Town, Cape Town, South Africa.
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Konno Y, Uriu K, Chikata T, Takada T, Kurita JI, Ueda MT, Islam S, Yang Tan BJ, Ito J, Aso H, Kumata R, Williamson C, Iwami S, Takiguchi M, Nishimura Y, Morita E, Satou Y, Nakagawa S, Koyanagi Y, Sato K. Two-step evolution of HIV-1 budding system leading to pandemic in the human population. Cell Rep 2024; 43:113697. [PMID: 38294901 DOI: 10.1016/j.celrep.2024.113697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/19/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The pandemic HIV-1, HIV-1 group M, emerged from a single spillover event of its ancestral lentivirus from a chimpanzee. During human-to-human spread worldwide, HIV-1 diversified into multiple subtypes. Here, our interdisciplinary investigation mainly sheds light on the evolutionary scenario of the viral budding system of HIV-1 subtype C (HIV-1C), a most successfully spread subtype. Of the two amino acid motifs for HIV-1 budding, the P(T/S)AP and YPxL motifs, HIV-1C loses the YPxL motif. Our data imply that HIV-1C might lose this motif to evade immune pressure. Additionally, the P(T/S)AP motif is duplicated dependently of the level of HIV-1 spread in the human population, and >20% of HIV-1C harbored the duplicated P(T/S)AP motif. We further show that the duplication of the P(T/S)AP motif is caused by the expansion of the CTG triplet repeat. Altogether, our results suggest that HIV-1 has experienced a two-step evolution of the viral budding process during human-to-human spread worldwide.
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Affiliation(s)
- Yoriyuki Konno
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Takayuki Chikata
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Toru Takada
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Saiful Islam
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Benjy Jek Yang Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Hirofumi Aso
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Ryuichi Kumata
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan; MIRAI, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Yorifumi Satou
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan; CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan.
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Kyobe S, Kisitu G, Mwesigwa S, Farirai J, Katagirya E, Retshabile G, Williams L, Mirembe A, Ketumile L, Wayengera M, Mukisa J, Sebetso G, Diphoko T, Amujal M, Kigozi E, Katabazi F, Oceng R, Mlotshwa B, Morapedi K, Nsangi B, Wampande E, Tsimako M, Brown C, Kasvosve I, Joloba M, Anabwani G, Mpoloka S, Mardon G, Kekitiinwa A, Hanchard NA, Kyosiimire-Lugemwa J, Matshaba M, Kiragga D. Long-term non-progression and risk factors for disease progression among children living with HIV in Botswana and Uganda: A retrospective cohort study. Int J Infect Dis 2024; 139:132-140. [PMID: 38036259 PMCID: PMC10843817 DOI: 10.1016/j.ijid.2023.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
OBJECTIVES We utilize a large retrospective study cohort derived from electronic medical records to estimate the prevalence of long-term non-progression (LTNP) and determine the factors associated with progression among children infected with HIV in Botswana and Uganda. METHODS Electronic medical records from large tertiary HIV clinical centers in Botswana and Uganda were queried to identify LTNP children 0-18 years enrolled between June 2003 and May 2014 and extract demographic and nutritional parameters. Multivariate subdistribution hazard analyses were used to examine demographic factors and nutritional status in progression in the pre-antiretroviral therapy era. RESULTS Between the two countries, 14,246 antiretroviral therapy-naïve children infected with HIV were enrolled into clinical care. The overall proportion of LTNP was 6.3% (9.5% in Botswana vs 5.9% in Uganda). The median progression-free survival for the cohort was 6.3 years, although this was lower in Botswana than in Uganda (6.6 vs 8.8 years; P <0.001). At baseline, the adjusted subdistribution hazard ratio (aHRsd) of progression was increased among underweight children (aHRsd 1.42; 95% confidence interval [CI]: 1.32-1.53), enrolled after 2010 (aHRsd 1.32; 95% CI 1.22-1.42), and those from Botswana (aHRsd 2; 95% CI 1.91-2.10). CONCLUSIONS In our study, the prevalence of pediatric LTNP was lower than that observed among adult populations, but progression-free survival was higher than expected. Underweight, year of enrollment into care, and country of origin are independent predictors of progression among children.
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Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Grace Kisitu
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - John Farirai
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Angela Mirembe
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Lesego Ketumile
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - John Mukisa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaseene Sebetso
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Thabo Diphoko
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Marion Amujal
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Katabazi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ronald Oceng
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Busisiwe Mlotshwa
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Morapedi
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Betty Nsangi
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Edward Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Chester Brown
- University of Tennessee Health Science Center, Memphis, USA
| | - Ishmael Kasvosve
- School of Allied Health Professionals, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda
| | - Sununguko Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, USA
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Neil A Hanchard
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, USA; Childhood Complex Disease Genomics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Dithan Kiragga
- Baylor College of Medicine Children's Foundation Uganda, Kampala, Uganda; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
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Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ. Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population. J Virol 2023; 97:e0095423. [PMID: 37747237 PMCID: PMC10617395 DOI: 10.1128/jvi.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
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Affiliation(s)
- Vanessa E. Schulz
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey F. Tuff
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Riley H. Tough
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lyle R. McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Paul J. McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Getaneh Y, Getnet F, Ning F, Rashid A, Liao L, Yi F, Shao Y. HIV-1 Disease Progression and Drug Resistance Mutations among Children on First-Line Antiretroviral Therapy in Ethiopia. Biomedicines 2023; 11:2293. [PMID: 37626789 PMCID: PMC10452141 DOI: 10.3390/biomedicines11082293] [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: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Background: High rates of disease progression and HIV drug resistance (HIVDR) among adults taking highly active antiretroviral treatment (HAART) in Sub-Saharan Africa were previously documented. However, children were generally not considered despite their greater risk. Hence, this study was aimed to evaluate HIV-1 disease progression and drug resistance mutation among children on first-line antiretroviral therapy in Ethiopia. Method: A longitudinal study was conducted among 551 HIV-positive children (<15 years old) recruited between 2017 and 2019 at 40 antiretroviral treatment delivery sites in Ethiopia. Disease progression was retrospectively measured over a 12-year (2007-2019) follow-up as the progress towards immunosuppression. Two consecutive viral load (VL) tests were conducted in 6-month intervals to assess virologic failure (VF). For children with VF, HIV-1 genotyping and sequencing was performed for the pol gene region using in-house assay validated at the Chinese Center for Disease Control and Prevention, and the Stanford HIVDB v9.0 algorithm was used for identification of drug resistance mutations. The Kaplan-Meier analysis and Cox proportional hazards regression model were used to estimate the rate and predictors of disease progression, respectively. Results: The disease progression rate was 6.3 per 100 person-years-observation (95% CI = 4.21-8.53). Overall immunosuppression (CD4 count < 200 cells/mm3) during the 12-year follow-up was 11.3% (95% CI = 7.5-15.1). Immunosuppression was significantly increased as of the mean duration of 10.5 (95% CI = 10.1-10.8) years (38.2%) to 67.8% at 12 years (p < 0.001). Overall, 14.5% had resistance to at least one drug, and 6.2% had multi-drug resistance. A resistance of 67.8% was observed among children with VF. Resistance to non-nucleotide reverse transcriptase inhibitors (NNRTI) and nucleotide reverse transcriptase inhibitors (NRTI) drugs were 11.4% and 10.1%, respectively. Mutations responsible for NRTI resistance were M184V (30.1%), K65R (12.1%), and D67N (5.6%). Moreover, NNRTI-associated mutations were K103N (14.8%), Y181C (11.8%), and G190A (7.7%). Children who had a history of opportunistic infection [AHR (95% CI) = 3.4 (1.8-6.2)], vitamin D < 20 ng/mL [AHR (95% CI) = 4.5 (2.1-9.9)], drug resistance [AHR (95% CI) = 2.2 (1.4-3.6)], and VF [AHR (95% CI) = 2.82 (1.21, 3.53)] had a higher hazard of disease progression; whereas, being orphan [AOR (95% CI) = 1.8 (1.2-3.1)], history of drug substitution [(AOR (95% CI) = 4.8 (2.1-6.5), hemoglobin < 12 mg/dL [AOR (95% CI) = 1.2 (1.1-2.1)] had higher odds of developing drug resistance. Conclusions: Immunosuppression was increasing over time and drug resistance was also substantially high. Enhancing routine monitoring of viral load and HIVDR and providing a vitamin-D supplement during clinical management could help improve the immunologic outcome. Limiting HAART substitution is also crucial for children taking HAART in Ethiopia.
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Affiliation(s)
- Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310027, China;
- Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
| | - Fentabil Getnet
- Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
- Takemi Program in International Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Feng Ning
- Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Abdur Rashid
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Feng Yi
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yiming Shao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310027, China;
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Asare K, Ngcapu S, Osman F, Vandormael A, Mindel A, Naicker N, Khanyile M, S Abdool Karim S, Tomita A, Garrett N. Incidence, recurrence, and prevalence of bacterial vaginosis from acute to chronic HIV infection in a prospective cohort of women in South Africa. Ann Epidemiol 2023; 82:33-39. [PMID: 37037344 PMCID: PMC10247472 DOI: 10.1016/j.annepidem.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/12/2023]
Abstract
PURPOSE We investigated the incidence, recurrence, prevalence, and risk factors for bacterial vaginosis (BV) diagnosis starting from acute HIV infection among South African women. METHODS The Centre for the AIDS Programme of Research in South Africa 002 study tested and treated women for BV (Nugent score 7-10) once/twice annually from acute to chronic HIV infection (2004-2020). We estimated BV incidence as the number of new cases and recurrence as the number of subsequent diagnoses per 100 person-years (PYs). We fitted Anderson-Gil Cox-proportional-hazard regression models to determine factors associated with BV incidence or recurrence. RESULTS Of 235 participants, the median age at enrollment was 25 years (Inter Quartile Range [IQR] 22-29). BV prevalence at enrollment was 50.6%. BV incidence was 23.9 cases per 100 PYs, and recurrence was 51.3 cases per 100 PYs. BV incidence/recurrence was associated with younger age (<25 years: adjusted hazard ratio [aHR] 1.70, 95% confidence interval [CI] 1.27-2.27), detectable HIV viral load (aHR 1.54, 95% CI 1.27-1.87) and lower CD4 count (<350 cells/μL: aHR 1.33, 95% CI 1.01-1.76). CONCLUSIONS Our findings underscore the need for early antiretroviral treatment initiation with diagnostic BV and sexually transmitted infection care, especially among younger women.
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Affiliation(s)
- Kwabena Asare
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Health Economics and HIV and AIDS Research Division (HEARD), University of KwaZulu-Natal, Durban, South Africa.
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Farzana Osman
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Alain Vandormael
- Heidelberg Institute of Global Health, Heidelberg University, Heidelberg, Germany
| | - Adrian Mindel
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nivashnee Naicker
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Mlungisi Khanyile
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Department of Epidemiology, Columbia University, New York, NY
| | - Andrew Tomita
- Centre for Rural Health, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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7
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Pre-infection plasma cytokines and chemokines as predictors of HIV disease progression. Sci Rep 2022; 12:2437. [PMID: 35165387 PMCID: PMC8844050 DOI: 10.1038/s41598-022-06532-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/02/2022] [Indexed: 01/13/2023] Open
Abstract
Previous studies have highlighted the role of pre-infection systemic inflammation on HIV acquisition risk, but the extent to which it predicts disease progression outcomes is less studied. Here we examined the relationship between pre-infection plasma cytokine expression and the rate of HIV disease progression in South African women who seroconverted during the CAPRISA 004 tenofovir gel trial. Bio-Plex 200 system was used to measure the expression of 47 cytokines/chemokines in 69 seroconvertors from the CAPRISA 004 trial. Cox proportional hazards regression analyses were used to measure associations between cytokine expression and CD4 decline prior to antiretroviral therapy initiation. Linear regression models were used to assess whether pre-infection cytokine expression were predictors of disease progression outcomes including peak and set-point viral load and CD4:CD8 ratio at less and greater than180 days post infection. Several cytokines were associated with increased peak HIV viral load (including IL-16, SCGFβ, MCP-3, IL-12p40, SCF, IFNα2 and IL-2). The strongest association with peak viral load was observed for SCGFβ, which was also inversely associated with lowest CD4:CD8 ratio < 180 days post infection and faster CD4 decline below 500 cells/µl (adjusted HR 4.537, 95% CI 1.475–13.954; p = 0.008) in multivariable analysis adjusting for age, study site, contraception, baseline HSV-2 status and trial arm allocation. Our results show that pre-infection systemic immune responses could play a role in HIV disease progression, especially in the early stages of infection.
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8
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Yirga AA, Melesse SF, Mwambi HG, Ayele DG. Application of quantile mixed-effects model in modeling CD4 count from HIV-infected patients in KwaZulu-Natal South Africa. BMC Infect Dis 2022; 22:20. [PMID: 34983387 PMCID: PMC8724661 DOI: 10.1186/s12879-021-06942-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CD4 cell count signifies the health of an individual's immune system. The use of data-driven models enables clinicians to accurately interpret potential information, examine the progression of CD4 count, and deal with patient heterogeneity due to patient-specific effects. Quantile-based regression models can be used to illustrate the entire conditional distribution of an outcome and identify various covariates effects at the respective location. METHODS This study uses the quantile mixed-effects model that assumes an asymmetric Laplace distribution for the error term. The model also incorporated multiple random effects to consider the correlation among observations. The exact maximum likelihood estimation was implemented using the Stochastic Approximation of the Expectation-Maximization algorithm to estimate the parameters. This study used the Centre of the AIDS Programme of Research in South Africa (CAPRISA) 002 Acute Infection Study data. In this study, the response variable is the longitudinal CD4 count from HIV-infected patients who were initiated on Highly Active Antiretroviral Therapy (HAART), and the explanatory variables are relevant baseline characteristics of the patients. RESULTS The analysis obtained robust parameters estimates at various locations of the conditional distribution. For instance, our result showed that baseline BMI (at [Formula: see text] 0.05: [Formula: see text]), baseline viral load (at [Formula: see text] 0.05: [Formula: see text] [Formula: see text]), and post-HAART initiation (at [Formula: see text] 0.05: [Formula: see text]) were major significant factors of CD4 count across fitted quantiles. CONCLUSIONS CD4 cell recovery in response to post-HAART initiation across all fitted quantile levels was observed. Compared to HIV-infected patients with low viral load levels at baseline, HIV-infected patients enrolled in the treatment with a high viral load level at baseline showed a significant negative effect on CD4 cell counts at upper quantiles. HIV-infected patients registered with high BMI at baseline had improved CD4 cell count after treatment, but physicians should not ignore this group of patients clinically. It is also crucial for physicians to closely monitor patients with a low BMI before and after starting HAART.
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Affiliation(s)
- Ashenafi A Yirga
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa.
| | - Sileshi F Melesse
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa
| | - Henry G Mwambi
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa
| | - Dawit G Ayele
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA
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9
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Orkin C, Ajana F, Kityo C, Koenig E, Natukunda E, Gandhi-Patel B, Wang H, Liu Y, Wei X, White K, Makadzange T, Pikora C, McNicholl I, Collins SE, Brainard D, Chuck SK. Brief Report: Efficacy and Safety of Bictegravir/Emtricitabine/Tenofovir Alafenamide in Females Living With HIV: An Integrated Analysis of 5 Trials. J Acquir Immune Defic Syndr 2021; 88:393-398. [PMID: 34506342 PMCID: PMC8547745 DOI: 10.1097/qai.0000000000002789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND We characterized the efficacy and safety of bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF) in a broad population of pediatric/adolescent/adult/elderly females living with HIV (FWH). SETTING Integrated analysis. METHODS Available data from 5 trials were integrated. Week 48 virologic suppression (HIV-1 RNA <50 copies/mL), resistance, adverse events (AEs), and laboratory parameters were assessed. RESULTS Three hundred and seventy-three FWH [304 virologically suppressed; 69 antiretroviral therapy (ART)-naive] received B/F/TAF [data from comparator regimens available for 306 individuals (236 virologically suppressed and 70 ART-naive participants)]. Virologic suppression rates with B/F/TAF at week 48 were high regardless of age in participants virologically suppressed at baseline (≥95%) and in ART-naive participants (≥87%). Virologic suppression rates were similar in B/F/TAF and comparator regimens (both virologically suppressed and ART-naive groups). Treatment-emergent resistance was not detected in the B/F/TAF group. AEs considered related to study drugs were experienced by 9.2% (B/F/TAF) and 5.5% (comparator regimen) of virologically suppressed participants and 15.9% (B/F/TAF) and 31.4% (comparator regimen) of ART-naive participants. For virologically suppressed and ART-naive FWH combined, only 1 of the 373 B/F/TAF-treated and 2 of the 306 comparator-regimen participants discontinued because of AEs (none were bone/renal/hepatic AEs); grade 3/4 AEs were experienced by 5.1% (B/F/TAF) and 7.8% (comparator regimen); and grade 3/4 elevation of low-density lipoprotein/total cholesterol occurred in 2.7%/0.3% (B/F/TAF) and 5.9%/2.0% (comparator regimen). At week 48, median changes from baseline estimated glomerular filtration rate in adults were <5 mL/min; results were similar in B/F/TAF and comparator-regimen groups. CONCLUSION B/F/TAF treatment was effective and well tolerated over 48 weeks, confirming B/F/TAF as an option for a broad population of FWH.
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Affiliation(s)
- Chloe Orkin
- Ambrose King Centre, The Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Faiza Ajana
- Centre Hospitalier de Tourcoing, Tourcoing, France
| | - Cissy Kityo
- Joint Clinical Research Centre, Kampala, Uganda
| | - Ellen Koenig
- Instituto Dominicano de Estudios Virologicos (IDEV), Santo Domingo, Dominican Republic; and
| | | | | | - Hui Wang
- Gilead Sciences, Foster City, CA
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10
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Additive quantile mixed effects modelling with application to longitudinal CD4 count data. Sci Rep 2021; 11:17945. [PMID: 34504147 PMCID: PMC8429740 DOI: 10.1038/s41598-021-97114-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
Quantile regression offers an invaluable tool to discern effects that would be missed by other conventional regression models, which are solely based on modeling conditional mean. Quantile regression for mixed-effects models has become practical for longitudinal data analysis due to the recent computational advances and the ready availability of efficient linear programming algorithms. Recently, quantile regression has also been extended to additive mixed-effects models, providing an efficient and flexible framework for nonparametric as well as parametric longitudinal forms of data analysis focused on features of the outcome beyond its central tendency. This study applies the additive quantile mixed model to analyze the longitudinal CD4 count of HIV-infected patients enrolled in a follow-up study at the Centre of the AIDS Programme of Research in South Africa. The objective of the study is to justify how the procedure developed can obtain robust nonlinear and linear effects at different conditional distribution locations. With respect to time and baseline BMI effect, the study shows a significant nonlinear effect on CD4 count across all fitted quantiles. Furthermore, across all fitted quantiles, the effect of the parametric covariates of baseline viral load, place of residence, and the number of sexual partners was found to be major significant factors on the progression of patients' CD4 count who had been initiated on the Highly Active Antiretroviral Therapy study.
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11
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Brooks K, Omondi FH, Liang RH, Sudderuddin H, Jones BR, Joy JB, Brumme CJ, Hunter E, Brumme ZL. Proviral Turnover During Untreated HIV Infection Is Dynamic and Variable Between Hosts, Impacting Reservoir Composition on ART. Front Microbiol 2021; 12:719153. [PMID: 34489909 PMCID: PMC8417368 DOI: 10.3389/fmicb.2021.719153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/30/2021] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) can persist as an integrated provirus, in a transcriptionally repressed state, within infected cells. This small yet enduring pool of cellular reservoirs that harbor replication-competent HIV is the main barrier to cure. Entry of viral sequences into cellular reservoirs begins shortly after infection, and cells containing integrated proviral DNA are extremely stable once suppressive antiretroviral therapy (ART) is initiated. During untreated HIV infection however, reservoir turnover is likely to be more dynamic. Understanding these dynamics is important because the longevity of the persisting proviral pool during untreated infection dictates reservoir composition at ART initiation. If the persisting proviral pool turns over slowly pre-ART, then HIV sequences seeded into it during early infection would have a high likelihood of persisting for long periods. However, if pre-ART turnover was rapid, the persisting proviral pool would rapidly shift toward recently circulating HIV sequences. One-way to estimate this turnover rate is from the age distributions of proviruses sampled shortly after therapy initiation: this is because, at the time of sampling, the majority of proviral turnover would have already occurred prior to ART. Recently, methods to estimate a provirus’ age from its sequence have made this possible. Using data from 12 individuals with HIV subtype C for whom proviral ages had been determined phylogenetically, we estimated that the average proviral half-life during untreated infection was 0.78 (range 0.45–2.38) years, which is >15 times faster than that of proviral DNA during suppressive ART. We further show that proviral turnover during untreated infection correlates with both viral setpoint and rate of CD4+ T-cell decline during this period. Overall, our results support dynamic proviral turnover pre-ART in most individuals, which helps explain why many individuals’ reservoirs are skewed toward younger HIV sequences. Broadly, our findings are consistent with the notion that active viral replication creates an environment less favorable to proviral persistence, while viral suppression creates conditions more favorable to persistence, where ART stabilizes the proviral pool by dramatically slowing its rate of decay. Strategies to inhibit this stabilizing effect and/or to enhance reservoir turnover during ART could represent additional strategies to reduce the HIV reservoir.
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Affiliation(s)
- Kelsie Brooks
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Richard H Liang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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12
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Ismail SD, Pankrac J, Ndashimye E, Prodger JL, Abrahams MR, Mann JFS, Redd AD, Arts EJ. Addressing an HIV cure in LMIC. Retrovirology 2021; 18:21. [PMID: 34344423 PMCID: PMC8330180 DOI: 10.1186/s12977-021-00565-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
HIV-1 persists in infected individuals despite years of antiretroviral therapy (ART), due to the formation of a stable and long-lived latent viral reservoir. Early ART can reduce the latent reservoir and is associated with post-treatment control in people living with HIV (PLWH). However, even in post-treatment controllers, ART cessation after a period of time inevitably results in rebound of plasma viraemia, thus lifelong treatment for viral suppression is indicated. Due to the difficulties of sustained life-long treatment in the millions of PLWH worldwide, a cure is undeniably necessary. This requires an in-depth understanding of reservoir formation and dynamics. Differences exist in treatment guidelines and accessibility to treatment as well as social stigma between low- and-middle income countries (LMICs) and high-income countries. In addition, demographic differences exist in PLWH from different geographical regions such as infecting viral subtype and host genetics, which can contribute to differences in the viral reservoir between different populations. Here, we review topics relevant to HIV-1 cure research in LMICs, with a focus on sub-Saharan Africa, the region of the world bearing the greatest burden of HIV-1. We present a summary of ART in LMICs, highlighting challenges that may be experienced in implementing a HIV-1 cure therapeutic. Furthermore, we discuss current research on the HIV-1 latent reservoir in different populations, highlighting research in LMIC and gaps in the research that may facilitate a global cure. Finally, we discuss current experimental cure strategies in the context of their potential application in LMICs.
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Affiliation(s)
- Sherazaan D Ismail
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Joshua Pankrac
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
| | - Emmanuel Ndashimye
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5C1, Canada
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melissa-Rose Abrahams
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Jamie F S Mann
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Bristol Veterinary School, University of Bristol, Langford House, Langford, Bristol, BS40 5DU, UK
| | - Andrew D Redd
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Eric J Arts
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada.
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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13
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Zhang J, Huang XJ, Tang WM, Chu Z, Hu Q, Liu J, Ding H, Han X, Zhang Z, Jiang YJ, Geng W, Xia W, Xu J, Shang H. Rapid Clinical Progression and Its Correlates Among Acute HIV Infected Men Who Have Sex With Men in China: Findings From a 5-Year Multicenter Prospective Cohort Study. Front Immunol 2021; 12:712802. [PMID: 34367176 PMCID: PMC8339583 DOI: 10.3389/fimmu.2021.712802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Background In the “treat all” era, there are few data on the nature of HIV clinical progression in middle-income countries. The aim of the current study was to prospectively analyze the clinical progression of HIV and its indicators among men in China with acute HIV who have sex with men. Methods From 2009–2014 a total of 400 men with acute HIV infection (AHI) were identified among 7,893 men who have sex with men via periodic pooled nucleic acid amplification testing, and they were assigned to an AHI prospective cohort in Beijing and Shenyang, China. Rapid progression was defined as two consecutive CD4+ T cell counts < 350/µL within 3–24 months post-infection. Kaplan−Meier and Cox-regression analyses were conducted to identify predictors of rapid progression. Results Among 400 men with AHI 46.5% were rapid progressors, 35.1% reached rapid progressor status by 12 months post-infection, and 63.9% reached rapid progressor status by 24 months. Rapid progression was associated with herpes simplex-2 virus coinfection (adjusted hazard ratio [aHR] 1.7, 95% confidence interval [CI] 1.2–2.3], depression (aHR 1.9, 95% CI 1.5–2.6), baseline CD4+ T cell count < 500/μL (aHR 3.5, 95% CI 2.4–5.1), higher baseline HIV viral load (aHR 1.6, 95% CI 1.2–2.3), acute symptoms lasting ≥ 2 weeks (aHR 1.6, 95% CI 1.1–2.2), higher body mass index (aHR 0.9, 95% CI 0.9–1.0), higher HIV viral load (aHR 1.7, 95% CI 1.4–2.1), set point viral load at 3 months (aHR 2.0, 95% CI 1.6–2.5), each 100-cell/μL decrease in CD4+ T cell count at 3 months (aHR 2.2, 95% CI 1.9–2.5), and baseline routine blood tests including white blood cell count < 5.32, hemoglobin ≥ 151, mean corpuscular hemoglobin ≥ 30.5, hemoglobin concentration ≥ 342, mean platelet count ≥ 342, lymphocytes ≥ 1.98, and mixed cell count ≥ 0.4 (all p < 0.05). Conclusion Almost half of the patients underwent rapid clinical progression within 2 years after HIV infection. A treat-all policy is necessary and should be strengthened globally. Rapid progression was correlated with herpes simplex-2 virus coinfection, depression, low CD4+ T cell counts, and high set point viral load in acute infection stage. Rapid progression can be identified via simple indicators such as body mass index and routine blood test parameters in low and middle-income countries.
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Affiliation(s)
- Jing Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiao-Jie Huang
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wei-Ming Tang
- Dermatology Hospital, Southern Medical University, Guangzhou, China.,University of North Carolina Project-China, Guangzhou, China.,School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Zhenxing Chu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Qinghai Hu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jing Liu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Haibo Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zining Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yong-Jun Jiang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Wenqing Geng
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Wei Xia
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junjie Xu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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14
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Yirga AA, Melesse SF, Mwambi HG, Ayele DG. Modelling CD4 counts before and after HAART for HIV infected patients in KwaZulu-Natal South Africa. Afr Health Sci 2020; 20:1546-1561. [PMID: 34394215 PMCID: PMC8351836 DOI: 10.4314/ahs.v20i4.7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND This study aims to make use of a longitudinal data modelling approach to analyze data on the number of CD4+cell counts measured repeatedly in HIV-1 Subtype C infected women enrolled in the Acute Infection Study of the Centre for the AIDS Programme of Research in South Africa. METHODOLOGY This study uses data from the CAPRISA 002 Acute Infection Study, which was conducted in South Africa. This cohort study observed N=235 incident HIV-1 positive women whose disease biomarkers were measured repeatedly at least four times on each participant. RESULTS From the findings of this study, post-HAART initiation, baseline viral load, and the prevalence of obese nutrition status were found to be major significant factors on the prognosis CD4+ count of HIV-infected patients. CONCLUSION Effective HAART initiation immediately after HIV exposure is necessary to suppress the increase of viral loads to induce potential ART benefits that accrue over time. The data showed evidence of strong individual-specific effects on the evolution of CD4+ counts. Effective monitoring and modelling of disease biomarkers are essential to help inform methods that can be put in place to suppress viral loads for maximum ART benefits that can be accrued over time at an individual level.
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Affiliation(s)
- Ashenfai A Yirga
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa
| | - Sileshi F Melesse
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa
| | - Henry G Mwambi
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa
| | - Dawit G Ayele
- Institute of Human Virology, University of Maryland, School of Medicine, USA
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15
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Yirga AA, Melesse SF, Mwambi HG, Ayele DG. Negative binomial mixed models for analyzing longitudinal CD4 count data. Sci Rep 2020; 10:16742. [PMID: 33028929 PMCID: PMC7541535 DOI: 10.1038/s41598-020-73883-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
It is of great interest for a biomedical analyst or an investigator to correctly model the CD4 cell count or disease biomarkers of a patient in the presence of covariates or factors determining the disease progression over time. The Poisson mixed-effects models (PMM) can be an appropriate choice for repeated count data. However, this model is not realistic because of the restriction that the mean and variance are equal. Therefore, the PMM is replaced by the negative binomial mixed-effects model (NBMM). The later model effectively manages the over-dispersion of the longitudinal data. We evaluate and compare the proposed models and their application to the number of CD4 cells of HIV-Infected patients recruited in the CAPRISA 002 Acute Infection Study. The results display that the NBMM has appropriate properties and outperforms the PMM in terms of handling over-dispersion of the data. Multiple imputation techniques are also used to handle missing values in the dataset to get valid inferences for parameter estimates. In addition, the results imply that the effect of baseline BMI, HAART initiation, baseline viral load, and the number of sexual partners were significantly associated with the patient's CD4 count in both fitted models. Comparison, discussion, and conclusion of the results of the fitted models complete the study.
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Affiliation(s)
- Ashenafi A Yirga
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
| | - Sileshi F Melesse
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Henry G Mwambi
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Dawit G Ayele
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD, USA
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16
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Dessie ZG, Zewotir T, Mwambi H, North D. Modeling Viral Suppression, Viral Rebound and State-Specific Duration of HIV Patients with CD4 Count Adjustment: Parametric Multistate Frailty Model Approach. Infect Dis Ther 2020; 9:367-388. [PMID: 32318999 PMCID: PMC7237593 DOI: 10.1007/s40121-020-00296-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Combination antiretroviral therapy has become the standard care of human immunodeficiency virus (HIV)-infected patients and has further led to a dramatically decreased progression probability to acquired immune deficiency syndrome (AIDS) for patients under such a therapy. However, responses of the patients to this therapy have recorded heterogeneous complexity and high dynamism. In this paper, we simultaneously model long-term viral suppression, viral rebound, and state-specific duration of HIV-infected patients. METHODS Full-parametric and semi-parametric Markov multistate models were applied to assess the effects of covariates namely TB co-infection, educational status, marital status, age, quality of life (QoL) scores, white and red blood cell parameters, and liver enzyme abnormality on long-term viral suppression, viral rebound and state-specific duration for HIV-infected individuals before and after treatment. Furthermore, two models, one including and another excluding the effect of the frailty, were presented and compared in this study. RESULTS Results from the diagnostic plots, Akaike information criterion (AIC) and likelihood ratio test showed that the Weibull multistate frailty model fitted significantly better than the exponential and semi-parametric multistate models. Viral rebound was found to be significantly associated with many sex partners, higher eosinophils count, younger age, lower educational level, higher monocyte counts, having abnormal neutrophils count, and higher liver enzyme abnormality. Furthermore, viral suppression was also found to be significantly associated with higher QoL scores, and having a stable sex partner. The analysis result also showed that patients with a stable sex partner, higher educational levels, higher QoL scores, lower eosinophils count, lower monocyte counts, and higher RBC indices were more likely to spend more time in undetectable viral load state. CONCLUSIONS To achieve and maintain the UNAIDS 90% suppression targets, additional interventions are required to optimize antiretroviral therapy outcomes, specifically targeting those with poor clinical characteristics, lower education, younger age, and those with many sex partners. From a methodological perspective, the parametric multistate approach with frailty is a flexible approach for modeling time-varying variables, allowing for dealing with heterogeneity between the sequence of transitions, as well as allowing for a reasonable degree of flexibility with a few additional parameters, which then aids in gaining a better insight into how factors change over time.
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Affiliation(s)
- Zelalem G Dessie
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa.
- College of Science, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Temesgen Zewotir
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
| | - Henry Mwambi
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
| | - Delia North
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
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Plasma concentration of injectable contraceptive correlates with reduced cervicovaginal growth factor expression in South African women. Mucosal Immunol 2020; 13:449-459. [PMID: 31896762 DOI: 10.1038/s41385-019-0249-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/10/2019] [Accepted: 12/15/2019] [Indexed: 02/06/2023]
Abstract
Long-acting injectable contraceptives have been associated with mucosal immune changes and increased HIV acquisition, but studies have often been hampered by the inaccuracy of self-reported data, unknown timing of injection, and interactions with mucosal transmission co-factors. We used mass spectrometry to quantify the plasma concentrations of injectable contraceptives in women from the CAPRISA004 study (n = 664), with parallel quantification of 48 cytokines and >500 host proteins in cervicovaginal lavage. Higher DMPA levels were associated with reduced CVL concentrations of GCSF, MCSF, IL-16, CTACK, LIF, IL-1α, and SCGF-β in adjusted linear mixed models. Dose-dependent relationships between DMPA concentration and genital cytokines were frequently observed. Unsupervised clustering of host proteins by DMPA concentration suggest that women with low DMPA had increases in proteins associated with mucosal fluid function, growth factors, and keratinization. Although DMPA was not broadly pro-inflammatory, DMPA was associated with increased IP-10 in HSV-2 seropositive and older women. DMPA-cytokine associations frequently differed by vaginal microbiome; in non-Lactobacillus-dominant women, DMPA was associated with elevated IL-8, MCP-1, and IP-10 concentrations. These data confirm a direct, concentration-dependant effect of DMPA on functionally important immune factors within the vaginal compartment. The biological effects of DMPA may vary depending on age, HSV-2 status, and vaginal microbiome composition.
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Dessie ZG, Zewotir T, Mwambi H, North D. Modelling immune deterioration, immune recovery and state-specific duration of HIV-infected women with viral load adjustment: using parametric multistate model. BMC Public Health 2020; 20:416. [PMID: 32228523 PMCID: PMC7106875 DOI: 10.1186/s12889-020-08530-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/16/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND CD4 cell and viral load count are highly correlated surrogate markers of human immunodeficiency virus (HIV) disease progression. In modelling the progression of HIV, previous studies mostly dealt with either CD4 cell counts or viral load alone. In this work, both biomarkers are in included one model, in order to study possible factors that affect the intensities of immune deterioration, immune recovery and state-specific duration of HIV-infected women. METHODS The data is from an ongoing prospective cohort study conducted among antiretroviral treatment (ART) naïve HIV-infected women in the province of KwaZulu-Natal, South Africa. Participants were enrolled in the acute HIV infection phase, then followed-up during chronic infection up to ART initiation. Full-parametric and semi-parametric Markov models were applied. Furthermore, the effect of the inclusion and exclusion viral load in the model was assessed. RESULTS Inclusion of a viral load component improves the efficiency of the model. The analysis results showed that patients who reported a stable sexual partner, having a higher educational level, higher physical health score and having a high mononuclear component score are more likely to spend more time in a good HIV state (particularly normal disease state). Patients with TB co-infection, with anemia, having a high liver abnormality score and patients who reported many sexual partners, had a significant increase in the intensities of immunological deterioration transitions. On the other hand, having high weight, higher education level, higher quality of life score, having high RBC parameters, high granulocyte component scores and high mononuclear component scores, significantly increased the intensities of immunological recovery transitions. CONCLUSION Inclusion of both CD4 cell count based disease progression states and viral load, in the time-homogeneous Markov model, assisted in modeling the complete disease progression of HIV/AIDS. Higher quality of life (QoL) domain scores, good clinical characteristics, stable sexual partner and higher educational level were found to be predictive factors for transition and length of stay in sequential adversity of HIV/AIDS.
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Affiliation(s)
- Zelalem G. Dessie
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
- College of Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Temesgen Zewotir
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
| | - Henry Mwambi
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
| | - Delia North
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
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Deletsu SD, Maina EK, Quaye O, Ampofo WK, Awandare GA, Bonney EY. High resistance to reverse transcriptase inhibitors among persons infected with human immunodeficiency virus type 1 subtype circulating recombinant form 02_AG in Ghana and on antiretroviral therapy. Medicine (Baltimore) 2020; 99:e18777. [PMID: 32049783 PMCID: PMC7035011 DOI: 10.1097/md.0000000000018777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/30/2019] [Accepted: 12/16/2019] [Indexed: 11/26/2022] Open
Abstract
This study sought to determine the dominant circulating human immunodeficiency virus type 1 (HIV-1) subtype and associated drug resistance mutations in Ghana.This cross-sectional study was conducted with archived samples collected from patients who received care at 2 hospitals in Ghana from 2014 to 2016. Blood samples were earlier processed into plasma and peripheral blood mononuclear cells and stored at -80 °C. Ribonucleic acid (RNA) was extracted from the archived plasma. Two HIV-1 genes; protease and reverse transcriptase, were amplified, sequenced using gene-specific primers and analyzed for subtype and drug resistance mutations using the Stanford HIV Database.Of 16 patient samples successfully sequenced, we identified the predominance of HIV-1 subtype CRF02_AG (11/16, 68%). Subtypes G (2/16, 13%), dual CRF02_AG/G (2/16, 13%), and CRF01_AE (1/16, 6%) were also observed. Major nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations, M184I/V, D67N, T215F, and K70R/E were found. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations, K103N, Y181C, V90I, F227L, and V106A were also prevalent. Additionally, and at a lower level, protease inhibitor (PI)-resistance mutations, M46I, I54 V, V82A, L90 M, and I471 V, were also present in the sequences from antiretroviral therapy (ART)-experienced individuals. Two NRTI-associated drug resistance mutations (DRMs) (D67N and T69N) were present in sequences from 1 ART-naive individual.HIV-1 subtype CRF02_AG was most frequently detected in this study thus confirming earlier reports of dominance of this subtype in the West-African sub-region and Ghana in particular. The detection of these drug resistance mutations in individuals on first-line regimen composed of NRTI and NNRTI is an indication of prolonged drug exposure without viral load monitoring. Routine viral load monitoring is necessary for early detection of virologic failure and drug resistance testing will inform appropriate choice of regimens for such patients.
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Affiliation(s)
- Selase D. Deletsu
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
| | - Edward K. Maina
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon-Accra, Ghana
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
| | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon-Accra, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
| | - Evelyn Y. Bonney
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon-Accra, Ghana
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20
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Sivro A, Schuetz A, Sheward D, Joag V, Yegorov S, Liebenberg LJ, Yende-Zuma N, Stalker A, Mwatelah RS, Selhorst P, Garrett N, Samsunder N, Balgobin A, Nawaz F, Cicala C, Arthos J, Fauci AS, Anzala AO, Kimani J, Bagaya BS, Kiwanuka N, Williamson C, Kaul R, Passmore JAS, Phanuphak N, Ananworanich J, Ansari A, Abdool Karim Q, Abdool Karim SS, McKinnon LR. Integrin α 4β 7 expression on peripheral blood CD4 + T cells predicts HIV acquisition and disease progression outcomes. Sci Transl Med 2019; 10:10/425/eaam6354. [PMID: 29367348 DOI: 10.1126/scitranslmed.aam6354] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 08/29/2017] [Accepted: 12/01/2017] [Indexed: 11/02/2022]
Abstract
The gastrointestinal (GI) mucosa is central to HIV pathogenesis, and the integrin α4β7 promotes the homing of immune cells to this site, including those that serve as viral targets. Data from simian immunodeficiency virus (SIV) animal models suggest that α4β7 blockade provides prophylactic and therapeutic benefits. We show that pre-HIV infection frequencies of α4β7+ peripheral blood CD4+ T cells, independent of other T cell phenotypes and genital inflammation, were associated with increased rates of HIV acquisition in South African women. A similar acquisition effect was observed in a Kenyan cohort and in nonhuman primates (NHPs) after intravaginal SIV challenge. This association was stronger when infection was caused by HIV strains containing V2 envelope motifs with a preference for α4β7 binding. In addition, pre-HIV α4β7+ CD4+ T cells predicted a higher set-point viral load and a greater than twofold increased rate of CD4+ T cell decline. These results were confirmed in SIV-infected NHPs. Increased frequencies of pre-HIV α4β7+ CD4+ T cells were also associated with higher postinfection expression of lipopolysaccharide binding protein, a microbial translocation marker, suggestive of more extensive gut damage. CD4+ T cells expressing α4β7 were rapidly depleted very early in HIV infection, particularly from the GI mucosa, and were not restored by early antiretroviral therapy. This study provides a link between α4β7 expression and HIV clinical outcomes in humans, in line with observations made in NHPs. Given the availability of a clinically approved anti-α4β7 monoclonal antibody for treatment of inflammatory bowel disease, these data support further evaluation of targeting α4β7 integrin as a clinical intervention during HIV infection.
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Affiliation(s)
- Aida Sivro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa.,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Alexandra Schuetz
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand.,U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute, Silver Spring, MD 20817, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Daniel Sheward
- Division of Medical Virology and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service, Cape Town 7925, South Africa
| | - Vineet Joag
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sergey Yegorov
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lenine J Liebenberg
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa
| | - Andrew Stalker
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ruth S Mwatelah
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Philippe Selhorst
- Division of Medical Virology and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service, Cape Town 7925, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa
| | - Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa
| | - Anisha Balgobin
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa
| | - Fatima Nawaz
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Anthony S Fauci
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Aggrey Omu Anzala
- Kenyan AIDS Vaccine Initiative, Nairobi 00202, Kenya.,Department of Medical Microbiology, University of Nairobi, Nairobi 00202, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.,Department of Medical Microbiology, University of Nairobi, Nairobi 00202, Kenya
| | - Bernard S Bagaya
- Uganda Virus Research Institute-International AIDS Vaccine Initiative HIV Vaccine Program, Plot 51-59, Nakiwogo Road, Entebbe, Uganda.,Department of Epidemiology and Biostatistics, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Noah Kiwanuka
- Uganda Virus Research Institute-International AIDS Vaccine Initiative HIV Vaccine Program, Plot 51-59, Nakiwogo Road, Entebbe, Uganda.,Department of Immunology and Molecular Biology, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Carolyn Williamson
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa.,Division of Medical Virology and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service, Cape Town 7925, South Africa
| | - Rupert Kaul
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,University Health Network, Toronto, Ontario M5G IL7, Canada
| | - Jo-Ann S Passmore
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa.,Division of Medical Virology and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service, Cape Town 7925, South Africa.,National Health Laboratory Services, Cape Town 8005, South Africa
| | - Nittaya Phanuphak
- South East Asia Research Collaboration in HIV (SEARCH), The Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute, Silver Spring, MD 20817, USA.,South East Asia Research Collaboration in HIV (SEARCH), The Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand.,University of Amsterdam, 1000 GG Amsterdam, Netherlands
| | - Aftab Ansari
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa.,Department of Epidemiology, Columbia University, New York, NY 10032, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa.,Department of Epidemiology, Columbia University, New York, NY 10032, USA
| | - Lyle R McKinnon
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa.,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.,Department of Medical Microbiology, University of Nairobi, Nairobi 00202, Kenya
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Ding ZD, Zheng JF, Song CB, Fu YJ, Xu JJ, Jiang YJ, Shang H, Zhang ZN. Decreased CD4 +CD8 low T cells in early HIV infection are associated with rapid disease progression. Cytokine 2019; 125:154801. [PMID: 31442680 DOI: 10.1016/j.cyto.2019.154801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/30/2019] [Accepted: 08/05/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND HIV rapid progressors (RPs) present with a rapid decline of CD4+ T cells within a few years of infection. Determining the underlying mechanisms throughout this decline is important to identify prognostic biomarkers and intervention strategies. Determining the numbers of CD4+ and CD8+ T cells is essential for monitoring the immune status of HIV infected patients. There are additional kinds of cell subtypes in T cells, but their relationship to the rapid progression of HIV disease is not well defined. METHODS Nineteen RPs and twenty-one chronic progressors (CPs) were enrolled in this study. Based on the intensity of CD4 and CD8 expression, different T cell subtypes were identified, including CD4+CD8+T cells, CD4-CD8- T cells, CD4+CD8low T cells and CD4-CD8low T cells. Alterations in these T cell subtypes in early HIV infection (within 120 days of infection) between RPs and CPs were measured, and the relationships between these subtypes and HIV disease progression were investigated. In addition, expression of IFN-γ in T cell subtypes after PMA stimulation was analyzed by flow cytometry. RESULTS We found that during early HIV infection, CD4+CD8low T cells both significantly decreased in numbers and percentages in RPs compared to CPs. Furthermore, baseline CD4+CD8low T cells positively correlated not only with baseline CD4+T cells but also with CD4+T cells 12 months after infection. Moreover, survival analysis indicated that low levels of baseline CD4+CD8low T cells significantly accelerated the decline in CD4+ T cells as well as increased viral loads. CD4+CD8low T cells secreted significantly more IFN-γ after PMA stimulation compared to CD4+CD8-T cells and CD4-CD8+T cells, which may be beneficial for the prevention of disease progression. CONCLUSIONS Our results identified that in early stage HIV-1 infection, a subtype of T cells, CD4+CD8low, are associated with subsequent disease progression.
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Affiliation(s)
- Zi-Dan Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China
| | - Jie-Fu Zheng
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China
| | - Cheng-Bo Song
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China
| | - Ya-Jing Fu
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China
| | - Jun-Jie Xu
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China
| | - Yong-Jun Jiang
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China.
| | - Zi-Ning Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang 110001, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou 310003, China.
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22
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Rossenkhan R, Rolland M, Labuschagne JPL, Ferreira RC, Magaret CA, Carpp LN, Matsen Iv FA, Huang Y, Rudnicki EE, Zhang Y, Ndabambi N, Logan M, Holzman T, Abrahams MR, Anthony C, Tovanabutra S, Warth C, Botha G, Matten D, Nitayaphan S, Kibuuka H, Sawe FK, Chopera D, Eller LA, Travers S, Robb ML, Williamson C, Gilbert PB, Edlefsen PT. Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment. Viruses 2019; 11:E607. [PMID: 31277299 PMCID: PMC6669737 DOI: 10.3390/v11070607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/19/2019] [Accepted: 06/27/2019] [Indexed: 12/16/2022] Open
Abstract
Knowledge of the time of HIV-1 infection and the multiplicity of viruses that establish HIV-1 infection is crucial for the in-depth analysis of clinical prevention efficacy trial outcomes. Better estimation methods would improve the ability to characterize immunological and genetic sequence correlates of efficacy within preventive efficacy trials of HIV-1 vaccines and monoclonal antibodies. We developed new methods for infection timing and multiplicity estimation using maximum likelihood estimators that shift and scale (calibrate) estimates by fitting true infection times and founder virus multiplicities to a linear regression model with independent variables defined by data on HIV-1 sequences, viral load, diagnostics, and sequence alignment statistics. Using Poisson models of measured mutation counts and phylogenetic trees, we analyzed longitudinal HIV-1 sequence data together with diagnostic and viral load data from the RV217 and CAPRISA 002 acute HIV-1 infection cohort studies. We used leave-one-out cross validation to evaluate the prediction error of these calibrated estimators versus that of existing estimators and found that both infection time and founder multiplicity can be estimated with improved accuracy and precision by calibration. Calibration considerably improved all estimators of time since HIV-1 infection, in terms of reducing bias to near zero and reducing root mean squared error (RMSE) to 5-10 days for sequences collected 1-2 months after infection. The calibration of multiplicity assessments yielded strong improvements with accurate predictions (ROC-AUC above 0.85) in all cases. These results have not yet been validated on external data, and the best-fitting models are likely to be less robust than simpler models to variation in sequencing conditions. For all evaluated models, these results demonstrate the value of calibration for improved estimation of founder multiplicity and of time since HIV-1 infection.
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Affiliation(s)
- Raabya Rossenkhan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Jan P L Labuschagne
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town 7535, South Africa
| | - Roux-Cil Ferreira
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frederick A Matsen Iv
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Erika E Rudnicki
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yuanyuan Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nonkululeko Ndabambi
- Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Murray Logan
- Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Ted Holzman
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa-Rose Abrahams
- Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Colin Anthony
- Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Christopher Warth
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Gordon Botha
- Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - David Matten
- Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Sorachai Nitayaphan
- Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Fred K Sawe
- Kenya Medical Research Institute/U.S. Army Medical Research Directorate-Africa/Kenya-Henry Jackson Foundation MRI, Kericho 20200, Kenya
| | - Denis Chopera
- Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE), Africa Health Research Institute, Durban 4001, South Africa
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Simon Travers
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town 7535, South Africa
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Carolyn Williamson
- Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Paul T Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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23
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Borzooee F, Joris KD, Grant MD, Larijani M. APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome. Front Immunol 2019; 9:3032. [PMID: 30687306 PMCID: PMC6338068 DOI: 10.3389/fimmu.2018.03032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022] Open
Abstract
APOBEC3G (A3G) is a host enzyme that mutates the genomes of retroviruses like HIV. Since A3G is expressed pre-infection, it has classically been considered an agent of innate immunity. We and others previously showed that the impact of A3G-induced mutations on the HIV genome extends to adaptive immunity also, by generating cytotoxic T cell (CTL) escape mutations. Accordingly, HIV genomic sequences encoding CTL epitopes often contain A3G-mutable “hotspot” sequence motifs, presumably to channel A3G action toward CTL escape. Here, we studied the depths and consequences of this apparent viral genome co-evolution with A3G. We identified all potential CTL epitopes in Gag, Pol, Env, and Nef restricted to several HLA class I alleles. We simulated A3G-induced mutations within CTL epitope-encoding sequences, and flanking regions. From the immune recognition perspective, we analyzed how A3G-driven mutations are predicted to impact CTL-epitope generation through modulating proteasomal processing and HLA class I binding. We found that A3G mutations were most often predicted to result in diminishing/abolishing HLA-binding affinity of peptide epitopes. From the viral genome evolution perspective, we evaluated enrichment of A3G hotspots at sequences encoding CTL epitopes and included control sequences in which the HIV genome was randomly shuffled. We found that sequences encoding immunogenic epitopes exhibited a selective enrichment of A3G hotspots, which were strongly biased to translate to non-synonymous amino acid substitutions. When superimposed on the known mutational gradient across the entire length of the HIV genome, we observed a gradient of A3G hotspot enrichment, and an HLA-specific pattern of the potential of A3G hotspots to lead to CTL escape mutations. These data illuminate the depths and extent of the co-evolution of the viral genome to subvert the host mutator A3G.
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Affiliation(s)
- Faezeh Borzooee
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Krista D Joris
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Michael D Grant
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
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24
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Ghosn J, Bayan T, Meixenberger K, Tran L, Frange P, d'Arminio Monforte A, Zangerle R, de Mendoza C, Krastinova E, Porter K, Meyer L, Chaix ML. CD4 T cell decline following HIV seroconversion in individuals with and without CXCR4-tropic virus. J Antimicrob Chemother 2018; 72:2862-2868. [PMID: 29091208 DOI: 10.1093/jac/dkx247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/22/2017] [Indexed: 11/12/2022] Open
Abstract
Background The natural clinical and immunological courses following HIV seroconversion with CXCR4-tropic or dual-mixed (X4/DM) viruses are controversial. We compared spontaneous immunological outcome in patients harbouring an X4/DM virus at the time of seroconversion with those harbouring a CCR5-tropic (R5) virus. Methods Data were included from patients participating in CASCADE, a large cohort collaboration of HIV seroconverters, with ≥2 years of follow-up since seroconversion. The HIV envelope gene was sequenced from frozen plasma samples collected at enrolment, and HIV tropism was determined using Geno2Pheno (false-positive rate 10%). The spontaneous CD4 T cell evolution was compared by modelling CD4 kinetics using linear mixed-effects models with random intercept and random slope. Results A total of 1387 patients were eligible. Median time between seroconversion and enrolment was 1 month (range 0-3). At enrolment, 202 of 1387 (15%) harboured an X4/DM-tropic virus. CD4 decrease slopes were not significantly different according to HIV-1 tropism during the first 30 months after seroconversion. No marked change in these results was found after adjusting for age, year of seroconversion and baseline HIV viral load. Time to antiretroviral treatment initiation was not statistically different between patients harbouring an R5 (20.76 months) and those harbouring an X4/DM-tropic virus (22.86 months, logrank test P = 0.32). Conclusions: In this large cohort collaboration, 15% of the patients harboured an X4/DM virus close to HIV seroconversion. Patients harbouring X4/DM-tropic viruses close to seroconversion did not have an increased risk of disease progression, estimated by the decline in CD4 T cell count or time to combined ART initiation.
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Affiliation(s)
- Jade Ghosn
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Inserm UMR-S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Université Pierre et Marie Curie, Paris, France
| | - Tatiana Bayan
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France
| | | | - Laurent Tran
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France.,AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Pierre Frange
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,AP-HP, Laboratoire de Microbiologie Clinique, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Antonella d'Arminio Monforte
- Infectious Diseases, University of Milan, San Paolo Hospital, Milano, Italy and Health Sciences, University of Milan, San Paolo Hospital, Milano, Italy
| | | | - Carmen de Mendoza
- Research Institute and University Hospital Puerta de Hierro, Majahonda, Madrid, Spain
| | - Evguenia Krastinova
- AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Kholoud Porter
- Medical Research Council Clinical Trials Unit, University College London, London, UK
| | - Laurence Meyer
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France.,AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Marie-Laure Chaix
- INSERM U941, Université Paris Diderot, Paris, France.,APHP, Laboratoire de Virologie, Hôpital Saint Louis, Paris, France
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25
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Tanko RF, Soares AP, Masson L, Garrett NJ, Samsunder N, Abdool Karim Q, Abdool Karim SS, Riou C, Burgers WA. Residual T cell activation and skewed CD8+ T cell memory differentiation despite antiretroviral therapy-induced HIV suppression. Clin Immunol 2018; 195:127-138. [PMID: 29883708 DOI: 10.1016/j.clim.2018.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/29/2018] [Accepted: 06/04/2018] [Indexed: 11/29/2022]
Abstract
HIV infection results in excessive T cell activation and dysfunction which may persist even during effective antiretroviral therapy (ART). The dynamics of immune 'deactivation' and extent to which T cell memory subsets normalize after ART are unclear. We longitudinally assessed the influence of 1 year of ART on the phenotype of T cells in HIV-infected African women, relative to matched HIV-uninfected women, using activation (CD38, HLA-DR) and differentiation markers (CD27, CD45RO). ART induced a substantial reduction in T cell activation, but remained higher than HIV-uninfected controls. ART largely normalized the distribution of CD4+ T cell memory subsets, while the distribution of CD8+ T cell memory subsets remained significantly skewed compared to HIV-uninfected individuals. Thus, there was a considerable but only partial reversal of T cell defects upon ART. Understanding T cell impairment may provide important insights into mechanisms of HIV pathogenesis in the era of ART.
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Affiliation(s)
- Ramla F Tanko
- Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Andreia P Soares
- Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Lindi Masson
- Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa; Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel J Garrett
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Natasha Samsunder
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Salim S Abdool Karim
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa.
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26
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Garrett N, Norman E, Leask K, Naicker N, Asari V, Majola N, Karim QA, Karim SSA. Acceptability of Early Antiretroviral Therapy Among South African Women. AIDS Behav 2018; 22:1018-1024. [PMID: 28224322 PMCID: PMC5565727 DOI: 10.1007/s10461-017-1729-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
WHO guidelines recommend immediate initiation of antiretroviral therapy (ART) for all individuals at HIV diagnosis regardless of CD4 count, but concerns remain about potential low uptake or poor adherence among healthy patients with high CD4 counts, especially in resource-limited settings. This study assessed the acceptability of earlier treatment among HIV-positive South African women, median age at enrollment 25 (IQR 22-30), in a 10 year prospective cohort study by (i) describing temporal CD4 count trends at initiation in relation to WHO guidance, (ii) virological suppression rates post-ART initiation at different CD4 count thresholds, and (iii) administration of a standardized questionnaire. 158/232 (68.1%) participants initiated ART between 2006 and 2015. Mean CD4 count at initiation was 217 cells/µl (range 135-372) before 2010, and increased to 531 cells/µl (range 272-1095) by 2015 (p < 0.001). Median viral load at ART initiation decreased over this period from 5.2 (IQR 4.6-5.6) to 4.1 (IQR 3.4-4.6) log copies/ml (p = 0.004). Virological suppression rates at 3, 6, 12 and 18 months were consistently above 85% with no statistically significant differences for participants starting ART at different CD4 count thresholds. A questionnaire assessing uptake of early ART amongst ART-naïve women, median age 28 (IQR 24-33), revealed that 40/51 (78.4%) were willing to start ART at CD4 ≥500. Of those unwilling, 6/11 (54.5%) started ART within 6 months of questionnaire administration. Temporal increases in CD4 counts, comparable virological suppression rates, and positive patient perceptions confirm high acceptability of earlier ART initiation for the majority of patients.
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Affiliation(s)
- Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa.
| | - Emily Norman
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa
- Department of Epidemiology, Columbia University, New York City, USA
| | - Kerry Leask
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa
| | - Nivashnee Naicker
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa
| | - Villeshni Asari
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa
| | - Nelisile Majola
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa
- Department of Epidemiology, Columbia University, New York City, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 2nd Floor, 719 Umbilo Road, Congella, Private Bag X7, Durban, 4013, South Africa
- Department of Epidemiology, Columbia University, New York City, USA
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27
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Moosa Y, Tanko RF, Ramsuran V, Singh R, Madzivhandila M, Yende-Zuma N, Abrahams MR, Selhorst P, Gounder K, Moore PL, Williamson C, Abdool Karim SS, Garrett NJ, Burgers WA. Case report: mechanisms of HIV elite control in two African women. BMC Infect Dis 2018; 18:54. [PMID: 29370775 PMCID: PMC5785875 DOI: 10.1186/s12879-018-2961-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 01/15/2018] [Indexed: 11/21/2022] Open
Abstract
Background The majority of people living with HIV require antiretroviral therapy (ART) for controlling viral replication, however there are rare HIV controllers who spontaneously and durably control HIV in the absence of treatment. Understanding what mediates viral control in these individuals has provided us with insights into the immune mechanisms that may be important to induce for a vaccine or functional cure for HIV. To date, few African elite controllers from high incidence settings have been described. We identified virological controllers from the CAPRISA 002 cohort of HIV-1 subtype C infected women in KwaZulu Natal, South Africa, two (1%) of whom were elite controllers. We examined the genetic, clinical, immunological and virological characteristics of these two elite HIV controllers in detail, to determine whether they exhibit features of putative viral control similar to those described for elite controllers reported in the literature. Case presentation In this case report, we present clinical features, CD4+ T cell and viral load trajectories for two African women over 7 years of HIV infection. Viral load became undetectable 10 months after HIV infection in Elite Controller 1 (EC1), and after 6 weeks in Elite Controller 2 (EC2), and remained undetectable for the duration of follow-up, in the absence of ART. Both elite controllers expressed multiple HLA Class I and II haplotypes previously associated with slower disease progression (HLA-A*74:01, HLA-B*44:03, HLA-B*81:01, HLA-B*57:03, HLA-DRB1*13). Fitness assays revealed that both women were infected with replication competent viruses, and both expressed higher mRNA levels of p21, a host restriction factor associated with viral control. HIV-specific T cell responses were examined using flow cytometry. EC1 mounted high frequency HIV-specific CD8+ T cell responses, including a B*81:01-restricted Gag TL9 response. Unusually, EC2 had evidence of pre-infection HIV-specific CD4+ T cell responses. Conclusion We identified some features typical of elite controllers, including high magnitude HIV-specific responses and beneficial HLA. In addition, we made the atypical finding of pre-infection HIV-specific immunity in one elite controller, that may have contributed to very early viral control. This report highlights the importance of studying HIV controllers in high incidence settings. Electronic supplementary material The online version of this article (10.1186/s12879-018-2961-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yumna Moosa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Ramla F Tanko
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Veron Ramsuran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Cancer Inflammation Program, Laboratory of Experimental Immunology, Leidos-Frederick, Incorporated, Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Ravesh Singh
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Mashudu Madzivhandila
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Melissa-Rose Abrahams
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Philippe Selhorst
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kamini Gounder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Carolyn Williamson
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nigel J Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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28
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Koch AS, Brites D, Stucki D, Evans JC, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Mizrahi V, Warner DF, Parkhill J, Gagneux S, Martin DP, Wilkinson RJ. The Influence of HIV on the Evolution of Mycobacterium tuberculosis. Mol Biol Evol 2017; 34:1654-1668. [PMID: 28369607 PMCID: PMC5455964 DOI: 10.1093/molbev/msx107] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 coinfected and uninfected individuals and analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favoring and disfavoring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favoring nonsynonymous substitutions within HIV-1 infected individuals. Among the 25,251 polymorphic codon sites analyzed, FUBAR revealed that 189-fold more were detectably evolving under persistent negative selection than were evolving under persistent positive selection. Three specific codon sites within the genes celA2b, katG, and cyp138 were identified by MEDS as displaying significant evidence of evolving under directional selection influenced by HIV-1 coinfection. All three genes encode proteins that may indirectly interact with human proteins that, in turn, interact functionally with HIV proteins. Unexpectedly, epitope encoding regions were enriched for sites displaying weak evidence of directional selection influenced by HIV-1. Although the low degree of genetic diversity observed in our M. tuberculosis data set means that these results should be interpreted carefully, the effects of HIV-1 on epitope evolution in M. tuberculosis may have implications for the design of M. tuberculosis vaccines that are intended for use in populations with high HIV-1 infection rates.
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Affiliation(s)
- Anastasia S Koch
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - David Stucki
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Joanna C Evans
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ronnett Seldon
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- University of Cape Town, and National Health Laboratory Service, Cape Town, South Africa
| | - Tolu Oni
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.,The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Darren P Martin
- Division of Computational Biology, Department of Integrated Biology Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Imperial College, London, United Kingdom.,Francis Crick Institute, London, United Kingdom
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29
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Naranbhai V, Carrington M. Host genetic variation and HIV disease: from mapping to mechanism. Immunogenetics 2017; 69:489-498. [PMID: 28695282 PMCID: PMC5537324 DOI: 10.1007/s00251-017-1000-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
Abstract
This review aims to provide a summary of current knowledge of host genetic effects on human immunodeficiency virus (HIV) disease. Mapping of simple single nucleotide polymorphisms (SNP) has been largely successful in HIV, but more complex genetic associations involving haplotypic or epigenetic variation, for example, remain elusive. Mechanistic insights explaining SNP associations are incomplete, but continue to be forthcoming. The number of robust immunogenetic correlates of HIV is modest and their discovery mostly predates the genome-wide era. Nevertheless, genome-wide evaluations have nicely validated the impact of HLA and CCR5 variants on HIV disease, and importantly, made clear the many false positive associations that were previously suggested by studies using the candidate gene approach. We describe how multiple HIV outcome measures such as acquisition, viral control, and immune decline have been studied in adults and in children, but that collectively these identify only the two replicable loci responsible for modifying HIV disease, CCR5, and HLA. Recent heritability estimates in this disease corroborate the modest impact of genetic determinants and their oligogenic nature. While the mechanism of protection afforded by genetic variants that diminish CCR5 expression is clear, new aspects of HLA class I-mediated protection continue to be uncovered. We describe how these genetic findings have enhanced insights into immunobiology, been clinically translated into CCR5 antagonists, allowed prioritization of antigens for vaccination efforts, and identified targets for genome-editing interventions. Finally, we describe how studies of genetically complex parts of the genome using new tools may begin revealing additional correlates.
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Affiliation(s)
- Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
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Replication Capacity of Viruses from Acute Infection Drives HIV-1 Disease Progression. J Virol 2017; 91:JVI.01806-16. [PMID: 28148791 DOI: 10.1128/jvi.01806-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/19/2017] [Indexed: 01/09/2023] Open
Abstract
The viral genotype has been shown to play an important role in HIV pathogenesis following transmission. However, the viral phenotypic properties that contribute to disease progression remain unclear. Most studies have been limited to the evaluation of Gag function in the context of a recombinant virus backbone. Using this approach, important biological information may be lost, making the evaluation of viruses obtained during acute infection, representing the transmitted virus, a more biologically relevant model. Here, we evaluate the roles of viral infectivity and the replication capacity of viruses from acute infection in disease progression in women who seroconverted in the CAPRISA 004 tenofovir microbicide trial. We show that viral replication capacity, but not viral infectivity, correlates with the set point viral load (Spearman r = 0.346; P = 0.045) and that replication capacity (hazard ratio [HR] = 4.52; P = 0.01) can predict CD4 decline independently of the viral load (HR = 2.9; P = 0.004) or protective HLA alleles (HR = 0.61; P = 0.36). We further demonstrate that Gag-Pro is not the main driver of this association, suggesting that additional properties of the transmitted virus play a role in disease progression. Finally, we find that although viruses from the tenofovir arm were 2-fold less infectious, they replicated at rates similar to those of viruses from the placebo arm. This indicates that the use of tenofovir gel did not select for viral variants with higher replication capacity. Overall, this study supports a strong influence of the replication capacity in acute infection on disease progression, potentially driven by interaction of multiple genes rather than a dominant role of the major structural gene gagIMPORTANCE HIV disease progression is known to differ between individuals, and defining which fraction of this variation can be attributed to the virus is important both clinically and epidemiologically. In this study, we show that the replication capacity of viruses isolated during acute infection predicts subsequent disease progression and drives CD4 decline independently of the viral load. This provides further support for the hypothesis that the replication capacity of the transmitted virus determines the initial damage to the immune system, setting the pace for later disease progression. However, we did not find evidence that the major structural gene gag drives this correlation, highlighting the importance of other genes in determining disease progression.
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Early evolution of human leucocyte antigen-associated escape mutations in variable Gag proteins predicts CD4+ decline in HIV-1 subtype C-infected women. AIDS 2017; 31:191-197. [PMID: 27755110 DOI: 10.1097/qad.0000000000001298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE HIV-1 escape from cytotoxic T-lymphocytes results in the accumulation of human leucocyte antigen (HLA)-associated mutations in the viral genome. To understand the contribution of early escape to disease progression, this study investigated the evolution and pathogenic implications of cytotoxic T-lymphocyte escape in a cohort followed from infection for 5 years. METHODS Viral loads and CD4 cell counts were monitored in 78 subtype C-infected individuals from onset of infection until CD4 cell count decline to less than 350 cells/μl or 5 years postinfection. The gag gene was sequenced and HLA-associated changes between enrolment and 12 months postinfection were mapped. RESULTS HLA-associated escape mutations were identified in 48 (62%) of the participants and were associated with CD4 decline to less than 350 cells/μl (P = 0.05). Escape mutations in variable Gag proteins (p17 and p7p6) had a greater impact on disease progression than escape in more conserved regions (p24) (P = 0.03). The association between HLA-associated escape mutations and CD4 decline was independent of protective HLA allele (B57, B58 : 01 and B81) expression. CONCLUSION The high frequency of escape contributed to rapid disease progression in this cohort. Although HLA-adaption in both conserved and variable Gag domains in the first year of infection was detrimental to long-term clinical outcome, escape in variable domains had greater impact.
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Tanko RF, Soares AP, Müller TL, Garrett NJ, Samsunder N, Abdool Karim Q, Abdool Karim SS, Riou C, Burgers WA. Effect of Antiretroviral Therapy on the Memory and Activation Profiles of B Cells in HIV-Infected African Women. THE JOURNAL OF IMMUNOLOGY 2016; 198:1220-1228. [PMID: 28039305 DOI: 10.4049/jimmunol.1601560] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/30/2016] [Indexed: 12/25/2022]
Abstract
Human immunodeficiency virus infection induces a wide range of effects in B cells, including skewed memory cell differentiation, compromised B cell function, and hypergammaglobulinemia. However, data on the extent to which these B cell abnormalities can be reversed by antiretroviral therapy (ART) are limited. To investigate the effect of ART on B cells, the activation (CD86) and differentiation (IgD, CD27, and CD38) profiles of B cells were measured longitudinally in 19 HIV-infected individuals before (median, 2 mo) and after ART initiation (median, 12 mo) and compared with 19 age-matched HIV-uninfected individuals using flow cytometry. Twelve months of ART restored the typical distribution of B cell subsets, increasing the proportion of naive B cells (CD27-IgD+CD38-) and concomitantly decreasing the immature transitional (CD27-IgD+CD38+), unswitched memory (CD27+IgD+CD38-), switched memory (CD27+IgD-CD38- or CD27-IgD-CD38-), and plasmablast (CD27+IgD-CD38high) subsets. However, B cell activation was only partially normalized post-ART, with the frequency of activated B cells (CD86+CD40+) reduced compared with pre-ART levels (p = 0.0001), but remaining significantly higher compared with HIV-uninfected individuals (p = 0.0001). Interestingly, unlike for T cell activation profiles, the extent of B cell activation prior to ART did not correlate with HIV plasma viral load, but positively associated with plasma sCD14 levels (p = 0.01, r = 0.58). Overall, ART partially normalizes the skewed B cell profiles induced by HIV, with some activation persisting. Understanding the effects of HIV on B cell dysfunction and restoration following ART may provide important insights into the mechanisms of HIV pathogenesis.
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Affiliation(s)
- Ramla F Tanko
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Andreia P Soares
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Tracey L Müller
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Nigel J Garrett
- Centre for the AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Natasha Samsunder
- Centre for the AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032; and
| | - Salim S Abdool Karim
- Centre for the AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032; and
| | - Catherine Riou
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Wendy A Burgers
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; .,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
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Mkhize NN, Durgiah R, Ashley V, Archary D, Garrett NJ, Karim QA, Karim SSA, Moore PL, Yates N, Passmore JAS, Tomaras GD, Morris L. Broadly neutralizing antibody specificities detected in the genital tract of HIV-1 infected women. AIDS 2016; 30:1005-14. [PMID: 26836790 PMCID: PMC4816677 DOI: 10.1097/qad.0000000000001038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Broadly neutralizing antibodies (bNAbs) targeting conserved epitopes on the HIV envelope glycoprotein have been identified in blood from HIV-1 infected women. We investigated whether antibodies in the genital tract from these women share similar epitope specificities and functional profiles as those in blood. METHODS Immunoglobulin (Ig)G and IgA antibodies were isolated from cervicovaginal lavages or Softcups from 13 HIV-infected women in the CAPRISA cohort using Protein G and Peptide M, respectively. Binding antibodies to envelope antigens were quantified by ELISA and binding antibody multiplex assay. Neutralizing antibody titers and epitope targets were measured using the TZM-bl assay with Env-pseudotyped wild-type and mutated viruses. RESULTS HIV-specific IgG, but not IgA, was detected in genital secretions and the ratio of total IgG to HIV-specific IgG was similar to plasma. HIV-specific IgG reacted with multiple envelope antigens, including V1V2, gp120, gp140 and gp41. Two women had high plasma titers of HIV-specific IgG3 which was also detected in their genital tract samples. IgG from the genital tract had neutralizing activity against both Tier 1 and Tier 2 primary HIV-isolates. Antibodies targeting well known glycan epitopes and the membrane proximal region of gp41 were detected in genital secretions, and matched specificities in plasma. CONCLUSIONS Women with plasma bNAbs have overlapping specificities in their genital secretions, indicating that these predominantly IgG isotype antibodies may transudate from blood to the genital tract. These data provide evidence that induction of systemic HIV-specific bNAbs can lead to antiviral immunity at the portal of entry.
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Affiliation(s)
- Nonhlanhla N. Mkhize
- National Institute for Communicable Diseases, Johannesburg, South Africa
- University of the Witwatersrand, Johannesburg, South Africa
| | - Raveshni Durgiah
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Vicki Ashley
- Duke Human Vaccine Institute and Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel J. Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Penny L. Moore
- National Institute for Communicable Diseases, Johannesburg, South Africa
- University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nicole Yates
- Duke Human Vaccine Institute and Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Jo-Ann S. Passmore
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, South Africa
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute and Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg, South Africa
- University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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Naranbhai V, de Assis Rosa D, Werner L, Moodley R, Hong H, Kharsany A, Mlisana K, Sibeko S, Garrett N, Chopera D, Carr WH, Abdool Karim Q, Hill AVS, Abdool Karim SS, Altfeld M, Gray CM, Ndung'u T. Killer-cell Immunoglobulin-like Receptor (KIR) gene profiles modify HIV disease course, not HIV acquisition in South African women. BMC Infect Dis 2016; 16:27. [PMID: 26809736 PMCID: PMC4727384 DOI: 10.1186/s12879-016-1361-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/18/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Killer-cell Immunoglobulin-like Receptors (KIR) interact with Human Leukocyte Antigen (HLA) to modify natural killer- and T-cell function. KIR are implicated in HIV acquisition by small studies that have not been widely replicated. A role for KIR in HIV disease progression is more widely replicated and supported by functional studies. METHODS To assess the role of KIR and KIR ligands in HIV acquisition and disease course, we studied at-risk women in South Africa between 2004-2010. Logistic regression was used for nested case-control analysis of 154 women who acquired vs. 155 who did not acquire HIV, despite high exposure. Linear mixed-effects models were used for cohort analysis of 139 women followed prospectively for a median of 54 months (IQR 31-69) until 2014. RESULTS Neither KIR repertoires nor HLA alleles were associated with HIV acquisition. However, KIR haplotype BB was associated with lower viral loads (-0.44 log10 copies/ml; SE = 0.18; p = 0.03) and higher CD4+ T-cell counts (+80 cells/μl; SE = 42; p = 0.04). This was largely explained by the protective effect of KIR2DL2/KIR2DS2 on the B haplotype and reciprocal detrimental effect of KIR2DL3 on the A haplotype. CONCLUSIONS Although neither KIR nor HLA appear to have a role in HIV acquisition, our data are consistent with involvement of KIR2DL2 in HIV control. Additional studies to replicate these findings are indicated.
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Affiliation(s)
- V Naranbhai
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa. .,Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa.
| | - D de Assis Rosa
- National Institute of Communicable Diseases, Sandringham, South Africa. .,University of the Witwatersrand, Johannesburg, South Africa.
| | - L Werner
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - R Moodley
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa.
| | - H Hong
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - A Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - K Mlisana
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - S Sibeko
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - N Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - D Chopera
- University of Cape Town, Cape Town, South Africa.
| | - W H Carr
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa. .,City University of New York - Medgar Evers College, New York, USA. .,Ragon Institute of MGH, MIT and Harvard University, Boston, USA.
| | - Q Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa. .,Mailman School of Public Health, Columbia University, New York, USA.
| | - A V S Hill
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - S S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa. .,Mailman School of Public Health, Columbia University, New York, USA.
| | - M Altfeld
- Ragon Institute of MGH, MIT and Harvard University, Boston, USA. .,Leibniz Institute for Experimental Virology, Heinrich Pette Institute, Hamburg, Germany.
| | - C M Gray
- National Institute of Communicable Diseases, Sandringham, South Africa. .,University of Cape Town, Cape Town, South Africa.
| | - T Ndung'u
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa. .,Ragon Institute of MGH, MIT and Harvard University, Boston, USA. .,KwaZulu-Natal Research Institute for Tuberculosis and HIV, University of KwaZulu-Natal, Durban, South Africa. .,Max Planck Institute for Infection Biology, Chariteplatz, D-10117, Berlin, Germany.
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Impact of HIV-1 Subtype on the Time to CD4+ T-Cell Recovery in Combination Antiretroviral Therapy (cART)-Experienced Patients. PLoS One 2015; 10:e0137281. [PMID: 26335136 PMCID: PMC4559476 DOI: 10.1371/journal.pone.0137281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/16/2015] [Indexed: 11/19/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtypes have been shown to differ in the rate of clinical progression. We studied the association between HIV-1 subtypes and the rate of CD4+ T-cell recovery in a longitudinal cohort of patients on combination antiretroviral therapy (cART). We studied 103 patients infected with CRF01_AE (69%) and subtype B (31%) who initiated cART between 2006 and 2013. Demographic data, CD4+ T-cell counts and HIV-1 viral load were abstracted from patient medical charts. Kaplan-Meier was used to estimate the time to CD4+ T-cell count increase to ≥350 between subtypes and effects of covariates were analysed using Cox proportional hazards. An 87% of the study population were male adults (mean age of 38.7 years old). Baseline CD4+ T-cell counts and viral loads, age at cART initiation, sex, ethnicity and co-infection did not differ significantly between subtypes. A shorter median time for CD4+ T-cell count increase to ≥350 cells/μL was observed for CRF01_AE (546 days; 95% confidence interval [CI], 186–906 days; P = .502) compared to subtype B (987 days; 95% CI, 894–1079 days). In multivariate analysis, female sex was significantly associated with a 2.7 times higher chance of achieving CD4+ T-cell recovery (adjusted hazard ratio [HR], 2.75; 95% CI, 1.21–6.22; P = .025) and both baseline CD4+ T-cell count (P = .001) and viral load (P = .001) were important predictors for CD4+ T-cell recovery. Immunological recovery correlated significantly with female sex, baseline CD4+ T-cell counts and viral load but not subtype.
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McGrath N, Lessells RJ, Newell ML. Time to eligibility for antiretroviral therapy in adults with CD4 cell count > 500 cells/μL in rural KwaZulu-Natal, South Africa. HIV Med 2015; 16:512-8. [PMID: 25959724 PMCID: PMC4682449 DOI: 10.1111/hiv.12255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2015] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Understanding of progression to antiretroviral therapy (ART) eligibility and associated factors remains limited. The objectives of this analysis were to determine the time to ART eligibility and to explore factors associated with disease progression in adults with early HIV infection. METHODS HIV-infected adults (≥ 18 years old) with CD4 cell count > 500 cells/μl were enrolled in the study at three primary health care clinics, and a sociodemographic, behavioural and partnership-level questionnaire was administered. Participants were followed 6-monthly and ART eligibility was determined using a CD4 cell count threshold of 350 cells/μl. Kaplan - Meier and Cox proportional hazard regression modelling were used in the analysis. RESULTS A total of 206 adults contributed 381 years of follow-up; 79 (38%) reached the ART eligibility threshold. Median time to ART eligibility was shorter for male patients (12.0 months) than for female patients (33.9 months). Male sex [adjusted hazard ratio (aHR) 3.13; 95% confidence interval (CI) 1.82-5.39], residing in a household with food shortage in the previous year (aHR 1.58; 95% CI 0.99-2.54), and taking nutritional supplements in the first 6 months after enrolment (aHR 2.06; 95% CI 1.11-3.83) were associated with shorter time to ART eligibility. Compared with reference CD4 cell count ≤ 559 cells/μl, higher CD4 cell count was associated with longer time to ART eligibility [aHR 0.46 (95% CI 0.25-0.83) for CD4 cell count 560-632 cells/μl; aHR 0.30 (95% CI 0.16-0.57) for CD4 cell count 633-768 cells/μl; and aHR 0.17 (95% CI 0.08-0.38) for CD4 cell count > 768 cells/μl]. CONCLUSIONS Over one in three adults with CD4 cell count > 500 cells/μl became eligible for ART at a CD4 cell count threshold of 350 cells/μl over a median of 2 years. The shorter time to ART eligibility in male patients suggests a possible need for sex-specific pre-ART care and monitoring strategies.
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Affiliation(s)
- N McGrath
- Academic Unit of Primary Care and Population Sciences, University of SouthamptonSouthampton, UK
- Department of Social Statistics and Demography, University of SouthamptonSouthampton, UK
- Africa Centre for Health and Population Studies, University of KwaZulu-NatalMtubatuba, South Africa
| | - RJ Lessells
- Africa Centre for Health and Population Studies, University of KwaZulu-NatalMtubatuba, South Africa
- Department of Clinical Research, London School of Hygiene and Tropical MedicineLondon, UK
| | - ML Newell
- Department of Social Statistics and Demography, University of SouthamptonSouthampton, UK
- Africa Centre for Health and Population Studies, University of KwaZulu-NatalMtubatuba, South Africa
- Academic Unit of Human Development and Health, University of SouthamptonSouthampton, UK
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Riou C, Tanko RF, Soares AP, Masson L, Werner L, Garrett NJ, Samsunder N, Karim QA, Karim SSA, Burgers WA. Restoration of CD4+ Responses to Copathogens in HIV-Infected Individuals on Antiretroviral Therapy Is Dependent on T Cell Memory Phenotype. THE JOURNAL OF IMMUNOLOGY 2015. [PMID: 26195814 DOI: 10.4049/jimmunol.1500803] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antiretroviral therapy (ART) induces rapid suppression of viral replication and a progressive replenishment of CD4(+) T cells in HIV-infected individuals. However, the effect of ART on restoring pre-existing memory CD4(+) T cells specific for common copathogens is still unclear. To better understand the dynamics of Ag-specific CD4(+) T cells during ART, we assessed the frequency, functional capacity, and memory profile of CD4(+) T cells specific for Mycobacterium tuberculosis and CMV in 15 HIV-infected individuals before and 1 y after ART initiation. After ART initiation, the frequency of M. tuberculosis-specific CD4(+) T cells showed little change, whereas CMV-specific CD4(+) T cells were significantly lower (p = 0.003). There was no difference in the polyfunctional or memory profile of Ag-specific CD4(+) T cells before and after ART. The replenishment of Ag-specific CD4(+) T cells correlated with the memory differentiation profile of these cells prior to ART. Pathogen-specific CD4(+) T cells exhibiting a late differentiated profile (CD45RO(+)CD27(-)) had a lower capacity to replenish (p = 0.019; r = -0.5) compared with cells with an early differentiated profile (CD45RO(+)CD27(+); p = 0.04; r = 0.45). In conclusion, restoration of copathogen-specific memory CD4(+) T cells during treated HIV infection is related to their memory phenotype, in which early differentiated cells (such as most M. tuberculosis-specific cells) have a higher replenishment capacity compared with late differentiated cells (such as most CMV-specific cells). These data identify an important, hitherto unrecognized, factor that may limit restoration of copathogen immunity in HIV-infected individuals on ART.
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Affiliation(s)
- Catherine Riou
- Division of Medical Virology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ramla F Tanko
- Division of Medical Virology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Andreia P Soares
- Division of Medical Virology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lindi Masson
- Division of Medical Virology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Lise Werner
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel J Garrett
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Natasha Samsunder
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Wendy A Burgers
- Division of Medical Virology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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