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Wan Z, Zhang C. How to report and make sense of a new HIV-1 circulating recombinant form? Front Microbiol 2024; 15:1343143. [PMID: 38450164 PMCID: PMC10915052 DOI: 10.3389/fmicb.2024.1343143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024] Open
Abstract
Co-circulation of multiple HIV-1 subtypes in the same high-risk groups leads to the on-going generation of various inter-subtype recombinants, including unique (URFs) and circulating (CRFs) recombinant forms, which brings a new challenge for the prevention and eradication of HIV/AIDS. Identification and prompt reporting of new CRFs will provide not only new insights into the understanding of genetic diversity and evolution of HIV-1, but also an early warning of potential prevalence of these variants. Currently, 140 HIV-1 CRFs have been described; however, their prevalence and clinical importance are less concerned. Apart from the mosaic genomic maps, less other valuable information, including the clinical and demographic data, genomic sequence characteristics, origin and evolutionary dynamics, as well as representative genomic fragments for determining the variants, are available for most of these CRFs. Accompanied with the growing increase of HIV-1 full-length genomic sequences, more and more CRFs will be identified in the near future due to the high recombination potential of HIV-1. Here, we discuss the prevalence and clinical importance of various HIV-1 CRFs and propose how to report and make sense of a new HIV-1 CRF.
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Affiliation(s)
- Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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2
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Chameettachal A, Mustafa F, Rizvi TA. Understanding Retroviral Life Cycle and its Genomic RNA Packaging. J Mol Biol 2023; 435:167924. [PMID: 36535429 DOI: 10.1016/j.jmb.2022.167924] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Members of the family Retroviridae are important animal and human pathogens. Being obligate parasites, their replication involves a series of steps during which the virus hijacks the cellular machinery. Additionally, many of the steps of retrovirus replication are unique among viruses, including reverse transcription, integration, and specific packaging of their genomic RNA (gRNA) as a dimer. Progress in retrovirology has helped identify several molecular mechanisms involved in each of these steps, but many are still unknown or remain controversial. This review summarizes our present understanding of the molecular mechanisms involved in various stages of retrovirus replication. Furthermore, it provides a comprehensive analysis of our current understanding of how different retroviruses package their gRNA into the assembling virions. RNA packaging in retroviruses holds a special interest because of the uniqueness of packaging a dimeric genome. Dimerization and packaging are highly regulated and interlinked events, critical for the virus to decide whether its unspliced RNA will be packaged as a "genome" or translated into proteins. Finally, some of the outstanding areas of exploration in the field of RNA packaging are highlighted, such as the role of epitranscriptomics, heterogeneity of transcript start sites, and the necessity of functional polyA sequences. An in-depth knowledge of mechanisms that interplay between viral and cellular factors during virus replication is critical in understanding not only the virus life cycle, but also its pathogenesis, and development of new antiretroviral compounds, vaccines, as well as retroviral-based vectors for human gene therapy.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates. https://twitter.com/chameettachal
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
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3
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Appah A, Beelen CJ, Kirkby D, Dong W, Shahid A, Foley B, Mensah M, Ganu V, Puplampu P, Amoah LE, Nii-Trebi NI, Brumme CJ, Brumme ZL. Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage. Viruses 2022; 15:128. [PMID: 36680168 PMCID: PMC9865111 DOI: 10.3390/v15010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.
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Affiliation(s)
- Anna Appah
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Brian Foley
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA
| | - Miriam Mensah
- Fevers Unit, Department of Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Vincent Ganu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Peter Puplampu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Linda E. Amoah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box LG 25, Ghana
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
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4
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Gutierrez B, Castelán Sánchez HG, Candido DDS, Jackson B, Fleishon S, Houzet R, Ruis C, Delaye L, Faria NR, Rambaut A, Pybus OG, Escalera-Zamudio M. Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America. Cell Host Microbe 2022; 30:1112-1123.e3. [PMID: 35853454 PMCID: PMC9212848 DOI: 10.1016/j.chom.2022.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/18/2022] [Accepted: 06/16/2022] [Indexed: 02/09/2023]
Abstract
Although recombination is a feature of coronavirus evolution, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation thus far. Here, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages to investigate the possibility of virus recombination among them. Our analyses reveal well-supported phylogenetic differences between the Orf1ab region encoding viral non-structural proteins and the rest of the genome, including Spike (S) protein and remaining reading frames. By accounting for several deletions in NSP6, Orf3a, and S, we conclude that the B.1.628 major cluster, now designated as lineage XB, originated from a recombination event between viruses of B.1.631 and B.1.634 lineages. This scenario is supported by the spatiotemporal distribution of these lineages across the USA and Mexico during 2021, suggesting that the recombination event originated in this geographical region. This event raises important questions regarding the role and potential effects of recombination on SARS-CoV-2 evolution.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.
| | - Hugo G Castelán Sánchez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Darlan da Silva Candido
- Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | | | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Luis Delaye
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Departamento de Ingeniería Genética, Unidad Irapuato, CINVESTAV, Irapuato, Mexico
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK; The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK; Department of Pathobiology, Royal Veterinary College, London, UK.
| | - Marina Escalera-Zamudio
- Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México.
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5
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Nii-Trebi NI, Matsuoka S, Kawana-Tachikawa A, Bonney EY, Abana CZ, Ofori SB, Mizutani T, Ishizaka A, Shiino T, Ohashi J, Naruse TK, Kimura A, Kiyono H, Ishikawa K, Ampofo WK, Matano T. Super high-resolution single-molecule sequence-based typing of HLA class I alleles in HIV-1 infected individuals in Ghana. PLoS One 2022; 17:e0269390. [PMID: 35653364 PMCID: PMC9162337 DOI: 10.1371/journal.pone.0269390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Polymorphisms in human leukocyte antigen (HLA) class I loci are known to have a great impact on disease progression in HIV-1 infection. Prevailing HIV-1 subtypes and HLA genotype distribution are different all over the world, and the HIV-1 and host HLA interaction could be specific to individual areas. Data on the HIV-1 and HLA interaction have been accumulated in HIV-1 subtype B- and C-predominant populations but not fully obtained in West Africa where HIV-1 subtype CRF02_AG is predominant. In the present study, to obtain accurate HLA typing data for analysis of HLA association with disease progression in HIV-1 infection in West African populations, HLA class I (HLA-A, -B, and -C) four-digit allele typing was performed in treatment-naïve HIV-1 infected individuals in Ghana (n = 324) by a super high-resolution single-molecule sequence-based typing (SS-SBT) using next-generation sequencing. Comparison of the SS-SBT-based data with those obtained by a conventional sequencing-based typing (SBT) revealed incorrect assignment of several alleles by SBT. Indeed, HLA-A*23:17, HLA-B*07:06, HLA-C*07:18, and HLA-C*18:02 whose allele frequencies were 2.5%, 0.9%, 4.3%, and 3.7%, respectively, were not determined by SBT. Several HLA alleles were associated with clinical markers, viral load and CD4+ T-cell count. Of note, the impact of HLA-B*57:03 and HLA-B*58:01, known as protective alleles against HIV-1 subtype B and C infection, on clinical markers was not observed in our cohort. This study for the first time presents SS-SBT-based four-digit typing data on HLA-A, -B, and -C alleles in Ghana, describing impact of HLA on viral load and CD4 count in HIV-1 infection. Accumulation of these data would facilitate high-resolution HLA genotyping, contributing to our understanding of the HIV-1 and host HLA interaction in Ghana, West Africa.
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Affiliation(s)
- Nicholas I. Nii-Trebi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Evelyn Y. Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Christopher Z. Abana
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson B. Ofori
- Department of Medicine, Koforidua Government Hospital, Eastern Region, Ghana
| | | | - Aya Ishizaka
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Teiichiro Shiino
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Sciences, University of Tokyo, Tokyo, Japan
| | - Taeko K. Naruse
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Kiyono
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba, Japan
- CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - William K. Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- * E-mail: (WKA); (TM)
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- * E-mail: (WKA); (TM)
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6
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He S, Song W, Guo G, Li Q, An M, Zhao B, Gao Y, Tian W, Wang L, Shang H, Han X. Multiple CRF01_AE/CRF07_BC Recombinants Enhanced the HIV-1 Epidemic Complexity Among MSM in Shenyang City, Northeast China. Front Microbiol 2022; 13:855049. [PMID: 35633698 PMCID: PMC9133626 DOI: 10.3389/fmicb.2022.855049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
The transmission of Unique Recombinant Forms (URFs) has complicated the molecular epidemic of HIV-1. This increasing genetic diversity has implications for prevention surveillance, diagnosis, and vaccine design. In this study, we characterized the HIV-1 URFs from 135 newly diagnosed HIV-1 infected cases between 2016 and 2020 in Shenyang, northeast China and analyzed the evolutionary relationship of them by phylogenetic and recombination approaches. Among 135 URFs, we found that the CRF01_AE/CRF07_BC recombinants were the most common (81.5%, 110/135), followed by CRF01_AE/B (11.9%, 16/135), B/C (3.7%, 5/135), and others (3.0%, 4/135). 94.8% (128/135) of patients infected by URFs were through homosexual contact. Among 110 URFs_0107, 60 (54.5%) formed 11 subclusters (branch support value = 1) and shared the consistent recombination structure, respectively. Four subclusters have caused small-scale spread among different high-risk populations. Although the recombination structures of URFs_0107 are various, the hotspots of recombinants gathered between position 2,508 and 2,627 (relative to the HXB2 position). Moreover, the CRF07_BC and CRF01AE fragments of URFs_0107 were mainly derived from the MSM population. In brief, our results reveal the complex recombinant modes and the high transmission risk of URFs_0107, which calls for more attention on the new URFs_0107 monitoring and strict control in the areas led by homosexual transmission route.
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Affiliation(s)
- Shan He
- 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Wei Song
- Department of Food Safety and Nutrition, Shenyang Center for Health Service and Administrative Law Enforcement (Shenyang Center for Disease Control and Prevention), Shenyang, China
| | - Gang Guo
- Department of Clinical Laboratory, The Sixth People’s Hospital of Shenyang, Shenyang, China
| | - Qiang Li
- Department of Clinical Laboratory, The Sixth People’s Hospital of Shenyang, Shenyang, China
| | - Minghui An
- 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Bin Zhao
- 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Yang Gao
- 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Wen Tian
- 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
| | - Lin Wang
- 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
- *Correspondence: Hong Shang,
| | - 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
- Chinese Academy of Medical Sciences Research Unit (No. 2019RU017), China Medical University, Shenyang, China
- Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China
- Xiaoxu Han,
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7
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Oluniyi PE, Ajogbasile FV, Zhou S, Fred-Akintunwa I, Polyak CS, Ake JA, Tovanabutra S, Iroezindu M, Rolland M, Happi CT. HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria. AIDS 2022; 36:137-146. [PMID: 34628443 PMCID: PMC8654252 DOI: 10.1097/qad.0000000000003098] [Citation(s) in RCA: 1] [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] [Received: 06/20/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE This study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country. METHODS We used an advanced next-generation sequencing platform, Primer ID, to: investigate the presence of high and low abundance drug resistance mutations; characterize preexisting Integrase Strand Transfer Inhibitor (INSTI) mutations in antiretroviral therapy (ART)-experienced but dolutegravir-naive individuals; detect recent HIV-1 infections and characterize subtype diversity from a cohort of people with HIV-1 (PWH). RESULTS HIV-1 subtype analysis revealed the predominance of CRF02_AG and subtype G in our study population. At detection sensitivity of 30% abundance, drug resistance mutations (DRMs) were identified in 3% of samples. At a sensitivity level of 10%, DRMs were identified in 27.3% of samples. We did not detect any major INSTI mutation associated with dolutegravir-resistance. Only one recent infection was detected in our study population. CONCLUSION Our study suggests that dolutegravir-containing antiretroviral regimens will be effective in Nigeria. Our study also further emphasizes the high genetic diversity of HIV-1 in Nigeria and that CRF02_AG and subtype G are the dominant circulating forms of HIV-1 in Nigeria. These two circulating forms of the virus are largely driving the epidemic in the country.
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Affiliation(s)
- Paul E. Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V. Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christina S. Polyak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Julie A. Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- HJF Medical Research International, Abuja, Nigeria
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Christian T. Happi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
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8
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Kapaata A, Balinda SN, Xu R, Salazar MG, Herard K, Brooks K, Laban K, Hare J, Dilernia D, Kamali A, Ruzagira E, Mukasa F, Gilmour J, Salazar-Gonzalez JF, Yue L, Cotten M, Hunter E, Kaleebu P. HIV-1 Gag-Pol Sequences from Ugandan Early Infections Reveal Sequence Variants Associated with Elevated Replication Capacity. Viruses 2021; 13:v13020171. [PMID: 33498793 PMCID: PMC7912664 DOI: 10.3390/v13020171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 01/05/2023] Open
Abstract
The ability to efficiently establish a new infection is a critical property for human immunodeficiency virus type 1 (HIV-1). Although the envelope protein of the virus plays an essential role in receptor binding and internalization of the infecting virus, the structural proteins, the polymerase and the assembly of new virions may also play a role in establishing and spreading viral infection in a new host. We examined Ugandan viruses from newly infected patients and focused on the contribution of the Gag-Pol genes to replication capacity. A panel of Gag-Pol sequences generated using single genome amplification from incident HIV-1 infections were cloned into a common HIV-1 NL4.3 pol/env backbone and the influence of Gag-Pol changes on replication capacity was monitored. Using a novel protein domain approach, we then documented diversity in the functional protein domains across the Gag-Pol region and identified differences in the Gag-p6 domain that were frequently associated with higher in vitro replication.
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Affiliation(s)
- Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Kimberly Herard
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kelsie Brooks
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kato Laban
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jonathan Hare
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Dario Dilernia
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | | | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Freddie Mukasa
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Ling Yue
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Matthew Cotten
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
- Correspondence: ; Tel.: +25-6701-509-685
| | - Eric Hunter
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
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Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Kirtley S, Gouws-Williams E, Ghys PD. Global and regional epidemiology of HIV-1 recombinants in 1990-2015: a systematic review and global survey. Lancet HIV 2020; 7:e772-e781. [PMID: 33128904 DOI: 10.1016/s2352-3018(20)30252-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Global HIV-1 genetic diversity and evolution form a major challenge to treatment and prevention efforts. An increasing number of distinct HIV-1 recombinants have been identified worldwide, but their contribution to the global epidemic is unknown. We aimed to estimate the global and regional distribution of HIV-1 recombinant forms during 1990-2015. METHODS We assembled a global HIV-1 molecular epidemiology database through a systematic literature review and a global survey. We searched the PubMed, Embase (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) databases for HIV-1 subtyping studies published from Jan 1, 1990, to Dec 31, 2015. Unpublished original HIV-1 subtyping data were collected through a survey among experts in the field who were members of the WHO-UNAIDS Network for HIV Isolation and Characterisation. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. Countries were grouped into 14 regions and analyses were done for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV in each country to generate regional and global estimates of numbers and proportions of HIV-1 recombinants in each time period. The systematic review is registered with PROSPERO, CRD42017067164. FINDINGS Our global data collection yielded an HIV-1 molecular epidemiology database of 383 519 samples from 116 countries in 1990-2015. We found that the proportion of recombinants increased over time, both globally and in most regions, reaching 22·8% (7 978 517 of 34 921 639) of global HIV-1 infections in 2010-15. Both the proportion and the number of distinct CRFs detected increased over time to 16·7% and 57 CRFs in 2010-15. The global and regional distribution of HIV-1 recombinants was diverse and evolved over time, and we found large regional variation in the numbers (0-44 CRFs), types (58 distinct CRFs), and proportions (0-80·5%) of HIV-1 recombinants. Globally, CRF02_AG was the most prevalent recombinant, accounting for 33·9% (2 701 364 of 7 978 517) of all recombinant infections in 2010-15. URFs accounted for 26·7% (2 131 450 of 7 978 517), CRF01_AE for 23·0% (1 838 433), and other CRFs for 16·4% (1 307 270) of all recombinant infections in 2010-15. Although other CRFs accounted for small proportions of infections globally (<1% each), they were prominent in regional epidemics, including in east and southeast Asia, west and central Africa, Middle East and north Africa, and eastern Europe and central Asia. In addition, in 2010-15, central Africa (21·3% [243 041 of 1 143 531]), west Africa (15·5% [838 476 of 5 419 010]), east Africa (12·6% [591 140 of 4 704 986]), and Latin America (9·6% [153 069 of 1 586 605]) had high proportions of URFs. INTERPRETATION HIV-1 recombinants are increasingly prominent in global and regional HIV epidemics, which has important implications for the development of an HIV vaccine and the design of diagnostic, resistance, and viral load assays. Continued and improved surveillance of the global molecular epidemiology of HIV is crucial. FUNDING None.
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Affiliation(s)
- Joris Hemelaar
- Nuffield Department of Population Health, University of Oxford, Oxford, UK; Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK.
| | - Ramyiadarsini Elangovan
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jason Yun
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Leslie Dickson-Tetteh
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Shona Kirtley
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Oxford, UK
| | | | - Peter D Ghys
- Strategic Information Department, UNAIDS, Geneva, Switzerland
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10
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Ogbenna AA, Meloni S, Inzaule S, Hamers RL, Sigaloff K, Osibogun A, Adeyemo TA, Okonkwo P, Samuels JO, Kanki PJ, Rinke de Wit TF, Akanmu AS. The impact of HIV-1 subtypes on virologic and immunologic treatment outcomes at the Lagos University Teaching Hospital: A longitudinal evaluation. PLoS One 2020; 15:e0238027. [PMID: 32841264 PMCID: PMC7447033 DOI: 10.1371/journal.pone.0238027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 08/10/2020] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION HIV is a highly diverse virus with significant genetic variability which may confer biologic differences that could impact on treatment outcomes. MATERIALS AND METHODS We studied the association between HIV subtypes and immunologic and virologic outcomes in a longitudinal cohort of 169 patients on combination antiretroviral therapy. Participants were followed up for 5 years. Demographic data, CD4 cell count and viral loads (VL) were extracted from medical records. Whole protease gene and codon 1-300 of the reverse transcriptase gene were sequenced and analysed. RESULTS Sixty-four percent of participants were females with a median age of 35 years. Twelve different subtypes were observed, the commonest being CRF 02_AG (55.0%) and subtypes G (23.1%). All subtypes showed steady rise in CD4 count and there was no difference in proportion who achieved CD4+ cell count rise of ≥100 cells/μL from baseline within 12 months' post-initiation of ART, or ≥350 cells/μL at 60 months' post-initiation. Median time to attaining a rise of ≥350 cells/μL was 24 months (6-48 months). The proportion that achieved undetectable VL at month 6 and 12 post-initiation of ART were comparable across subtypes. At end of 5th year, there was no statistical difference in proportion with virologic failure. CONCLUSION No association between HIV subtypes and immunologic or virologic response to therapy was observed, suggesting that current first-line ART may have similar efficacy across subtype predominating in South-West Nigeria.
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Affiliation(s)
- Ann Abiola Ogbenna
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Seema Meloni
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Seth Inzaule
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | - Raph L. Hamers
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kim Sigaloff
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, Amsterdam, Netherlands
| | - Akin Osibogun
- Department of Community Health and Primary Care, College of Medicine, Faculty of Clinical Sciences, University of Lagos, Lagos, Nigeria
| | - Titilope Adenike Adeyemo
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | | | - Phyllis J. Kanki
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Tobias F. Rinke de Wit
- Department of Global Health, Amsterdam UMC, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | - Alani Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, Faculty of Clinical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
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Wei H, Yu D, Geng X, He Y. Defective HIV-1 envelope gene promotes the evolution of the infectious strain through recombination in vitro. BMC Infect Dis 2020; 20:569. [PMID: 32753067 PMCID: PMC7401196 DOI: 10.1186/s12879-020-05288-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/26/2020] [Indexed: 11/10/2022] Open
Abstract
Background HIV-1 produces defective mutants in the process of reproduction. The significance of the mutants has not been well investigated. Methods The plasmids of wild type (HIV-1NL4–3) and Env-defective (HIV-1SG3ΔEnv) HIV-1 were co-transfected into HEK293T cells. The progeny virus was collected to infect MT4 cells. The env gene and near-full-length genome (NFLG) of HIV-1 were amplified and sequenced. The phylogenetic diversity, recombinant patterns and hotspots, and the functionality of HIV-1 Env were determined. Results A total of 42 env genes and 8 NFLGs were successfully amplified and sequenced. Five types of recombinant patterns of env were identified and the same recombinant sites were detected in different patterns. The recombination hotspots were found distributing mainly in conservative regions of env. The recombination between genes of HIV-1NL4–3 and HIV-1SG3Δenv increased the variety of viral quasispecies and resulted in progeny viruses with relative lower infectious ability than that of HIVNL4–3. The defective env genes as well as NFLG could be detected after 20 passages. Conclusion The existence of the defective HIV-1 promotes the phylogenetic evolution of the virus, thus increasing the diversity of virus population. The role of defective genes may be converted from junk genes to useful materials and cannot be neglected in the study of HIV-1 reservoir.
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Affiliation(s)
- Huamian Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Danwei Yu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiuzhu Geng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China. .,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
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12
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Obeng BM, Bonney EY, Asamoah-Akuoko L, Nii-Trebi NI, Mawuli G, Abana CZY, Sagoe KWC. Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana. Virol J 2020; 17:114. [PMID: 32709248 PMCID: PMC7378406 DOI: 10.1186/s12985-020-01386-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Background Detection of HIV-1 transmitted drug resistance (TDR) and subtype diversity (SD) are public health strategies to assess current HIV-1 regimen and ensure effective therapeutic outcomes of antiretroviral therapy (ART) among HIV-1 patients. Globally, limited data exist on TDR and SD among blood donors. In this study, drug resistance mutations (DRMs) and SD amongst HIV-1 sero-positive blood donors in Accra, Ghana were characterized. Methods Purposive sampling method was used to collect 81 HIV sero-positive blood samples from the Southern Area Blood Center and confirmed by INNO-LIA as HIV-1 and/or HIV-2. Viral RNA was only extracted from plasma samples confirmed as HIV-1 positive. Complementary DNA (cDNA) was synthesized using the RNA as a template and subsequently amplified by nested PCR with specific primers. The expected products were verified, purified and sequenced. Neighbour-joining tree with the Kimura’s 2-parameter distances was generated with the RT sequences using Molecular Evolutionary Genetic Analysis version 6.0 (MEGA 6.0). Results Out of the 81 plasma samples, 60 (74%) were confirmed as HIV-1 sero-positive by INNO-LIA HIVI/II Score kit with no HIV-2 and dual HIV-1/2 infections. The remaining samples, 21 (26%) were confirmed as HIV sero-negative. Of the 60 confirmed positive samples, (32) 53% and (28) 47% were successfully amplified in the RT and PR genes respectively. Nucleotide sequencing of amplified samples revealed the presence of major drug resistance mutations in two (2) samples; E138A in one sample and another with K65R. HIV-1 Subtypes including subtypes A, B, CRF02_AG and CRF09_cpx were found. Conclusion This study found major drug resistance mutations, E138A and K65R in the RT gene that confer high level resistance to most NNRTIs and NRTI respectively. CRF02_AG was most predominant, the recorded percentage of subtype B and the evolutionary relationship inferred by phylogenetic analysis may suggest possible subtype importation. However, a more prospective and detailed analysis is needed to establish this phenomenon. The data obtained would inform the selection of drugs for ART initiation to maximize therapeutic options in drug-naïve HIV-1 patients in Ghana.
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Affiliation(s)
- Billal Musah Obeng
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana. .,Department of Medical Microbiology, School of Medicine and Dentistry, University of Ghana, Accra, Ghana.
| | - Evelyn Yayra Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana
| | | | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Gifty Mawuli
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana
| | - Christopher Zaab-Yen Abana
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana
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Pre-treatment drug resistance and HIV-1 genetic diversity in the rural and urban settings of Northwest-Cameroon. PLoS One 2020; 15:e0235958. [PMID: 32692778 PMCID: PMC7373288 DOI: 10.1371/journal.pone.0235958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/26/2020] [Indexed: 01/08/2023] Open
Abstract
Background With the scale-up of antiretroviral therapy (ART), pre-treatment drug resistance (PDR) appears ≥10% amongst ART-initiators in many developing countries, including Cameroon. Northwest region-Cameroon having the second epidemiological burden of HIV infection, generating data on PDR in these geographical settings, will enhance evidence-based decision-making. Objectives We sought to ascertain levels of PDR and HIV-1 clade dispersal in rural and urban settings, and their potential association with subtype distribution and CD4-staging. Methods A cross-sectional study was conducted from February to May 2017 among patients recently diagnosed with HIV-infection and initiating ART at the Bamenda regional Hospital (urban setting) and the Mbingo Baptist hospital (rural setting). Protease and reverse transcriptase sequencing was performed using an in-house protocol and pre-treatment drug resistance mutations were interpreted using Stanford HIVdb.v8.3. Phylogeny was performed for subtype assignation. Results A total of 61 patient sequences were generated from ART initiators (median age: 37 years old; 57.4% female; median CD4 cell count: 184 [IQR: 35–387] in urban vs. 161 [IQR: 96–322] cells/mm3 in rural). Overall, the level of PDR was 9.8% (6/61). Of note, burden of PDR was almost doubled in urban (12.9% [4/31]) compared to rural setting 6.7% (2/30), p = 0.352). Fifteen (15) PDR mutations were found among four patients the urban settings [6 resistance mutations to NRTIs:[M41L (2), E44D (1), K65R (1), K70E (1), M184V/I (2), K219R (1)] and 6 resistance mutations to NNRTIs: K103N (1), E138A/G (2), V179E (1), M230L (1), K238T (1), P225H (1)] against two (02) mutations found in two patients in the rural setting[2 resistant mutations to NNRTIs: E138A (1) and Y188H (1)]. The rural setting showed more genetic diversity (8 subtypes) than the urban setting (5 subtypes), with CRF02_AG being the most prevalent clade (72.1% [44/61]). Of note, level of PDR was similar between patients infected with CRF02_AG and non-CRF02_AG infected (9.1% [4/44]) vs. 11.8% [2/17]), p = 1.000). Moreover, PDR appeared higher in patients with CD4 cell count <200 cells/mm3 compared to those with CD4 cell count ≥200 cells/mm3 (14.7% [5/34]) vs. 3.7% [1/27]), p = 0.214). Conclusions PDR is at a moderate rate in the Northwest region of Cameroon, with higher burden within urban populations. CRF02_AG is the most predominant clade in both urban and rural settings. No effect of HIV molecular epidemiology and CD4-staging on the presence of PDR in patients living in these settings was found. Our findings suggest close monitoring, NNRTI-sparing regimens or sequencing for patients initiating ART, especially in urban settings.
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14
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Epigenetics, N-myrystoyltransferase-1 and casein kinase-2-alpha modulates the increased replication of HIV-1 CRF02_AG, compared to subtype-B viruses. Sci Rep 2019; 9:10689. [PMID: 31337802 PMCID: PMC6650493 DOI: 10.1038/s41598-019-47069-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/05/2019] [Indexed: 02/04/2023] Open
Abstract
HIV subtypes distribution varies by geographic regions; this is likely associated with differences in viral fitness but the predictors and underlying mechanisms are unknown. Using in-vitro, in-vivo, and ex-vivo approaches, we found significantly higher transactivation and replication of HIV-1-CRF02_AG (prevalent throughout West-Central Africa), compared to subtype-B. While CRF02_AG-infected animals showed higher viremia, subtype-B-infected animals showed significantly more weight loss, lower CD4+ T-cells and lower CD4/CD8 ratios, suggesting that factors other than viremia contribute to immunosuppression and wasting syndrome in HIV/AIDS. Compared to HIV-1-subtype-B and its Tat proteins(Tat.B), HIV-1-CRF02_AG and Tat.AG significantly increased histone acetyl-transferase activity and promoter histones H3 and H4 acetylation. Silencing N-myrystoyltransferase(NMT)-1 and casein-kinase-(CK)-II-alpha prevented Tat.AG- and HIV-1-CRF02_AG-mediated viral transactivation and replication, but not Tat.B- or HIV-1-subtype-B-mediated effects. Tat.AG and HIV-1-CRF02_AG induced the expression of NMT-1 and CKII-alpha in human monocytes and macrophages, but Tat.B and HIV-1-subtype-B had no effect. These data demonstrate that NMT1, CKII-alpha, histone acetylation and histone acetyl-transferase modulate the increased replication of HIV-1-CRF02_AG. These novel findings demonstrate that HIV genotype influence viral replication and provide insights into the molecular mechanisms of differential HIV-1 replication. These studies underline the importance of considering the influence of viral genotypes in HIV/AIDS epidemiology, replication, and eradication strategies.
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Kostaki EG, Karamitros T, Bobkova M, Oikonomopoulou M, Magiorkinis G, Garcia F, Hatzakis A, Paraskevis D. Spatiotemporal Characteristics of the HIV-1 CRF02_AG/CRF63_02A1 Epidemic in Russia and Central Asia. AIDS Res Hum Retroviruses 2018; 34:415-420. [PMID: 29455562 DOI: 10.1089/aid.2017.0233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eastern European countries, including Russia, Ukraine, and other former Soviet Union (FSU) countries, have experienced a human immunodeficiency virus (HIV) epidemic spreading mostly among people who inject drugs (PWID). We aimed to investigate the origin and the dispersal patterns of HIV-1 CRF02_AG in Russia and other FSU countries. We studied 136 CRF02_AG sequences originating from Russia, and FSU countries along with a globally sampled dataset of 3,580 CRF02_AG sequences. Maximum-likelihood phylogeny reconstruction with bootstrap evaluation was conducted in RAxML. Bayesian phylogeographic analysis was performed in BEAST v1.8 using the discrete trait model. We found that all CRF02_AG sequences from Russia and other FSU countries formed a single monophyletic cluster within CRF02_AG radiation. The Russian/FSU clade was classified as CRF63_02A1. Sequences from the FSU countries clustered further within distinct subclades (two from Russia, three from Uzbekistan, and one Kazakhstan) according to the geographic origin of sampling. Molecular clock analysis revealed that the time to the most recent common ancestor (tMRCA) of the CRF63_02A1 epidemic was in 1996 [95% higher posterior density (95% HPD): 1992-1999], while for the two Russian subclades, tMRCA was estimated in 2003 (95% HPD: 2001-2004) and in 2007 (95% HPD: 2005-2008). Phylogeographic analysis suggested that the potential origin of the epidemic was in Uzbekistan. Early dispersal of CRF63_02A1 occurred in Kazakhstan and Uzbekistan and thereafter the epidemic spread to Russia. Notably, spillover transmissions to Russia kept occurring from both countries. Previous studies have shown that Russia and Ukraine have provided the source for the PWID-driven, HIV-1 subtype-A epidemic, spreading across the FSU countries (AFSU). In great contrast, CRF63_02A1 established an epidemic in central Asia (Uzbekistan and Kazakhstan), from where it subsequently disseminated to Russia. Our study suggests that cross-border transmissions among PWID occur bidirectionally between Russian and other FSU populations. These results are of public health importance and suggest that prevention actions have to be reinforced in this area to assist the management of high-risk practices.
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Affiliation(s)
- Evangelia-Georgia Kostaki
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | | | - Marina Bobkova
- 3 Ivanovsky Institute of Virology , FSBI "N.F. Gamaleya FRCEM" of the Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Martha Oikonomopoulou
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | - Gkikas Magiorkinis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
- 2 Department of Zoology, University of Oxford , Oxford, United Kingdom
| | - Federico Garcia
- 4 Servicio de Microbiología, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada, Cohorte de Adultos de la Red de Investigación en SIDA-CoRIS, Instituto de Investigación Ibs , Granada, Granada (Andalucía), Spain
| | - Angelos Hatzakis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | - Dimitrios Paraskevis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
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Jumare J, Ndembi N, El-Kamary SS, Magder L, Hungerford L, Burdo T, Eyzaguirre LM, Dakum P, Umlauf A, Cherner M, Abimiku A, Charurat M, Blattner WA, Royal W. Cognitive Function Among Antiretroviral Treatment-Naive Individuals Infected With Human Immunodeficiency Virus Type 1 Subtype G Versus CRF02_AG in Nigeria. Clin Infect Dis 2018; 66:1448-1453. [PMID: 29182762 PMCID: PMC5905588 DOI: 10.1093/cid/cix1019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022] Open
Abstract
Background Human immunodeficiency virus type 1 (HIV-1) subtype has been shown to be associated with disease progression. We compared cognitive function between individuals infected with HIV-1 subtype G and CRF02_AG in Nigeria. Methods For this cross-sectional study, samples were analyzed from 146 antiretroviral-naive participants. Genotypic analysis of plasma HIV RNA was performed by nested polymerase chain reaction of protease and reverse transcriptase genes, and sequences were aligned with curated HIV-1 subtype references. Cognitive status was determined using demographically adjusted T scores and global deficit score (GDS) obtained from a comprehensive neuropsychological test battery. Results A total of 76 (52.1%) participants were infected with CRF02_AG, 48 (32.8%) with subtype G, and 22 (15.1%) with other HIV-1 strains. In a multivariable linear regression adjusting for plasma HIV RNA, CD4 count, and depression score, mean global T score was lower among subtype G-infected compared with CRF02_AG-infected participants (mean difference, -3.0 [95% confidence interval {CI}, -5.2, to -.7]; P = .011). Also, T scores were significantly lower among subtype G- than CRF02_AG-infected participants for the speed of information processing, executive function, and verbal fluency ability domains. Adjusting for similar variables in a logistic regression, the odds of global cognitive impairment (GDS ≥0.5) were 2.2 times higher among subtype G compared with CRF02_AG-infected participants (odds ratio, 2.2 [95% CI, .9-5.4]; P = .078). Conclusions Cognitive performance was significantly worse among antiretroviral-naive individuals with HIV-1 subtype G vs CRF02_AG infection. Further studies are required to characterize the mechanistic basis for these differences.
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Affiliation(s)
| | | | | | | | | | - Tricia Burdo
- School of Medicine, Temple University, Philadelphia, Pennsylvania
| | | | - Patrick Dakum
- School of Medicine, University of Maryland, Baltimore
| | - Anya Umlauf
- School of Medicine, University of California, San Diego
| | | | | | - Man Charurat
- School of Medicine, University of Maryland, Baltimore
| | | | - Walter Royal
- School of Medicine, University of Maryland, Baltimore
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17
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Villabona Arenas CJ, Vidal N, Ahuka Mundeke S, Muwonga J, Serrano L, Muyembe JJ, Boillot F, Delaporte E, Peeters M. Divergent HIV-1 strains (CRF92_C2U and CRF93_cpx) co-circulating in the Democratic Republic of the Congo: Phylogenetic insights on the early evolutionary history of subtype C. Virus Evol 2017; 3:vex032. [PMID: 29250430 PMCID: PMC5724398 DOI: 10.1093/ve/vex032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular epidemiological studies revealed that the epicenter of the HIV pandemic was Kinshasa, the capital city of the Democratic Republic of the Congo (DRC) in Central Africa. All known subtypes and numerous complex recombinant strains co-circulate in the DRC. Moreover, high intra-subtype diversity has been also documented. During two previous surveys on HIV-1 antiretroviral drug resistance in the DRC, we identified two divergent subtype C lineages in the protease and partial reverse transcriptase gene regions. We sequenced eight near full-length genomes and classified them using bootscanning and likelihood-based phylogenetic analyses. Four strains are more closely related to subtype C although within the range of inter sub-subtype distances. However, these strains also have small unclassified fragments and thus were named CRF92_C2U. Another strain is a unique recombinant of CRF92_C2U with an additional small unclassified fragment and a small divergent subtype A fragment. The three remaining strains represent a complex mosaic named CRF93_cpx. CRF93_cpx have two fragments of divergent subtype C sequences, which are not conventional subtype C nor the above described C2, and multiple divergent subtype A-like fragments. We then inferred the time-scaled evolutionary history of subtype C following a Bayesian approach and a partitioned analysis using major genomic regions. CRF92_C2U and CRF93_cpx had the most recent common ancestor with conventional subtype C around 1932 and 1928, respectively. A Bayesian demographic reconstruction corroborated that the subtype C transition to a faster phase of exponential growth occurred during the 1950s. Our analysis showed considerable differences between the newly discovered early-divergent strains and the conventional subtype C and therefore suggested that this virus has been diverging in humans for several decades before the HIV/M diversity boom in the 1950s.
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Affiliation(s)
- C J Villabona Arenas
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - N Vidal
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - S Ahuka Mundeke
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France.,Institut National de Recherche Biomédicale, Av. De la Démocratie 5345, Kinshasa, Democratic Republic of the Congo.,Cliniques Universitaires de Kinshasa, Route de Kimwenza, Kinshasa, Congo, Democratic Republic of Congo
| | - J Muwonga
- Cliniques Universitaires de Kinshasa, Route de Kimwenza, Kinshasa, Congo, Democratic Republic of Congo.,Laboratoire National de Référence du SIDA, Kinshasa, Democratic Republic of Congo
| | - L Serrano
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - J J Muyembe
- Institut National de Recherche Biomédicale, Av. De la Démocratie 5345, Kinshasa, Democratic Republic of the Congo.,Cliniques Universitaires de Kinshasa, Route de Kimwenza, Kinshasa, Congo, Democratic Republic of Congo
| | - F Boillot
- Alter-Santé Internationale and Développement, Montpellier, 34090, France
| | - E Delaporte
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
| | - M Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, Université de Montpellier, 911 Avenue Agropolis, Montpellier, 34394, France
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18
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Joshi A, Cox EK, Sedano MJ, Punke EB, Lee RT, Maurer-Stroh S, Kaur P, Ng OT, Garg H. HIV-1 subtype CRF01_AE and B differ in utilization of low levels of CCR5, Maraviroc susceptibility and potential N-glycosylation sites. Virology 2017; 512:222-233. [PMID: 29020646 DOI: 10.1016/j.virol.2017.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/18/2017] [Accepted: 09/30/2017] [Indexed: 10/18/2022]
Abstract
HIV subtypes not only predominate in different geographical regions but also differ in key phenotypic characteristics. To determine if genotypic and/or phenotypic differences in the Envelope (Env) glycoprotein can explain subtype related differences, we cloned 37 full length Envs from Subtype B and AE HIV infected individuals from Singapore. Our data demonstrates that CRF01_AE Envs have lower Potential N Glycosylation Sites and higher risk of ×4 development. Phenotypically, CRF01_AE were less infectious than subtype B Envs in cells expressing low levels of CCR5. Moreover, the Maraviroc IC50 was higher for subtype B Envs and correlated with infectivity in low CCR5 expressing cells as well as PNGS. Specifically, the glycosylation site N301 in the V3 loop was seen less frequently in AE subtype and CXCR4 topic viruses. CRF01_AE differs from B subtype in terms of CCR5 usage and Maraviroc susceptibility which may have implications for HIV pathogenesis and virus evolution.
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Affiliation(s)
- Anjali Joshi
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX, USA.
| | - Emily K Cox
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Melina J Sedano
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Erin B Punke
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Raphael Tc Lee
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Palvinder Kaur
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore
| | - Oon Tek Ng
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore
| | - Himanshu Garg
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX, USA.
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19
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Sallam M, Şahin GÖ, Ingman M, Widell A, Esbjörnsson J, Medstrand P. Genetic characterization of human immunodeficiency virus type 1 transmission in the Middle East and North Africa. Heliyon 2017; 3:e00352. [PMID: 28725873 PMCID: PMC5506879 DOI: 10.1016/j.heliyon.2017.e00352] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA. METHODS A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988-2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences. The REGA and COMET tools were used to determine HIV-1 subtypes and circulating recombinant forms. Maximum Likelihood and Bayesian phylogenetic analyses were used to identify and date HIV-1 transmission clusters. RESULTS At least 21 HIV-1 subtypes and recombinant forms were prevalent in the MENA. Subtype B was the most common variant (39%), followed by CRF35_AD (19%) and CRF02_AG (14%). The most common genetic region was pol, and 675 partial pol sequences (average of 1005 bp) were eligible for detailed phylogenetic analysis. Fifty-four percent of the MENA sequences formed HIV-1 transmission clusters. Whereas numerous clusters were country-specific, some clusters indicated transmission links between countries for subtypes B, C and CRF02_AG. This was more common in North Africa compared with the Middle East (p < 0.001). Recombinant forms had a larger proportion of clustering compared to pure subtypes (p < 0.001). The largest MENA clusters dated back to 1991 (an Algerian CRF06_cpx cluster of 43 sequences) and 2002 (a Tunisian CRF02_AG cluster of 48 sequences). CONCLUSIONS We found an extensive HIV-1 diversity in the MENA and a high proportion of sequences in transmission clusters. This study highlights the need for preventive measures in the MENA to limit HIV-1 spread in this region.
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Affiliation(s)
- Malik Sallam
- Lund University, Faculty of Medicine, Department of Translational Medicine, Malmö, Sweden
| | - Gülşen Özkaya Şahin
- Lund University, Faculty of Medicine, Department of Translational Medicine, Malmö, Sweden
- Laboratory Medicine Skåne, Lund, Sweden
| | - Mikael Ingman
- Lund University, Faculty of Medicine, Department of Translational Medicine, Malmö, Sweden
| | - Anders Widell
- Lund University, Faculty of Medicine, Department of Translational Medicine, Malmö, Sweden
| | - Joakim Esbjörnsson
- Lund University, Faculty of Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Patrik Medstrand
- Lund University, Faculty of Medicine, Department of Translational Medicine, Malmö, Sweden
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20
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Sun Y, Qiao Y, Zhu Y, Chong H, He Y. Identification of a novel HIV-1-neutralizing antibody from a CRF07_BC-infected Chinese donor. Oncotarget 2017; 8:63047-63063. [PMID: 28968970 PMCID: PMC5609902 DOI: 10.18632/oncotarget.18594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 05/29/2017] [Indexed: 01/11/2023] Open
Abstract
The identification of human monoclonal antibodies (mAbs) able to neutralize a broad spectrum of primary HIV-1 isolates is highly important for understanding the immune response of HIV-1 infection and developing vaccines and therapeutics. In this study, we isolated a novel human mAb termed Y498 from a phage display antibody library constructed with the PBMC samples of a CRF07_BC-infected Chinese donor whose sera exhibited broadly neutralizing activity. Y498 cross-reacted with diverse Env antigens and neutralized 30% of 70 tested HIV-1 isolates. It efficiently blocked the binding of soluble CD4 to gp120 and competed with the CD4-binding site (CD4bs)-specific mAbs. By combining molecular docking and site-directed mutagenesis, the epitope of Y498 was characterized to contain three antigenic sites on gp120, including the CD4 binding loop in C3, the β23 in C4 and the β24-α5 in C5, which overlap the binding sites of CD4 and CD4bs-directed mAbs (b12, VRC01, A16). Therefore, Y498 is a novel neutralizing human mAb targeting a conformation-dependent CD4bs-based epitope, and its isolation and characterization could provide helpful information for elucidating human immune response to HIV-1 infection and designing effective vaccines and immunotherapeutics.
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Affiliation(s)
- Youxiang Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuanyuan Qiao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuanmei Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huihui Chong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuxian He
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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21
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Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression. J Virol 2017; 91:JVI.00253-17. [PMID: 28424286 DOI: 10.1128/jvi.00253-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/30/2017] [Indexed: 11/20/2022] Open
Abstract
There are marked differences in the spread and prevalence of HIV-1 subtypes worldwide, and differences in clinical progression have been reported. However, the biological reasons underlying these differences are unknown. Gag-protease is essential for HIV-1 replication, and Gag-protease-driven replication capacity has previously been correlated with disease progression. We show that Gag-protease replication capacity correlates significantly with that of whole isolates (r = 0.51; P = 0.04), indicating that Gag-protease is a significant contributor to viral replication capacity. Furthermore, we investigated subtype-specific differences in Gag-protease-driven replication capacity using large well-characterized cohorts in Africa and the Americas. Patient-derived Gag-protease sequences were inserted into an HIV-1 NL4-3 backbone, and the replication capacities of the resulting recombinant viruses were measured in an HIV-1-inducible reporter T cell line by flow cytometry. Recombinant viruses expressing subtype C Gag-proteases exhibited substantially lower replication capacities than those expressing subtype B Gag-proteases (P < 0.0001); this observation remained consistent when representative Gag-protease sequences were engineered into an HIV-1 subtype C backbone. We identified Gag residues 483 and 484, located within the Alix-binding motif involved in virus budding, as major contributors to subtype-specific replicative differences. In East African cohorts, we observed a hierarchy of Gag-protease-driven replication capacities, i.e., subtypes A/C < D < intersubtype recombinants (P < 0.0029), which is consistent with reported intersubtype differences in disease progression. We thus hypothesize that the lower Gag-protease-driven replication capacity of subtypes A and C slows disease progression in individuals infected with these subtypes, which in turn leads to greater opportunity for transmission and thus increased prevalence of these subtypes.IMPORTANCE HIV-1 subtypes are unevenly distributed globally, and there are reported differences in their rates of disease progression and epidemic spread. The biological determinants underlying these differences have not been fully elucidated. Here, we show that HIV-1 Gag-protease-driven replication capacity correlates with the replication capacity of whole virus isolates. We further show that subtype B displays a significantly higher Gag-protease-mediated replication capacity than does subtype C, and we identify a major genetic determinant of these differences. Moreover, in two independent East African cohorts we demonstrate a reproducible hierarchy of Gag-protease-driven replicative capacity, whereby recombinants exhibit the greatest replication, followed by subtype D, followed by subtypes A and C. Our data identify Gag-protease as a major determinant of subtype differences in disease progression among HIV-1 subtypes; furthermore, we propose that the poorer viral replicative capacity of subtypes A and C may paradoxically contribute to their more efficient spread in sub-Saharan Africa.
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22
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Jackson PE, Tebit DM, Rekosh D, Hammarskjold ML. Rev-RRE Functional Activity Differs Substantially Among Primary HIV-1 Isolates. AIDS Res Hum Retroviruses 2016; 32:923-34. [PMID: 27147495 DOI: 10.1089/aid.2016.0047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The HIV-1 replication cycle requires the nucleocytoplasmic export of intron-containing viral RNAs, a process that is ordinarily restricted. HIV overcomes this by means of the viral Rev protein, which binds to an RNA secondary structure called the Rev response element (RRE) present in all unspliced or incompletely spliced viral RNA transcripts. The resulting mRNP complex is exported through interaction with cellular factors. The Rev-RRE binding interaction is increasingly understood to display remarkable structural plasticity, but little is known about how Rev-RRE sequence differences affect functional activity. To study this issue, we utilized a lentiviral vector assay in which vector titer is dependent on the activity of selected Rev-RRE pairs. We found that Rev-RRE functional activity varies significantly (up to 24-fold) between naturally occurring viral isolates. The activity differences of the Rev-RRE cognate pairs track closely with Rev, but not with RRE activity. This variation in Rev activity is not correlated with differences in Rev steady state protein levels. These data suggest that Rev sequence differences drive substantial variation in Rev-RRE functional activity between patients. Such variation may play a role in viral adaptation to different immune milieus within and between patients and may be significant in the establishment of latency. The identification of differences in Rev-RRE functional activity in naturally occurring isolates may also permit more efficient production of lentiviral vectors.
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Affiliation(s)
- Patrick E. Jackson
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - Denis M. Tebit
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - David Rekosh
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
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23
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Gasser R, Hamoudi M, Pellicciotta M, Zhou Z, Visdeloup C, Colin P, Braibant M, Lagane B, Negroni M. Buffering deleterious polymorphisms in highly constrained parts of HIV-1 envelope by flexible regions. Retrovirology 2016; 13:50. [PMID: 27473399 PMCID: PMC4967302 DOI: 10.1186/s12977-016-0285-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023] Open
Abstract
Background Covariation is an essential process that leads to coevolution of parts of proteins and genomes. In organisms subject to strong selective pressure, coevolution is central to keep the balance between the opposite requirements of antigenic variation and retention of functionality. Being the viral component most exposed to the external environment, the HIV-1 glycoprotein gp120 constitutes the main target of the immune response. Accordingly its more external portions are characterised by extensive sequence heterogeneity fostering constant antigenic variation. Results We report that a single polymorphism, present at the level of the viral population in the conserved internal region C2, was sufficient to totally abolish Env functionality when introduced in an exogenous genetic context. The prominent defect of the non-functional protein is a block occurring after recognition of the co-receptor CCR5, likely due to an interference with the subsequent conformational changes that lead to membrane fusion. We also report that the presence of compensatory polymorphisms at the level of the external and hypervariable region V3 fully restored the functionality of the protein. The functional revertant presents different antigenic profiles and sensitivity to the entry inhibitor TAK 779. Conclusions Our data suggest that variable regions, besides harbouring intrinsic extensive antigenic diversity, can also contribute to sequence diversification in more structurally constrained parts of the gp120 by buffering the deleterious effect of polymorphisms, further increasing the genetic flexibility of the protein and the antigenic repertoire of the viral population.
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Affiliation(s)
- Romain Gasser
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France
| | - Meriem Hamoudi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France.,U1016, UMR 8104, INSERM-CNRS, Institut Cochin, Université Paris Descartes, Paris, France
| | - Martina Pellicciotta
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France
| | - Zhicheng Zhou
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
| | | | - Philippe Colin
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
| | | | - Bernard Lagane
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Matteo Negroni
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France.
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24
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Fernandes-Cardoso J, Süffert TA, Correa MDG, Jobim LFJ, Jobim M, Salim PH, Arruda MB, Boullosa LT, Tanuri A, Porto LC, Ferreira OC. Association between KIR genotypes and HLA-B alleles on viral load in Southern Brazilian individuals infected by HIV-1 subtypes B and C. Hum Immunol 2016; 77:854-860. [PMID: 27346697 DOI: 10.1016/j.humimm.2016.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 11/15/2022]
Abstract
There is a great variety of HIV-1 subtypes circulating in Brazil, including subtype C, whose prevalence is on the rise, particularly in the southern region. Many host and viral genetic factors may be involved in this trend. We evaluated the influence of human leukocyte antigen (HLA) class I alleles and killer-cell immunoglobulin-like receptor (KIR) genotypes on viral set point and T-CD4(+) parameters in 84 treatment-naïve HIV-1-positive individuals. Frequency data in the infected group were compared to data of 548 healthy control subjects. Individuals with the KIR AA genotype had a higher viral load (VL) than individuals with the KIR Bx genotype. The HIV-1 group was subdivided into three subgroups according to HLA-B allele presence: those with protection to disease alleles (HLA-B(+)), accelerated disease progression alleles (HLA-B(-)), or neither (HLA-B(o)) were grouped. We observed a significant effect of the HLA-B allele presence on VL. The HLA-B(+) group had significantly lower VL than the HLA-B(-) group and trended toward a lower VL than the HLA-B(o) group. There were significant differences between groups expressing extreme VL values: KIR-AA+HLA-B(-) vs. KIR Bx+HLA-B(+) and KIR-AA+HLA-B(o)vs. KIR Bx+HLA-B(+). The relationship of KIR/HLA host genetics with slow HIV disease progression in southern Brazil may be useful for vaccine developers, epidemiologists, and clinicians.
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Affiliation(s)
- Juliana Fernandes-Cardoso
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Theodoro Armando Süffert
- Serviço de Assistência Especializada em DST/AIDS, Prefeitura Municipal de Porto Alegre, Porto Alegre, Brazil
| | - Maria da Gloria Correa
- Serviço de Assistência Especializada em DST/AIDS, Prefeitura Municipal de Porto Alegre, Porto Alegre, Brazil
| | | | - Mariana Jobim
- Departamento de Imunologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | - Monica Barcelos Arruda
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lidia Theodoro Boullosa
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Cristóvão Porto
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando C Ferreira
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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25
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Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, Liitsola K, Björkman P, Bratt G, Gisslén M, Sönnerborg A, Nielsen C, Medstrand P, Albert J. HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries. Virus Evol 2016; 2:vew010. [PMID: 27774303 PMCID: PMC4989887 DOI: 10.1093/ve/vew010] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics. Analysis of the eight dominating subtypes and CRFs in the Nordic countries (A, B, C, D, G, CRF01_AE, CRF02_AG, and CRF06_cpx) showed that the subtype B proportion decreased while the CRF proportion increased over the study period. A majority (57 per cent) of the Nordic sequences formed transmission clusters, with evidence of mixing both geographically and between transmission groups. Detailed analyses showed multiple occasions of transmissions from MSM to heterosexuals and that active transmission clusters more often involved single than multiple Nordic countries. The strongest geographical link was between Denmark and Sweden. Finally, Denmark had a larger proportion of heterosexual domestic spread of HIV-1 subtype B (75 per cent) compared with Sweden (49 per cent) and Finland (57 per cent). We describe different HIV-1 transmission patterns between countries and transmission groups in a large geographical region. Our results may have implications for public health interventions in targeting HIV-1 transmission networks and identifying where to introduce such interventions.
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Affiliation(s)
- Joakim Esbjörnsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
| | - Mattias Mild
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Anne Audelin
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Helena Skar
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
| | - Louise Bruun Jørgensen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Per Björkman
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Göran Bratt
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Claus Nielsen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - SPREAD/ESAR Programme
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Jan Albert
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Abstract
PURPOSE OF REVIEW An improved understanding of how recombination affects the evolutionary history of HIV is crucial to understand its current and future evolution. The present review aims to disentangle the manifold effects of recombination on HIV by discussing its effects on the evolutionary history and the adaptive potential of HIV in the context of concepts from evolutionary genetics and genomics. RECENT FINDINGS The increasing occurrence of secondary contacts between divergent subtype populations (during coinfection) results in increased observations of recombinants worldwide. Recombination is heterogeneous along the HIV genome. Consequences of recombination of HIV evolution are, in combination with other demographic processes, expected to either homogenize the genetic composition of HIV populations (homogenization) or provide the potential for novel adaptations (diversification). New methods in population genomics allow deep characterization of recombinant genome (the segment composition and origin) and their evolutionary trajectories. SUMMARY HIV recombinants increase worldwide and invade geographical regions where pure subtypes were previously predominant. This trend is expected to continue in the future, as ease to travel worldwide increases opportunities for recombination between divergent HIV strains. While the effects of recombination in HIV are much researched, more effort is required to characterize current HIV recombinant composition and dynamics. This can be achieved with new population genetic and genomic methods.
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Tongo M, Dorfman JR, Abrahams MR, Mpoudi-Ngole E, Burgers WA, Martin DP. Near full-length HIV type 1M genomic sequences from Cameroon : Evidence of early diverging under-sampled lineages in the country. EVOLUTION MEDICINE AND PUBLIC HEALTH 2015; 2015:254-65. [PMID: 26354000 PMCID: PMC4600344 DOI: 10.1093/emph/eov022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/25/2015] [Indexed: 12/30/2022]
Abstract
Background: Cameroon is the country in which HIV-1 group M (HIV-1M) likely originated and is today a major hotspot of HIV-1M genetic diversity. It remains unclear, however, whether the highly divergent HIV-1M lineages found in this country arose during the earliest phases of the global HIV-1M epidemic, or whether they arose more recently as a result of recombination events between globally circulating HIV-1M lineages. Methodology: To differentiate between these two possibilities, we performed phylogenetic analyses of the near full genome sequences of nine newly sequenced divergent HIV-1M isolates and 15 previously identified, apparently unique recombinant forms (URFs) from Cameroon. Results: Although two of the new genome sequences were clearly classifiable within subtype G, the remaining seven were highly divergent and phylogenetically branched either outside of, or very near the bases of clades containing the well characterised globally circulating viral lineages that they were most closely related to. Recombination analyses further revealed that these divergent viruses were likely complex URFs. We show, however that substantial portions (>1 Kb) of three of the new genome sequences and 15 of the previously characterised Cameroonian URFs have apparently been derived from divergent parental viruses that branch phylogenetically near the bases of the major HIV-1M clades. Conclusions and implications: Our analyses indicate the presence in Cameroon of contemporary descendants of numerous early-diverging HIV-1M lineages. Further efforts to sample and sequence viruses from such lineages could be crucial both for retracing the earliest evolutionary steps during the emergence of HIV-1M in humans, and accurately reconstructing the ancestral sequences of the major globally circulating HIV-1M lineages.
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Affiliation(s)
- Marcel Tongo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology and Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon
| | - Jeffrey R Dorfman
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Eitel Mpoudi-Ngole
- Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon
| | | | - 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; and
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Chang CH, Kist NC, Stuart Chester TL, Sreenu VB, Herman M, Luo M, Lunn D, Bell J, Plummer FA, Ball TB, Katzourakis A, Iversen AKN. HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression. Sci Rep 2015; 5:11253. [PMID: 26082240 PMCID: PMC4469978 DOI: 10.1038/srep11253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/11/2015] [Indexed: 11/15/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL) responses against the HIV Gag protein are associated with lowering viremia; however, immune control is undermined by viral escape mutations. The rapid viral mutation rate is a key factor, but recombination may also contribute. We hypothesized that CTL responses drive the outgrowth of unique intra-patient HIV-recombinants (URFs) and examined gag sequences from a Kenyan sex worker cohort. We determined whether patients with HLA variants associated with effective CTL responses (beneficial HLA variants) were more likely to carry URFs and, if so, examined whether they progressed more rapidly than patients with beneficial HLA-variants who did not carry URFs. Women with beneficial HLA-variants (12/52) were more likely to carry URFs than those without beneficial HLA variants (3/61) (p < 0.0055; odds ratio = 5.7). Beneficial HLA variants were primarily found in slow/standard progressors in the URF group, whereas they predominated in long-term non-progressors/survivors in the remaining cohort (p = 0.0377). The URFs may sometimes spread and become circulating recombinant forms (CRFs) of HIV and local CRF fragments were over-represented in the URF sequences (p < 0.0001). Collectively, our results suggest that CTL-responses associated with beneficial HLA variants likely drive the outgrowth of URFs that might reduce the positive effect of these CTL responses on disease progression.
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Affiliation(s)
- Chih-Hao Chang
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicolaas C Kist
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Tammy L Stuart Chester
- National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada
| | - Vattipally B Sreenu
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Melissa Herman
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Ma Luo
- 1] National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada [2] Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel Lunn
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - John Bell
- Office of the Regius Professor of Medicine, The Richard Doll Building, University of Oxford, Oxford, United Kingdom
| | - Francis A Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - T Blake Ball
- 1] National HIV and Retrovirology Laboratories, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada [2] Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada [3] Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Astrid K N Iversen
- 1] Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom [2] Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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Turk G, Carobene MG. Deciphering How HIV-1 Intersubtype Recombination Shapes Viral Fitness and Disease Progression. EBioMedicine 2015; 2:188-9. [PMID: 26137559 PMCID: PMC4484815 DOI: 10.1016/j.ebiom.2015.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 02/16/2015] [Accepted: 02/16/2015] [Indexed: 01/30/2023] Open
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Yao Y, Xin R, Yang J, Xu Y, Zhang J, Xia Y, Pan X, Guo Z, Song Y. Trends of subtype variation of human immunodeficiency virus type 1 in Zhejiang Province, China. Virus Genes 2014; 50:22-8. [PMID: 25410050 DOI: 10.1007/s11262-014-1136-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
Abstract
The epidemic characteristics of human immunodeficiency virus type 1 (HIV-1) in Zhejiang Province have not been systematically identified. This study presented a dynamic analysis of HIV-1 subtype variation in Zhejiang from 2004 to 2008, based on the surveillance of molecular epidemiology or drug resistance. CRF01_AE was the major strain (43.5 %) spreading across the province, second by B/B' (17.9 %), CRF07_BC (17.1 %), and CRF08_BC (13.7 %). The strains were mainly transmitted by heterosexual contact. Novel recombinant strains and vertical transmission were occasionally reported. Floating population from other provinces accounted for a significant number of HIV-1 cases in Zhejiang. These data may provide us rational intervention strategy for further control of HIV dissemination.
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Affiliation(s)
- Yaping Yao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
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Boullosa J, Bachu M, Bila D, Ranga U, Süffert T, Sasazawa T, Tanuri A. Genetic diversity in HIV-1 subtype C LTR from Brazil and Mozambique generates new transcription factor-binding sites. Viruses 2014; 6:2495-504. [PMID: 24960272 PMCID: PMC4074939 DOI: 10.3390/v6062495] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/12/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022] Open
Abstract
The HIV-1 subtype C has been substituting the subtype B population in southern Brazil. This phenomenon has been previously described in other countries, suggesting that subtype C may possess greater fitness than other subtypes. The HIV-1 long-terminal repeat (LTR) is an important regulatory region critical for the viral life cycle. Sequence insertions immediately upstream of the viral enhancer are known as the most frequent naturally occurring length polimorphisms (MFNLP). Previous reports demonstrated that the MFNLP could lead to the duplication of transcription factor binding sites (TFBS) enhancing the activity of the HIV-1 subtype C LTR. Here, we amplified and sequenced the LTR obtained from proviral DNA samples collected from patients infected with subtype C from the Southern Region of Brazil (naïve or treatment failure) and Mozambique (only naïve). We confirm the presence of different types of insertions in the LTR sequences of both the countries leading to the creation of additional TFBS. In the Brazilian clinical samples, the frequency of the sequence insertion was significantly higher in subjects experiencing treatment failure than in antiretroviral naïve patients.
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Affiliation(s)
- José Boullosa
- Department of Genetics, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373. Edifício do Centro de Ciências da Saúde, Bloco A, sala A2-121, Cidade Universitária, Cep: 21.941-902, Brazil.
| | - Mahesh Bachu
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560 064, Jakkur Post, Bangalore, India.
| | - Dulce Bila
- Department of Genetics, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373. Edifício do Centro de Ciências da Saúde, Bloco A, sala A2-121, Cidade Universitária, Cep: 21.941-902, Brazil.
| | - Udaykumar Ranga
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560 064, Jakkur Post, Bangalore, India.
| | - Theodoro Süffert
- Prefeitura Municipal de Porto Alegre, Rio Grande do Sul, 90010-170, Brazil.
| | - Tomoko Sasazawa
- Prefeitura Municipal de Curitiba, Paraná, 80000-000, Brazil.
| | - Amilcar Tanuri
- Department of Genetics, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373. Edifício do Centro de Ciências da Saúde, Bloco A, sala A2-121, Cidade Universitária, Cep: 21.941-902, Brazil.
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Rubio AE, Abraha A, Carpenter CA, Troyer RM, Reyes-Rodríguez ÁL, Salomon H, Arts EJ, Tebit DM. Similar replicative fitness is shared by the subtype B and unique BF recombinant HIV-1 isolates that dominate the epidemic in Argentina. PLoS One 2014; 9:e92084. [PMID: 24727861 PMCID: PMC3984079 DOI: 10.1371/journal.pone.0092084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/18/2014] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 epidemic in South America is dominated by pure subtypes (mostly B and C) and more than 7 BF and BC recombinant forms. In Argentina, circulating recombinant forms (CRFs) comprised of subtypes B and F make up more than 50% of HIV infections. For this study, 28 HIV-1 primary isolates were obtained from patients in Buenos Aires, Argentina and initially classified into subtype B (n = 9, 32.1%), C (n = 1, 3.6%), and CRFs (n = 18, 64.3%) using partial pol and vpu-env sequences, which proved to be inconsistent and inaccurate for these phylogenetic analyses. Near full length genome sequences of these primary HIV-1 isolates revealed that nearly all intersubtype BF recombination sites were unique and countered previous "CRF" B/F classifications. The majority of these Argentinean HIV-1 isolates were CCR5-using but 4 had a dual/mixed tropism as predicted by both phenotypic and genotypic assays. Comparison of the replicative fitness of these BF primary HIV-1 isolates to circulating B, F, and C HIV-1 using pairwise competitions in peripheral blood mononuclear cells (PBMCs) indicated a similarity in fitness of these BF recombinants to subtypes B and F HIV-1 (of the same co-receptor usage) whereas subtype C HIV-1 was significantly less fit than all as previously reported. These results suggest that the multitude of BF HIV-1 strains present within the Argentinean population do not appear to have gained replicative fitness following recent B and F recombination events.
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Affiliation(s)
- Andrea E. Rubio
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Awet Abraha
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Crystal A. Carpenter
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Ryan M. Troyer
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Ángel L. Reyes-Rodríguez
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Horacio Salomon
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Eric J. Arts
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Denis M. Tebit
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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Fonjungo PN, Kalish ML, Schaefer A, Rayfield M, Mika J, Rose LE, Heslop O, Soudré R, Pieniazek D. Recombinant viruses initiated the early HIV-1 epidemic in Burkina Faso. PLoS One 2014; 9:e92423. [PMID: 24647246 PMCID: PMC3960253 DOI: 10.1371/journal.pone.0092423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/22/2014] [Indexed: 11/28/2022] Open
Abstract
We analyzed genetic diversity and phylogenetic relationships among 124 HIV-1 and 19 HIV-2 strains in sera collected in 1986 from patients of the state hospital in Ouagadougou, Burkina Faso. Phylogenetic analysis of the HIV-1 env gp41 region of 65 sequences characterized 37 (56.9%) as CRF06_cpx strains, 25 (38.5%) as CRF02_AG, 2 (3.1%) as CRF09_cpx, and 1 (1.5%) as subtype A. Similarly, phylogenetic analysis of the protease (PR) gene region of 73 sequences identified 52 (71.2%) as CRF06_cpx, 15 (20.5%) as CRF02_AG, 5 (6.8%) as subtype A, and 1 (1.4%) was a unique strain that clustered along the B/D lineage but basal to the node connecting the two lineages. HIV-2 PR or integrase (INT) groups A (n = 17 [89.5%]) and B (n = 2 [10.5%]) were found in both monotypic (n = 11) and heterotypic HIV-1/HIV-2 (n = 8) infections, with few HIV-2 group B infections. Based on limited available sampling, evidence suggests two recombinant viruses, CRF06_cpx and CRF02_AG, appear to have driven the beginning of the mid-1980s HIV-1 epidemic in Burkina Faso.
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Affiliation(s)
- Peter N. Fonjungo
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
- Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Marcia L. Kalish
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Amanda Schaefer
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Mark Rayfield
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Jennifer Mika
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Laura E. Rose
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Orville Heslop
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
| | - Robert Soudré
- Unité de Formation et de Recherche en Sciences de la Santé (UFR/SDS), Université de Ouagadougou, Ouagadougou, Burkina Faso
| | - Danuta Pieniazek
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Atlanta, Georgia, United States of America
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Agyingi L, Mayr LM, Kinge T, Orock GE, Ngai J, Asaah B, Mpoame M, Hewlett I, Nyambi P. The evolution of HIV-1 group M genetic variability in Southern Cameroon is characterized by several emerging recombinant forms of CRF02_AG and viruses with drug resistance mutations. J Med Virol 2013; 86:385-93. [PMID: 24248638 DOI: 10.1002/jmv.23846] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2013] [Indexed: 11/06/2022]
Abstract
The HIV epidemic in Cameroon is marked by a broad genetic diversity dominated by circulating recombinant forms (CRFs). Studies performed more than a decade ago in urban settings of Southern Cameroon revealed a dominance of the CRF02_AG and clade A variants in >90% of the infected subjects; however, little is known about the evolving viral variants circulating in this region. To document circulating HIV viral diversity, four regions of the viral genome (gag, PR, reverse transcriptase, env) in 116 HIV-1 positive individuals in Limbe, Southern Cameroon, were PCR-amplified. Sequences obtained at the RT and protease regions were analyzed for mutations that conferred drug resistance using the Stanford Drug Resistance Database. The present study reveals a broad genetic diversity characterized by several unique recombinant forms (URF) accounting for 36% of infections, 48.6% of patients infected with CRF02_AG, and the emergence of CRF22_01A1 in 7.2% of patients. Three out of 15 (20%) treated patients and 13 out of 93 (13.9%) drug naïve patients harbor drug resistance mutations to RT inhibitors, while 3.2% of drug naïve patients harbor drug resistance mutations associated with protease inhibitors. The high proportion (13.9%) of drug resistance mutations among the drug naïve patients reveals the ongoing transmission of these viruses in this region of Cameroon and highlights the need for drug resistance testing before starting treatment for patients infected with HIV-1.
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Affiliation(s)
- Lucy Agyingi
- Faculty of Science, University of Dschang, West Region, Cameroon; Department of Pathology, New York University School of Medicine, New York, New York
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Hamoudi M, Simon-Loriere E, Gasser R, Negroni M. Genetic diversity of the highly variable V1 region interferes with Human Immunodeficiency Virus type 1 envelope functionality. Retrovirology 2013; 10:114. [PMID: 24156625 PMCID: PMC3826872 DOI: 10.1186/1742-4690-10-114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 10/13/2013] [Indexed: 11/10/2022] Open
Abstract
Background The HIV envelope (Env) promotes viral entry in the host cell. During this process, Env undergoes several conformational changes to ensure its function. At the same time, the gp120 component of Env is the protein of the virus presenting the largest genetic diversity. Understanding how the virus maintains the balance between the competing requirements for maintenance of functionality and antigenic variation of this protein is central for the comprehension of its strategies of evolution and can highlight vulnerable aspects of its replication cycle. We focused on the variable domains V1 and V2 of the HIV-1 gp120 that are involved in conformational changes and are critical for viral escape from antibody neutralization. Results Despite the extensive sequence diversity found in the epidemic for these regions and their location on the external face of the protein, we observed that replacing V1V2 of one primary isolate with that of another severely interferes with Env functionality in more than half of the cases studied. Similar results were obtained for intra- and intersubtype chimeras. These observations are indicative of an interference of genetic diversity in these regions with Env functionality. Therefore, despite the extensive sequence diversity that characterizes these regions in the epidemic, our results show that functional constraints seem to limit their genetic variation. Defects in the V1V2 chimeras were not relieved by the insertion of the V3 region from the same isolate, suggesting that the decrease in functionality is not due to perturbation of potential coevolution networks between V1V2 and V3. Within the V1V2 domain, the sequence of the hypervariable loop of the V1 domain seems to be crucial for the functionality of the protein. Conclusions Besides the well-documented role of V1V2 in the interplay with the immune response, this work shows that V1 is also involved in the selection of functional envelopes. By documenting a compromise between the opposing forces of sequence diversification and retention of functionality, these observations improve our understanding of the evolutionary trajectories of the HIV-1 envelope gene.
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Affiliation(s)
| | | | | | - Matteo Negroni
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, Cedex, France.
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Palm AA, Esbjörnsson J, Månsson F, Kvist A, Isberg PE, Biague A, da Silva ZJ, Jansson M, Norrgren H, Medstrand P. Faster progression to AIDS and AIDS-related death among seroincident individuals infected with recombinant HIV-1 A3/CRF02_AG compared with sub-subtype A3. J Infect Dis 2013; 209:721-8. [PMID: 23935204 DOI: 10.1093/infdis/jit416] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) is divided into subtypes and circulating recombinant forms (CRFs) but the impact of subtype/CRF on disease progression is not fully understood. METHODS We determined the HIV-1 subtype/CRF of 152 seroincident individuals from Guinea-Bissau, based on the C2-V3 region of env. Disease progression was measured as time from estimated seroconversion to AIDS and AIDS-related death. Hazard ratios (HRs) were calculated using a Cox proportional hazard model, adjusting for gender and age at seroconversion. RESULTS The major subtypes/CRFs identified were CRF02_AG (53%), A3 (29%), and A3/02 (a recombinant of A3 and CRF02_AG) (13%). Infection with A3/02 was associated with a close to 3-fold increased risk of AIDS and AIDS-related death compared to A3 (HR = 2.6 [P = 0.011] and 2.9 [P = 0.032], respectively). The estimated time from seroconversion to AIDS and AIDS-related death was 5.0 and 8.0 years for A3/02, 6.2 and 9.0 years for CRF02_AG, and 7.2 and 11.3 years for A3. CONCLUSION Our results show that there are differences in disease progression between HIV-1 A-like subtypes/CRFs. Individuals infected with A3/02 have among the fastest progression rates to AIDS reported to date. Determining the HIV-1 subtype of infected individuals could be important in the management of HIV-1 infections.
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Inference of global HIV-1 sequence patterns and preliminary feature analysis. Virol Sin 2013; 28:228-38. [PMID: 23913180 DOI: 10.1007/s12250-013-3348-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from nonsoutheastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.
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Touloumi G, Pantazis N, Pillay D, Paraskevis D, Chaix ML, Bucher HC, Kücherer C, Zangerle R, Kran AMB, Porter K. Impact of HIV-1 subtype on CD4 count at HIV seroconversion, rate of decline, and viral load set point in European seroconverter cohorts. Clin Infect Dis 2013; 56:888-97. [PMID: 23223594 DOI: 10.1093/cid/cis1000] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype may influence disease progression. We compared CD4 lymphocyte cell count levels at seroconversion, decline rates and viral load set point in individuals infected with different HIV-1 subtypes. METHODS We used data from the Concerted Action on SeroConversion to AIDS and Death in Europe (CASCADE) collaboration, restricted to those infected since 1996, aged ≥15 years, and applied mixed effects models for CD4 cell count decline and median regression for viral load set point (mean level 6-24 months from seroconversion). RESULTS The analysis included 3364 seroconverters with known HIV-1 subtypes. Compared with subtype B, CD4 at seroconversion was significantly higher for subtype CRF01 and lower for subtype C. Subsequent CD4 decline was significantly slower for subtypes A and CRF02 and marginally slower for subtype C compared with B. Mean CD4 loss at 2 years of seroconversion for white men exposed through sex between men, aged 30-39 years, having seroconverted since 2006, enrolled within 6 months of seroconversion, and without acute infection was 88, 142, 100, 130, 103, and 167 cells/µL for subtypes A, B, C, CRF01_AE, CRF02_AG, and G, respectively. In adjusted analysis, median viral load set point and time to clinical AIDS/death did not differ significantly by subtype, although all subtypes, except C, tended to have lower levels compared with B. CONCLUSIONS HIV-1 subtype significantly influences seroconversion CD4 cell levels and decline rates but not viral load set point. These findings may be helpful to HIV-positive individuals and their attending physicians in understanding disease progression.
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Affiliation(s)
- Giota Touloumi
- Department of Hygiene, Epidemiology and Medical Statistics, Athens University Medical School, Greece.
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Hemelaar J. Implications of HIV diversity for the HIV-1 pandemic. J Infect 2012; 66:391-400. [PMID: 23103289 DOI: 10.1016/j.jinf.2012.10.026] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/21/2012] [Indexed: 11/17/2022]
Abstract
HIV-1 genetic variability within individuals and populations plays a central role in the HIV pandemic. Multiple zoonotic transmissions of SIV to humans have resulted in distinct HIV lineages in humans which have further diversified within the population over time. High rates of mutation and recombination during HIV reverse transcription create a genetic diversity in the host which is subject to selection pressures by the immune response and antiretroviral treatment. The global distribution of HIV genetic variants and the impact of HIV diversity on pathogenesis, transmission and clinical management are reviewed. Finally, the key role of escape mutations in the immune response to HIV is discussed as well as the major challenge which HIV-1 diversity poses to HIV vaccine development.
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Affiliation(s)
- Joris Hemelaar
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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Rusine J, Jurriaans S, van de Wijgert J, Cornelissen M, Kateera B, Boer K, Karita E, Mukabayire O, de Jong M, Ondoa P. Molecular and phylogeographic analysis of human immuno-deficiency virus type 1 strains infecting treatment-naive patients from Kigali, Rwanda. PLoS One 2012; 7:e42557. [PMID: 22905148 PMCID: PMC3419187 DOI: 10.1371/journal.pone.0042557] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/09/2012] [Indexed: 01/18/2023] Open
Abstract
This study aimed at describing the genetic subtype distribution of HIV-1 strains circulating in Kigali and their epidemiological link with the HIV-1 strains from the five countries surrounding Rwanda. One hundred and thirty eight pol (RT and PR) sequences from 116 chronically- and 22 recently-infected antiretroviral therapy (ART)-naïve patients from Kigali were generated and subjected to HIV drug resistance (HIV-DR), phylogenetic and recombinant analyses in connection with 366 reference pol sequences from Rwanda, Burundi, Kenya, Democratic Republic of Congo, Tanzania and Uganda (Los Alamos database). Among the Rwandan samples, subtype A1 predominated (71.7%), followed by A1/C recombinants (18.1%), subtype C (5.8%), subtype D (2.9%), one A1/D recombinant (0.7%) and one unknown subtype (0.7%). Thirteen unique and three multiple A1/C recombinant forms were identified. No evidence for direct transmission events was found within the Rwandan strains. Molecular characteristics of HIV-1 were similar between chronically and recently-infected individuals and were not significantly associated with demographic or social factors. Our report suggests that the HIV-1 epidemic in Kigali is characterized by the emergence of A1/C recombinants and is not phylogenetically connected with the HIV-1 epidemic in the five neighboring countries. The relatively low level of transmitted HIV-DR mutations (2.9%) reported here indicates the good performance of the ART programme in Rwanda. However, the importance of promoting couples' counseling, testing and disclosure during HIV prevention strategies is highlighted.
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Affiliation(s)
- John Rusine
- National Reference Laboratory, Kigali, Rwanda
| | - Suzanne Jurriaans
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Janneke van de Wijgert
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Marion Cornelissen
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Brenda Kateera
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Kimberly Boer
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | | | | | - Menno de Jong
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Pascale Ondoa
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- * E-mail:
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In Silico and In Vitro Comparison of HIV-1 Subtypes B and CRF02_AG Integrases Susceptibility to Integrase Strand Transfer Inhibitors. Adv Virol 2012; 2012:548657. [PMID: 22829822 PMCID: PMC3398581 DOI: 10.1155/2012/548657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 04/16/2012] [Accepted: 04/30/2012] [Indexed: 01/18/2023] Open
Abstract
Most antiretroviral medical treatments were developed and tested principally on HIV-1 B nonrecombinant strain, which represents less than 10% of the worldwide HIV-1-infected population. HIV-1 circulating recombinant form CRF02_AG is prevalent in West Africa and is becoming more frequent in other countries. Previous studies suggested that the HIV-1 polymorphisms might be associated to variable susceptibility to antiretrovirals. This study is pointed to compare the susceptibility to integrase (IN) inhibitors of HIV-1 subtype CRF02_AG IN respectively to HIV-1 B. Structural models of B and CRF02_AG HIV-1 INs as unbound enzymes and in complex with the DNA substrate were built by homology modeling. IN inhibitors—raltegravir (RAL), elvitegravir (ELV) and L731,988—were docked onto the models, and their binding affinity for both HIV-1 B and CRF02_AG INs was compared. CRF02_AG INs were cloned and expressed from plasma of integrase strand transfer inhibitor (INSTI)-naïve infected patients. Our in silico and in vitro studies showed that the sequence variations between the INs of CRF02_AG and B strains did not lead to any notable difference in the structural features of the enzyme and did not impact the susceptibility to the IN inhibitors. The binding modes and affinities of INSTI inhibitors to B and CRF02_AG INs were found to be similar. Although previous studies suggested that several naturally occurring variations of CRF02_AG IN might alter either IN/vDNA interactions or INSTIs binding, our study demonstrate that these variations do affect neither IN activity nor its susceptibility to INSTIs.
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Miri L, Ouladlahsen A, Kettani A, Bensghir R, Marhoum Elfilali K, Wakrim L. Characterization of protease resistance-associated mutations in HIV type 1 drug-naive patients following the increasing prevalence of the CRF02_AG strain in Morocco. AIDS Res Hum Retroviruses 2012; 28:571-7. [PMID: 22145994 DOI: 10.1089/aid.2011.0225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The purpose of this study was to investigate the amino acid substitutions in the protease of HIV-1 B and non-B subtypes and evaluate whether the emergence of resistance-associated mutations (RAMs) could have a significant correlation with the increasing prevalence of CRF02_AG strains in Morocco. A total of 162 protease gene sequences were successfully amplified from drug-naive HIV-1-infected individuals. We identified eight (sub)subtypes and CRFs: B(66%), A1(3.7%), C(1.2%), F1(0.6%), F2(0.6%), G(1.2%), CRF02_AG(25.3%), and CRF01_AE(1.2%). Phylogenetic analysis of CRF02_AG strains showed that 9.8% of isolates had a closer connection with reference strains from Morocco and 15.4% clustered with reference strains from eight West African and three European countries. When compared to the B subtype, patients with the CRF02_AG strain had a significantly higher prevalence of mutations associated with resistance to some antiprotease drugs, mainly tipranavir (TPV): H69K (97% vs. 5%; p<0.0001), L89M (95% vs. 1%; p<0.0001), and M36I/L (93% vs. 44%; p<0.0001). Most of the CRF02_AG strains (97%) significantly showed at least two TPV-RAMs (p=0.002) compared to the B subtype (7%). Multivariate analysis revealed that CRF02_AG infection was the only factor highly associated with the occurrence of more than two TPV-RAMs (C=0.42; p<0.0001). These results support the importance of transmitted drug resistance mutations (M36I/L, H69K, and L89M) in the protease gene of HIV-1 CRF02_AG isolates. This HIV drug resistance transmission before protease inhibitor (PI) exposure raises concern about its influence on the susceptibility of CRF02_AG strains to some PIs, especially tipranavir, which will soon be introduced as part of the second line therapeutic regimens in Morocco.
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Affiliation(s)
- Lamia Miri
- Laboratoire de Virologie, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Ahd Ouladlahsen
- Service des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Recherche sur les Lipoprotéines et l'Athérosclérose, Faculté des Sciences Ben M'sik, Casablanca, Morocco
| | - Rajaa Bensghir
- Service des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | | | - Lahcen Wakrim
- Laboratoire de Virologie, Institut Pasteur du Maroc, Casablanca, Morocco
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Faria NR, Suchard MA, Abecasis A, Sousa JD, Ndembi N, Bonfim I, Camacho RJ, Vandamme AM, Lemey P. Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2012; 12:453-60. [PMID: 21565285 PMCID: PMC4677783 DOI: 10.1016/j.meegid.2011.04.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 12/18/2022]
Abstract
Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XX century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to investigate the spatiotemporal patterns of the CRF02_AG clade. By explicitly integrating prevalence counts and genetic population size estimates we date the epidemic emergence of CRF02_AG at 1973.1 (1972.1, 1975.3, 95% CI). To infer the phylogeographic signature of this clade at a regional scale, we analyze pol and env time-stamped sequence data from 10 countries using a Bayesian phylogeographic approach based on an asymmetric discretized diffusion model. Our data confirms a spatial origin of CRF02_AG in the Democratic Republic of Congo (DRC) and suggests that viral dissemination to Cameroon occurred at an early stage of the evolutionary history of CRF02_AG. We find considerable support for epidemiological linkage between neighbour countries. Compilation of ethnographic data suggested that well-supported viral migration did not reflect sustained human migratory flows. Finally, using sequence data from 15 locations in Cameroon, we use relaxed random walk models to explore the spatiotemporal dynamics of CRF02_AG at a finer geographical detail. Phylogeographic dispersal in continuous space reveals that at least two distinct CRF02_AG lineages are circulating in overlapping regions that are evolving at different evolutionary and diffusion rates. In conclusion, by combining molecular and epidemiological data, our results provide a time scale for CRF02_AG, early 70s, place its spatial root in the DRC within the putative root of group-M diversity and propose a scenario of chance-exportation events for the spatiotemporal patterns of a successful HIV-1 lineage both at a regional and country-scale.
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Affiliation(s)
- Nuno R Faria
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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Fenyö EM, Esbjörnsson J, Medstrand P, Jansson M. Human immunodeficiency virus type 1 biological variation and coreceptor use: from concept to clinical significance. J Intern Med 2011; 270:520-31. [PMID: 21929694 DOI: 10.1111/j.1365-2796.2011.02455.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
There is ample evidence for intra-patient evolution of the human immunodeficiency virus type 1 (HIV-1) biological phenotype during the pathogenic process. Evolution often involves switch of coreceptor use from CCR5 to CXCR4, but change to more flexible use of CCR5 occurs over time even in patients with maintained CCR5 use. The increasing use of entry inhibitors in the clinic, often specific for one or the other HIV-1 coreceptor or with different binding properties to CCR5, calls for virus testing in patients prior to treatment initiation. Cell lines expressing CCR5/CXCR4 chimeric receptors are tools for testing viruses for mode of CCR5 use. It is conceivable that small-molecule entry inhibitors that differentially bind to CCR5 can be matched for best effect against HIV-1 with different modes of CCR5 use, thereby allowing an individualized drug choice specifically tailored for each patient.
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Affiliation(s)
- E M Fenyö
- Department of Laboratory Medicine, Division of Medical Microbiology, Lund, Sweden.
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45
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The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America. AIDS Res Treat 2011; 2011:154945. [PMID: 22162803 PMCID: PMC3226295 DOI: 10.1155/2011/154945] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 08/19/2011] [Indexed: 12/03/2022] Open
Abstract
The South American human immunodeficiency virus type 1 (HIV-1) epidemic is driven by several subtypes (B, C, and F1) and circulating and unique recombinant forms derived from those subtypes. Those variants are heterogeneously distributed around the continent in a country-specific manner. Despite some inconsistencies mainly derived from sampling biases and analytical constrains, most of studies carried out in the area agreed in pointing out specificities in the evolutionary dynamics of the circulating HIV-1 lineages. In this paper, we covered the theoretical basis, and the application of bioinformatics methods to reconstruct the HIV spatial-temporal dynamics, unveiling relevant information to understand the origin, geographical dissemination and the current molecular scenario of the HIV epidemic in the continent, particularly in the countries of Southern Cone.
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Véras NMC, Santoro MM, Gray RR, Tatem AJ, Presti AL, Olearo F, Cappelli G, Colizzi V, Takou D, Torimiro J, Russo G, Callegaro A, Salpini R, D'Arrigo R, Perno CF, Goodenow MM, Ciccozzi M, Salemi M. Molecular epidemiology of HIV type 1 CRF02_AG in Cameroon and African patients living in Italy. AIDS Res Hum Retroviruses 2011; 27:1173-82. [PMID: 21453131 DOI: 10.1089/aid.2010.0333] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 CRF02_AG accounts for >50% of infected individuals in Cameroon. CRF02_AG prevalence has been increasing both in Africa and Europe, particularly in Italy because of migrations from the sub-Saharan region. This study investigated the molecular epidemiology of CRF02_AG in Cameroon by employing Bayesian phylodynamics and analyzed the relationship between HIV-1 CRF02_AG isolates circulating in Italy and those prevalent in Africa to understand the link between the two epidemics. Among 291 Cameroonian reverse transcriptase sequences analyzed, about 70% clustered within three distinct clades, two of which shared a most recent common ancestor, all related to sequences from Western Africa. The major Cameroonian clades emerged during the mid-1970s and slowly spread during the next 30 years. Little or no geographic structure was detected within these clades. One of the major driving forces of the epidemic was likely the high accessibility between locations in Southern Cameroon contributing to the mobility of the population. The remaining Cameroonian sequences and the new strains isolated from Italian patients were interspersed mainly within West and Central African sequences in the tree, indicating a continuous exchange of CRF02_AG viral strains between Cameroon and other African countries, as well as multiple independent introductions in the Italian population. The evaluation of the spread of CRF02_AG may provide significant insight about the future dynamics of the Italian and European epidemic.
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Affiliation(s)
- Nazle Mendonca Collaço Véras
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
| | - Rebecca R. Gray
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | - Andrew J. Tatem
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | | | | | | | - Vittorio Colizzi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Desiré Takou
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Judith Torimiro
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Gianluca Russo
- Department of Tropical and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Romina Salpini
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
| | - Roberta D'Arrigo
- Monitoring Unit of Antiretroviral Therapies, INMI, Lazzaro Spallanzani, Rome, Italy
| | - Carlo-Federico Perno
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
- Monitoring Unit of Antiretroviral Therapies, INMI, Lazzaro Spallanzani, Rome, Italy
| | - Maureen M. Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
| | | | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
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Delviks-Frankenberry K, Galli A, Nikolaitchik O, Mens H, Pathak VK, Hu WS. Mechanisms and factors that influence high frequency retroviral recombination. Viruses 2011; 3:1650-1680. [PMID: 21994801 PMCID: PMC3187697 DOI: 10.3390/v3091650] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/18/2011] [Accepted: 08/25/2011] [Indexed: 01/25/2023] Open
Abstract
With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development.
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Affiliation(s)
- Krista Delviks-Frankenberry
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; E-Mails: (K.D.-F.); (V.K.P.)
| | - Andrea Galli
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; E-Mails: (A.G.); (O.N.)
- Copenhagen Hepatitis C Program, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre 2650, Denmark
| | - Olga Nikolaitchik
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; E-Mails: (A.G.); (O.N.)
| | - Helene Mens
- Department of Epidemic Diseases, Rigshospitalet, København 2100, Denmark; E-Mail:
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; E-Mails: (K.D.-F.); (V.K.P.)
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; E-Mails: (A.G.); (O.N.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-301-846-1250; Fax: +1-301-846-6013
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Ragupathy V, Zhao J, Wood O, Tang S, Lee S, Nyambi P, Hewlett I. Identification of new, emerging HIV-1 unique recombinant forms and drug resistant viruses circulating in Cameroon. Virol J 2011; 8:185. [PMID: 21513545 PMCID: PMC3118203 DOI: 10.1186/1743-422x-8-185] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/23/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The HIV epidemic in Cameroon is characterized by a high degree of viral genetic diversity with circulating recombinant forms (CRFs) being predominant. The goal of our study was to determine recent trends in virus evolution and emergence of drug resistance in blood donors and HIV positive patients. METHODOLOGY Blood specimens of 73 individuals were collected from three cities and a few villages in Cameroon and viruses were isolated by co-cultivation with PBMCs. Nested PCR was performed for gag p17 (670 bp) pol (840 bp) and Env gp41 (461 bp) genes. Sequences were phylogenetically analyzed using a reference set of sequences from the Los Alamos database. RESULTS Phylogenetic analysis based on partial sequences revealed that 65% (n = 48) of strains were CRF02_AG, 4% (n = 3) subtype F2, 1% each belonged to CRF06 (n = 1), CRF11 (n = 1), subtype G (n = 1), subtype D (n = 1), CRF22_01A1 (n = 1), and 26% (n = 18) were Unique Recombinant Forms (URFs). Most URFs contained CRF02_AG in one or two HIV gene fragments analyzed. Furthermore, pol sequences of 61 viruses revealed drug resistance in 55.5% of patients on therapy and 44% of drug naïve individuals in the RT and protease regions. Overall URFs that had a primary HIV subtype designation in the pol region showed higher HIV-1 p24 levels than other recombinant forms in cell culture based replication kinetics studies. CONCLUSIONS Our results indicate that although CRF02_AG continues to be the predominant strain in Cameroon, phylogenetically the HIV epidemic is continuing to evolve as multiple recombinants of CRF02_AG and URFs were identified in the individuals studied. CRF02_AG recombinants that contained the pol region of a primary subtype showed higher replicative advantage than other variants. Identification of drug resistant strains in drug-naïve patients suggests that these viruses are being transmitted in the population studied. Our findings support the need for continued molecular surveillance in this region of West Central Africa and investigating impact of variants on diagnostics, viral load and drug resistance assays on an ongoing basis.
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Affiliation(s)
- Viswanath Ragupathy
- Lab of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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Selhorst P, Vazquez AC, Terrazas-Aranda K, Michiels J, Vereecken K, Heyndrickx L, Weber J, Quiñones-Mateu ME, Ariën KK, Vanham G. Human immunodeficiency virus type 1 resistance or cross-resistance to nonnucleoside reverse transcriptase inhibitors currently under development as microbicides. Antimicrob Agents Chemother 2011; 55:1403-13. [PMID: 21282453 PMCID: PMC3067143 DOI: 10.1128/aac.01426-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 11/29/2010] [Accepted: 01/19/2011] [Indexed: 11/20/2022] Open
Abstract
Microbicides based on nonnucleoside reverse transcriptase inhibitors (NNRTIs) are currently being developed to protect women from HIV acquisition through sexual contact. However, the large-scale introduction of these products raises two major concerns. First, when these microbicides are used by undiagnosed HIV-positive women, they could potentially select for viral resistance, which may compromise subsequent therapeutic options. Second, NNRTI-based microbicides that are inactive against NNRTI-resistant strains might promote the selective transmission of these viruses. In order to address these concerns, drug resistance was selected in vitro by the serial passage of three viral isolates from subtypes B and C and CRF02_AG (a circulating recombinant form) in activated peripheral blood mononuclear cells (PBMCs) under conditions of increasing concentrations of three NNRTIs (i.e., TMC120, UC781, and MIV-160) that are currently being developed as candidate microbicides. TMC120 and MIV-160 displayed a high genetic barrier to resistance development, whereas resistance to UC781 emerged rapidly, similarly to efavirenz and nevirapine. Phenotypically, the selected viruses appeared to be highly cross-resistant to current first-line therapeutic NNRTIs (i.e., delavirdine, nevirapine, and efavirenz), although they retained some susceptibility to the more recently developed NNRTIs lersivirine and etravirine. The ability of UC781, TMC120, and MIV-160 to inhibit the in vitro-selected NNRTI-resistant viruses was also limited, although residual activity could be observed for the candidate microbicide NNRTI MIV-170. Interestingly, only four p2/p7/p1/p6/PR/RT/INT recombinant NNRTI-resistant viruses (i.e., TMC120-resistant VI829, EFV-resistant VI829, MIV-160-resistant VI829, and EFV-resistant MP568) showed impairments in replicative fitness. Overall, these in vitro analyses demonstrate that due to potential cross-resistance, the large-scale introduction of single-NNRTI-based microbicides should be considered with caution.
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Affiliation(s)
- Philippe Selhorst
- Department of Microbiology, Virology Unit, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium.
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HIV-1 molecular epidemiology in Guinea-Bissau, West Africa: origin, demography and migrations. PLoS One 2011; 6:e17025. [PMID: 21365013 PMCID: PMC3041826 DOI: 10.1371/journal.pone.0017025] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 01/19/2011] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 epidemic in West Africa has been dominated by subtype A and the recombinant form CRF02_AG. Little is known about the origins and the evolutionary history of HIV-1 in this region. We employed Maximum likelihood and Bayesian methods in combination with temporal and spatial information to reconstruct the HIV-1 subtype distribution, demographic history and migration patterns over time in Guinea-Bissau, West Africa. We found that CRF02_AG and subsubtype A3 were the dominant forms of HIV-1 in Guinea-Bissau and that they were introduced into the country on at least six different occasions between 1976 and 1981. These estimates also corresponded well with the first reported HIV-1 cases in Guinea-Bissau. Migration analyses suggested that (1) the HIV-1 epidemic started in the capital Bissau and then dispersed into more rural areas, and (2) the epidemic in Guinea-Bissau was connected to both Cameroon and Mali. This is the first study that describes the HIV-1 molecular epidemiology in a West African country by combining the results of subtype distribution with analyses of epidemic origin and epidemiological linkage between locations. The multiple introductions of HIV-1 into Guinea-Bissau, during a short time-period of five years, coincided with and were likely influenced by the major immigration wave into the country that followed the end of the independence war (1963-1974).
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