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Capoferri AA, Lamers SL, Grabowski MK, Rose R, Wawer MJ, Serwadda D, Gray RH, Quinn TC, Kigozi G, Kagaayi J, Laeyendecker O, Abeler-Dörner L, Ayles H, Bonsall D, Bowden R, Calvez V, Cohen M, Denis A, Frampton D, de Oliveira T, Essex M, Fidler S, Fraser C, Golubchik T, Hayes R, Herbeck JT, Hoppe A, Kaleebu P, Kellam P, Kityo C, Leigh-Brown A, Lingappa JR, Novitsky V, Paton N, Pillay D, Rambaut A, Ratmann O, Seeley J, Ssemwanga D, Tanser F. Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda. AIDS Res Hum Retroviruses 2020; 36:467-474. [PMID: 31914792 DOI: 10.1089/aid.2019.0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset (n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.
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Affiliation(s)
- Adam A. Capoferri
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mary Kate Grabowski
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Maria J. Wawer
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Ronald H. Gray
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Thomas C. Quinn
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | | | | | - Oliver Laeyendecker
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
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Billings E, Sanders-Buell E, Bose M, Kijak GH, Bradfield A, Crossler J, Arroyo MA, Maboko L, Hoffmann O, Geis S, Birx DL, Kim JH, Michael NL, Robb ML, Hoelscher M, Tovanabutra S. HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania. AIDS Res Hum Retroviruses 2017; 33:373-381. [PMID: 27841669 PMCID: PMC5372774 DOI: 10.1089/aid.2016.0111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In preparation for vaccine trials, HIV-1 genetic diversity was surveyed between 2002 and 2006 through the Cohort Development study in the form of a retrospective and prospective observational study in and around the town of Mbeya in Tanzania's Southwest Highlands. This study describes the molecular epidemiology of HIV-1 strains obtained from 97 out of 106 incident HIV-1 infections identified in three subpopulations of participants (one rural, two urban) from the Mbeya area. Near full-genome or half-genome sequencing showed a subtype distribution of 40% C, 17% A1, 1% D, and 42% inter-subtype recombinants. Compared to viral subtyping results previously obtained from the retrospective phase of this study, the overall proportion of incident viral strains did not change greatly during the study course, suggesting maturity of the epidemic. A comparison to a current Phase I-II vaccine being tested in Africa shows ∼17% amino acid sequence difference between the gp120 of the vaccine and subtype C incident strains. Phylogenetic and recombinant breakpoint analysis of the incident strains revealed the emergence of CRF41_CD and many unique recombinants, as well as the presence of six local transmission networks most of which were confined to the rural subpopulation. In the context of vaccine cohort selection, these results suggest distinct infection transmission dynamics within these three geographically close subpopulations. The diversity and genetic sequences of the HIV-1 strains obtained during this study will greatly contribute to the planning, immunogen selection, and analysis of vaccine-induced immune responses observed during HIV-1 vaccine trials in Tanzania and neighboring countries.
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Affiliation(s)
- Erik Billings
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
| | - Eric Sanders-Buell
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
| | - Meera Bose
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
| | - Gustavo H. Kijak
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
| | - Andrea Bradfield
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
| | - Jacqueline Crossler
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
| | - Miguel A. Arroyo
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Oliver Hoffmann
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Steffen Geis
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich (LMU), Munich, Germany
| | - Deborah L. Birx
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jerome H. Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Nelson L. Michael
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Merlin L. Robb
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich (LMU), Munich, Germany
- German Centre for Infection Research (DZIF), Munich partner site, Munich, Germany
| | - Sodsai Tovanabutra
- United States Military HIV Research Program/Henry M. Jackson Foundation, Silver Spring, Maryland
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Hawkins C, Ulenga N, Liu E, Aboud S, Mugusi F, Chalamilla G, Sando D, Aris E, Carpenter D, Fawzi W. HIV virological failure and drug resistance in a cohort of Tanzanian HIV-infected adults. J Antimicrob Chemother 2016; 71:1966-74. [PMID: 27076106 DOI: 10.1093/jac/dkw051] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/05/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES There are few data on ART failure rates and drug resistance from Tanzania, where there is a wide diversity of non-B HIV subtypes. We assessed rates and predictors of virological failure in HIV-infected Tanzanians and describe drug resistance patterns in a subgroup of these patients. METHODS ART-naive, HIV-1-infected adults enrolled in a randomized controlled trial between November 2006 and 2008 and on ≥24 weeks of first-line NNRTI-containing ART were included. Population-based genotyping of HIV-1 protease and reverse transcriptase was performed on stored plasma from patients with virological failure (viral load >1000 copies/mL at ≥24 weeks of ART) and at baseline, where available. RESULTS A total of 2403 patients [median (IQR) age 37 (32-43) years; 70% female] were studied. The median (IQR) baseline CD4+ T cell count was 128 (62-190) cells/μL. Predominant HIV subtypes were A, C and D (92.2%). The overall rate of virological failure was 14.9% (95% CI 13.2%-16.1%). In adjusted analyses, significant predictors of virological failure were lower CD4+ T cell count (P = 0.01) and non-adherence to ART (P < 0.01). Drug resistance mutations were present in 87/115 samples (75.7%); the most common were M184V/I (52.2%) and K103N (35%). Thymidine analogue mutations were uncommon (5.2%). The prevalence of mutations in 45 samples pre-ART was 22%. CONCLUSIONS High levels of early ART failure and drug resistance were observed among Tanzanian HIV-1-infected adults enrolled in a well-monitored study. Initiating treatment early and ensuring optimal adherence are vital for the success and durability of first-line ART in these settings.
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Affiliation(s)
- Claudia Hawkins
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nzovu Ulenga
- Management and Development for Health, Dar es Salaam, Tanzania Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Enju Liu
- Departments of Nutrition, Epidemiology, Biostatistics, and Global Health and Population, Harvard School of Public Health, Boston, MA, USA
| | - Said Aboud
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ferdinand Mugusi
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - David Sando
- Management and Development for Health, Dar es Salaam, Tanzania
| | - Eric Aris
- Management and Development for Health, Dar es Salaam, Tanzania
| | | | - Wafaie Fawzi
- Department of Global Health and Population, Harvard School of Public Health, Boston, MA, USA
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Lai A, Bozzi G, Franzetti M, Binda F, Simonetti FR, De Luca A, Micheli V, Meraviglia P, Bagnarelli P, Di Biagio A, Monno L, Saladini F, Zazzi M, Zehender G, Ciccozzi M, Balotta C. HIV-1 A1 Subtype Epidemic in Italy Originated from Africa and Eastern Europe and Shows a High Frequency of Transmission Chains Involving Intravenous Drug Users. PLoS One 2016; 11:e0146097. [PMID: 26752062 PMCID: PMC4709132 DOI: 10.1371/journal.pone.0146097] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/14/2015] [Indexed: 12/04/2022] Open
Abstract
Background Subtype A accounts for only 12% of HIV-1 infections worldwide but predominates in Russia and Former Soviet Union countries of Eastern Europe. After an early propagation via heterosexual contacts, this variant spread explosively among intravenous drug users. A distinct A1 variant predominates in Greece and Albania, which penetrated directly from Africa. Clade A1 accounts for 12.5% of non-B subtypes in Italy, being the most frequent after F1 subtype. Aim Aim of this study was to investigate the circulation of A1 subtype in Italy and trace its origin and diffusion through phylogenetic and phylodynamic approaches. Results The phylogenetic analysis of 113 A1 pol sequences included in the Italian ARCA database, indicated that 71 patients (62.8%) clustered within 5 clades. A higher probability to be detected in clusters was found for patients from Eastern Europe and Italy (88.9% and 60.4%, respectively) compared to those from Africa (20%) (p < .001). Higher proportions of clustering sequences were found in intravenous drug users with respect to heterosexuals (85.7% vs. 59.3%, p = .056) and in women with respect to men (81.4% vs. 53.2%, p < .006). Subtype A1 dated phylogeny indicated an East African origin around 1961. Phylogeographical reconstruction highlighted 3 significant groups. One involved East European and some Italian variants, the second encompassed some Italian and African strains, the latter included the majority of viruses carried by African and Italian subjects and all viral sequences from Albania and Greece. Conclusions Subtype A1 originated in Central Africa and spread among East European countries in 1982. It entered Italy through three introduction events: directly from East Africa, from Albania and Greece, and from the area encompassing Moldavia and Ukraine. As in previously documented A1 epidemics of East European countries, HIV-1 A1 subtype spread in Italy in part through intravenous drug users. However, Eastern European women contributed to the penetration of such variant, probably through sex work.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
- * E-mail:
| | - Giorgio Bozzi
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Marco Franzetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesca Binda
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesco R. Simonetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Andrea De Luca
- Division of Infectious Diseases, Siena University Hospital, Siena, Italy
| | - Valeria Micheli
- Laboratory of Microbiology, ‘L. Sacco’ Hospital, Milan, Italy
| | - Paola Meraviglia
- 2nd Division of Infectious Diseases, ‘L. Sacco’ Hospital, Milan, Italy
| | - Patrizia Bagnarelli
- Department of Biomedical Science, Section of Microbiology, Laboratory of Virology, University Politecnica delle Marche, Ancona, Italy
| | | | - Laura Monno
- Division of Infectious Disease, University of Bari, Bari, Italy
| | | | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
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