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Gotora PT, van der Sluis R, Williams ME. HIV-1 Tat amino acid residues that influence Tat-TAR binding affinity: a scoping review. BMC Infect Dis 2023; 23:164. [PMID: 36932337 PMCID: PMC10020771 DOI: 10.1186/s12879-023-08123-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/27/2023] [Indexed: 03/19/2023] Open
Abstract
HIV-1 remains a global health concern and to date, nearly 38 million people are living with HIV. The complexity of HIV-1 pathogenesis and its subsequent prevalence is influenced by several factors including the HIV-1 subtype. HIV-1 subtype variation extends to sequence variation in the amino acids of the HIV-1 viral proteins. Of particular interest is the transactivation of transcription (Tat) protein due to its key function in viral transcription. The Tat protein predominantly functions by binding to the transactivation response (TAR) RNA element to activate HIV-1 transcriptional elongation. Subtype-specific Tat protein sequence variation influences Tat-TAR binding affinity. Despite several studies investigating Tat-TAR binding, it is not clear which regions of the Tat protein and/or individual Tat amino acid residues may contribute to TAR binding affinity. We, therefore, conducted a scoping review on studies investigating Tat-TAR binding. We aimed to synthesize the published data to determine (1) the regions of the Tat protein that may be involved in TAR binding, (2) key Tat amino acids involved in TAR binding and (3) if Tat subtype-specific variation influences TAR binding. A total of thirteen studies met our inclusion criteria and the key findings were that (1) both N-terminal and C-terminal amino acids outside the basic domain (47-59) may be important in increasing Tat-TAR binding affinity, (2) substitution of the amino acids Lysine and Arginine (47-59) resulted in a reduction in binding affinity to TAR, and (3) none of the included studies have investigated Tat subtype-specific substitutions and therefore no commentary could be made regarding which subtype may have a higher Tat-TAR binding affinity. Future studies investigating Tat-TAR binding should therefore use full-length Tat proteins and compare subtype-specific variations. Studies of such a nature may help explain why we see differential pathogenesis and prevalence when comparing HIV-1 subtypes.
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Silva GPSA, Oliveira RC, de Souza JSM, Giovanetti M, Guimarães ML, Brites C, Monteiro-Cunha JP. Tracing the relationship among HIV-1 sub-subtype F1 strains: a phylodynamic perspective. Mem Inst Oswaldo Cruz 2023; 117:e220109. [PMID: 36700579 PMCID: PMC9870255 DOI: 10.1590/0074-02760220109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/17/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The human immunodeficiency virus type 1, F1 sub-subtype (HIV-1 F1) circulates in three continents: Africa, Europe, and South America. In Brazil, this sub-subtype co-circulates with subtypes B and C and several recombinant forms, mainly BF1 variants. OBJECTIVES This study aimed to reconstruct the dynamic history of HIV-1 F1 in Brazil. METHODS HIV-1 near full-length genome and pol gene nucleotide sequences available in public databases were assembled in two datasets (POL671 and NFLG53) to cover the largest number of F1 sub-subtype sequences. Phylodynamic and temporal analyses were performed. FINDINGS Two main strains of the F1 sub-subtype are circulating worldwide. The first (F1.I) was found among Brazilian samples (75%) and the second (F1.II) among Romanian (62%) and other European and African isolates. The F1 subtype epidemic in Brazil originated from a single entry into the country around 1970. This ancestral sample is related to samples isolated in European countries (France, Finland, and Belgium), which are possibly of African origin. Moreover, further migration (1998 CI: 1994-2003) of strains from Brazil to Europe (Spain and the UK) was observed. Interestingly, all different recombinant BF patterns found, even those from outside Brazil, present the same F1 lineage (F1.I) as an ancestor, which could be related to the acquisition of adaptive advantages for the recombinant progenies. MAIN CONCLUSIONS These findings are important for the understanding of the origin and dynamics of the F1 sub-subtype and a consequent better and greater understanding of the HIV-1 F1 and BF epidemic that still spreads from Brazil to other countries.
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Affiliation(s)
| | - Rodrigo Cunha Oliveira
- Universidade Federal da Bahia, Departamento de Bioquímica e Biofísica, Salvador, BA, Brasil
| | | | - Marta Giovanetti
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Laboratório de Genética Celular e Molecular, Belo Horizonte, MG, Brasil
| | - Monick Lindenmeyer Guimarães
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Carlos Brites
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, BA, Brasil
| | - Joana Paixão Monteiro-Cunha
- Universidade Federal da Bahia, Departamento de Bioquímica e Biofísica, Salvador, BA, Brasil,+ Corresponding author:
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Asia LK, Jansen Van Vuren E, Williams ME. The influence of viral protein R amino acid substitutions on clinical outcomes in people living with HIV: A systematic review. Eur J Clin Invest 2022; 53:e13943. [PMID: 36579370 DOI: 10.1111/eci.13943] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/17/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND The HIV viral protein R (Vpr) is a multifunction protein involved in the pathophysiology of HIV-1. Recent evidence has suggested that Vpr amino acid substitutions influence the pathophysiology of HIV-1 and clinical outcomes in people living with HIV (PLWH). Several studies have linked Vpr amino acid substitutions to clinical outcomes in PLWH; however, there is no clear consensus as to which amino acids or amino acid substitutions are most important in the pathophysiology and clinical outcomes in PLWH. We, therefore, conducted a systematic review of studies investigating Vpr amino acid substitutions and clinical outcomes in PLWH. METHODS PubMed, Scopus and Web of Science databases were searched according to PRISMA guidelines using a search protocol designed specifically for this study. RESULTS A total of 22 studies were included for data extraction, comprising 14 cross-sectional and 8 longitudinal studies. Results indicated that Vpr amino acid substitutions were associated with specific clinical outcomes, including disease progressions, neurological outcomes and treatment status. Studies consistently showed that the Vpr substitution 63T was associated with slower disease progression, whereas 77H and 85P were associated with no significant contribution to disease progression. CONCLUSIONS Vpr-specific amino acid substitutions may be contributors to clinical outcomes in PLWH, and future studies should consider investigating the Vpr amino acid substitutions highlighted in this review.
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Affiliation(s)
- Levanco K Asia
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Esmé Jansen Van Vuren
- Hypertension in Africa Research Team (HART), North-West University, Potchefstroom, South Africa.,South African Medical Research Council: Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Monray E Williams
- Human Metabolomics, North-West University, Potchefstroom, South Africa
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Giovanetti M, Ciccozzi M, Parolin C, Borsetti A. Molecular Epidemiology of HIV-1 in African Countries: A Comprehensive Overview. Pathogens 2020; 9:pathogens9121072. [PMID: 33371264 PMCID: PMC7766877 DOI: 10.3390/pathogens9121072] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) originated in non-human primates in West-central Africa and continues to be a major global public health issue, having claimed almost 33 million lives so far. In Africa, it is estimated that more than 20 million people are living with HIV/Acquired Immunodeficiency Syndrome (AIDS) and that more than 730,000 new HIV-1 infections still occur each year, likely due to low access to testing. The high genetic variability of HIV-1, due to a fast replication cycle and high mutation rate, may cause the generation of many viral variants in a single infected patient during a single day. Therefore, the active monitoring and characterization of the HIV-1 subtypes and recombinant forms circulating through African countries poses a significant challenge to more specific diagnoses, treatments, care, and intervention strategies. In this review, a concise characterization of all the subtypes and recombinant forms circulating in Africa is presented to highlight the magnitude of the HIV-1 threat among the African countries and to understand virus genetic diversity and dispersion dynamics better.
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Affiliation(s)
- Marta Giovanetti
- Reference Laboratory of Flavivirus, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Massimo Ciccozzi
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Cristina Parolin
- Department of Molecular, Medicine University of Padova, 35121 Padova, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy
- Correspondence: ; Tel.: +39-06-49903082
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Rubio-Garrido M, González-Alba JM, Reina G, Ndarabu A, Barquín D, Carlos S, Galán JC, Holguín Á. Current and historic HIV-1 molecular epidemiology in paediatric and adult population from Kinshasa in the Democratic Republic of Congo. Sci Rep 2020; 10:18461. [PMID: 33116151 PMCID: PMC7595211 DOI: 10.1038/s41598-020-74558-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/30/2020] [Indexed: 12/22/2022] Open
Abstract
HIV-1 diversity may impact monitoring and vaccine development. We describe the most recent data of HIV-1 variants and their temporal trends in the Democratic Republic of Congo (DRC) from 1976 to 2018 and in Kinshasa from 1983–2018. HIV-1 pol sequencing from dried blood collected in Kinshasa during 2016–2018 was done in 340 HIV-infected children/adolescents/adults to identify HIV-1 variants by phylogenetic reconstructions. Recombination events and transmission clusters were also analyzed. Variant distribution and genetic diversity were compared to historical available pol sequences from the DRC in Los Alamos Database (LANL). We characterized 165 HIV-1 pol variants circulating in Kinshasa (2016–2018) and compared them with 2641 LANL sequences from the DRC (1976–2012) and Kinshasa (1983–2008). During 2016–2018 the main subtypes were A (26.7%), G (9.7%) and C (7.3%). Recombinants accounted for a third of infections (12.7%/23.6% Circulant/Unique Recombinant Forms). We identified the first CRF47_BF reported in Africa and four transmission clusters. A significant increase of subtype A and sub-subtype F1 and a significant reduction of sub-subtype A1 and subtype D were observed in Kinshasa during 2016–2018 compared to variants circulating in the city from 1983 to 2008. We provide unique and updated information related to HIV-1 variants currently circulating in Kinshasa, reporting the temporal trends of subtypes/CRF/URF during 43 years in the DRC, and providing the most extensive data on children/adolescents.
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Affiliation(s)
- Marina Rubio-Garrido
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP, 28034, Madrid, Spain
| | - José María González-Alba
- Virology Section, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp, 28034, Madrid, Spain
| | - Gabriel Reina
- Microbiology Department, Clínica Universidad de Navarra, Navarra Institute for Health Research (IdiSNA), Institute of Tropical Health, Universidad de Navarra (ISTUN), 31008, Pamplona, Spain.
| | - Adolphe Ndarabu
- Monkole Hospital, Kinshasa, Democratic Republic of the Congo
| | - David Barquín
- Microbiology Department, Clínica Universidad de Navarra, Navarra Institute for Health Research (IdiSNA), Institute of Tropical Health, Universidad de Navarra (ISTUN), 31008, Pamplona, Spain
| | - Silvia Carlos
- Department of Preventive Medicine and Public Health, Navarra Institute for Health Research (IdiSNA), Institute of Tropical Health, Universidad de Navarra (ISTUN), Pamplona, 31008, Spain
| | - Juan Carlos Galán
- Virology Section, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp, 28034, Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP, 28034, Madrid, Spain.
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Gibson KM, Steiner MC, Rentia U, Bendall ML, Pérez-Losada M, Crandall KA. Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Viruses 2020; 12:E758. [PMID: 32674515 PMCID: PMC7412389 DOI: 10.3390/v12070758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.
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Affiliation(s)
- Keylie M. Gibson
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Margaret C. Steiner
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Uzma Rentia
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Matthew L. Bendall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4169-007 Vairão, Portugal
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
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Foley BT, Leitner T, Paraskevis D, Peeters M. Primate immunodeficiency virus classification and nomenclature: Review. INFECTION GENETICS AND EVOLUTION 2016; 46:150-158. [PMID: 27789390 DOI: 10.1016/j.meegid.2016.10.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 12/25/2022]
Abstract
The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. This review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.
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Affiliation(s)
- Brian T Foley
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Dimitrios Paraskevis
- National and Kapodistrian University of Athens, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, Athens, Greece
| | - Martine Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France; IBC, Computational Biology Institute, 34095 Montpellier, France
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Jia L, Li L, Li H, Liu S, Wang X, Bao Z, Li T, Zhuang D, Liu Y, Li J. Recombination pattern reanalysis of some HIV-1 circulating recombination forms suggest the necessity and difficulty of revision. PLoS One 2014; 9:e107349. [PMID: 25203725 PMCID: PMC4159329 DOI: 10.1371/journal.pone.0107349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 08/09/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Recombination is one of the major mechanisms underlying the generation of HIV-1 variability. Currently 61 circulating recombinant forms of HIV-1 have been identified. With the development of recombination detection techniques and accumulation of HIV-1 reference stains, more accurate mosaic structures of circulating recombinant forms (CRFs), like CRF04 and CRF06, have undergone repeated analysis and upgrades. Such revisions may also be necessary for other CRFs. Unlike previous studies, whose results are based primarily on a single recombination detection program, the current study was based on multiple recombination analysis, which may have produced more impartial results. METHODS Representative references of 3 categories of intersubtype recombinants were selected, including BC recombinants (CRF07 and CRF08), BG recombinants (CRF23 and CRF24), and BF recombinants (CRF38 and CRF44). They were reanalyzed in detail using both the jumping profile hidden Markov model and RDP3. RESULTS The results indicate that revisions and upgrades are very necessary and the entire re-analysis suggested 2 types of revision: (i) length of inserted fragments; and (ii) number of inserted fragments. The reanalysis also indicated that determination of small regions of about 200 bases or fewer should be performed with more caution. CONCLUSION Results indicated that the involvement of multiple recombination detection programs is very necessary. Additionally, results suggested two major challenges, one involving the difficulty of accurately determining the locations of breakpoints and the second involving identification of small regions of about 200 bases or fewer with greater caution. Both indicate the complexity of HIV-1 recombination. The resolution would depend critically on development of a recombination analysis algorithm, accumulation of HIV-1 stains, and a higher sequencing quality. With the changes in recombination pattern, phylogenetic relationships of some CRFs may also change. All these results may be critical to understand the role of recombination in a complex and dynamic HIV evolution.
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Affiliation(s)
- Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
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Velasco-de-Castro CA, Grinsztejn B, Veloso VG, Bastos FI, Pilotto JH, Fernandes N, Morgado MG. HIV-1 diversity and drug resistance mutations among people seeking HIV diagnosis in voluntary counseling and testing sites in Rio de Janeiro, Brazil. PLoS One 2014; 9:e87622. [PMID: 24498155 PMCID: PMC3907471 DOI: 10.1371/journal.pone.0087622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/27/2013] [Indexed: 11/19/2022] Open
Abstract
The remarkable viral diversity remains a big challenge to the development of HIV vaccines and optimal therapy worldwide. In the latest years, as a consequence of the large expansion of highly active antiretroviral therapy (HAART) availability worldwide, an increase in transmitted drug resistance mutations (TDRM) has been observed, varying according the region. This study assessed HIV-1 diversity and TDRM profile over time among newly HIV-1 diagnosed individuals from Rio de Janeiro, Brazil. Blood samples were collected from individuals seeking HIV diagnosis in four voluntary counseling and testing (VCTs) sites located in the Rio de Janeiro Metropolitan Area, in 2005-2007. Recent (RS) and long-term (LTS) HIV-1 seroconverters were distinguished using BED-CEIA. Pol viral sequences were obtained for 102 LTS identified in 2005 and 144 RS from 2005-2007. HIV-1 subtype and pol recombinant genomes were determined using Rega HIV-1 Subtyping Tool and by phylogenetic inferences and bootscanning analyses. Surveillance of HIV-1 TDRM to protease and reverse transcriptase inhibitors were performed according to the Calibrated Population Resistance (CPR) Tool 6.0. Overall, subtype B remains the most prevalent in Rio de Janeiro in both LTS and RS HIV-1 infected individuals. An increased proportion of recombinant samples was detected over time, especially in RS heterosexual men, due to the emergence of CRF02_AG and URF samples bearing a subtype K fragment. The prevalence of HIV-1 samples carrying TDRM was high and similar between LTS and RS (15.7% vs 14.6%) or age (<25yo 17.9% vs >25yo 16.6%) along the study period. The high resistance levels detected in both populations are of concern, especially considering the dynamics of HIV-1 diversity over time. Our results suggest that the incorporation of resistance testing prior to HAART initiation should be highly considered, as well as permanent surveillance, aiming to carefully monitoring HIV-1 diversity, with focus on CRF/URF emergence and putative transmission.
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Affiliation(s)
- Carlos A. Velasco-de-Castro
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Laboratório de Virologia, Departamento de Patologia Clínica, Instituto Fernandes Figueira, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- * E-mail: (MGM); (CAVdC)
| | - Beatriz Grinsztejn
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Valdiléa G. Veloso
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Francisco I. Bastos
- Instituto de Comunicação e Informação Científica e Tecnológica em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Laboratório de Informação em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil, and Imperial College London (CAPES visiting researcher # 17551-12-8), London, United Kingdom
| | - José H. Pilotto
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Hospital Geral de Nova Iguaçu, Nova Iguaçu, RJ, Brasil
| | - Nilo Fernandes
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Mariza G. Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- * E-mail: (MGM); (CAVdC)
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10
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Ivanov IA, Beshkov D, Shankar A, Hanson DL, Paraskevis D, Georgieva V, Karamacheva L, Taskov H, Varleva T, Elenkov I, Stoicheva M, Nikolova D, Switzer WM. Detailed molecular epidemiologic characterization of HIV-1 infection in Bulgaria reveals broad diversity and evolving phylodynamics. PLoS One 2013; 8:e59666. [PMID: 23527245 PMCID: PMC3602066 DOI: 10.1371/journal.pone.0059666] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 02/20/2013] [Indexed: 11/19/2022] Open
Abstract
Limited information is available to describe the molecular epidemiology of HIV-1 in Bulgaria. To better understand the genetic diversity and the epidemiologic dynamics of HIV-1 we analyzed 125 new polymerase (pol) sequences from Bulgarians diagnosed through 2009 and 77 pol sequences available from our previous study from persons infected prior to 2007. Epidemiologic and demographic information was obtained from each participant and phylogenetic analysis was used to infer HIV-1 evolutionary histories. 120 (59.5%) persons were infected with one of five different HIV-1 subtypes (A1, B, C, F1 and H) and 63 (31.2%) persons were infected with one of six different circulating recombinant forms (CRFs; 01_AE, 02_AG, 04_cpx, 05_DF, 14_BG, and 36_cpx). We also for the first time identified infection with two different clusters of unique A-like and F-like sub-subtype variants in 12 persons (5.9%) and seven unique recombinant forms (3.5%), including a novel J/C recombinant. While subtype B was the major genotype identified and was more prevalent in MSM and increased between 2000–2005, most non-B subtypes were present in persons ≥45 years old. CRF01_AE was the most common non-B subtype and was higher in women and IDUs relative to other risk groups combined. Our results show that HIV-1 infection in Bulgaria reflects the shifting distribution of genotypes coincident with the changing epidemiology of the HIV-1 epidemic among different risk groups. Our data support increased public health interventions targeting IDUs and MSM. Furthermore, the substantial and increasing HIV-1 genetic heterogeneity, combined with fluctuating infection dynamics, highlights the importance of sustained and expanded surveillance to prevent and control HIV-1 infection in Bulgaria.
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Affiliation(s)
- Ivailo Alexiev Ivanov
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria.
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Dwivedi SK, Sengupta S. Classification of HIV-1 sequences using profile Hidden Markov Models. PLoS One 2012; 7:e36566. [PMID: 22623958 PMCID: PMC3356369 DOI: 10.1371/journal.pone.0036566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 04/10/2012] [Indexed: 11/19/2022] Open
Abstract
Accurate classification of HIV-1 subtypes is essential for studying the dynamic spatial distribution pattern of HIV-1 subtypes and also for developing effective methods of treatment that can be targeted to attack specific subtypes. We propose a classification method based on profile Hidden Markov Model that can accurately identify an unknown strain. We show that a standard method that relies on the construction of a positive training set only, to capture unique features associated with a particular subtype, can accurately classify sequences belonging to all subtypes except B and D. We point out the drawbacks of the standard method; namely, an arbitrary choice of threshold to distinguish between true positives and true negatives, and the inability to discriminate between closely related subtypes. We then propose an improved classification method based on construction of a positive as well as a negative training set to improve discriminating ability between closely related subtypes like B and D. Finally, we show how the improved method can be used to accurately determine the subtype composition of Common Recombinant Forms of the virus that are made up of two or more subtypes. Our method provides a simple and highly accurate alternative to other classification methods and will be useful in accurately annotating newly sequenced HIV-1 strains.
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Affiliation(s)
- Sanjiv K. Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- School of Sciences, Indian Institute of Technology, Indore, Indore, India
| | - Supratim Sengupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal, India
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12
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Huang A, Hogan JW, Istrail S, Delong A, Katzenstein DA, Kantor R. Global analysis of sequence diversity within HIV-1 subtypes across geographic regions. Future Virol 2012; 7:505-517. [PMID: 22822410 DOI: 10.2217/fvl.12.37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AIMS: HIV-1 sequence diversity can affect host immune responses and phenotypic characteristics such as antiretroviral drug resistance. Current HIV-1 sequence diversity classification uses phylogeny-based methods to identify subtypes and recombinants, which may overlook distinct subpopulations within subtypes. While local epidemic studies have characterized sequence-level clustering within subtypes using phylogeny, identification of new genotype - phenotype associations are based on mutational correlations at individual sequence positions. We perform a systematic, global analysis of position-specific pol gene sequence variation across geographic regions within HIV-1 subtypes to characterize subpopulation differences that may be missed by standard subtyping methods and sequence-level phylogenetic clustering analyses. MATERIALS #ENTITYSTARTX00026; METHODS: Analysis was performed on a large, globally diverse, cross-sectional pol sequence dataset. Sequences were partitioned into subtypes and geographic subpopulations within subtypes. For each subtype, we identified positions that varied according to geography using VESPA (viral epidemiology signature pattern analysis) to identify sequence signature differences and a likelihood ratio test adjusted for multiple comparisons to characterize differences in amino acid (AA) frequencies, including minority mutations. Synonymous nonsynonymous analysis program (SNAP) was used to explore the role of evolutionary selection witihin subtype C. RESULTS: In 7693 protease (PR) and reverse transcriptase (RT) sequences from untreated patients in multiple geographic regions, 11 PR and 11 RT positions exhibited sequence signature differences within subtypes. Thirty six PR and 80 RT positions exhibited within-subtype geography-dependent differences in AA distributions, including minority mutations, at both conserved and variable loci. Among subtype C samples from India and South Africa, nine PR and nine RT positions had significantly different AA distributions, including one PR and five RT positions that differed in consensus AA between regions. A selection analysis of subtype C using SNAP demonstrated that estimated rates of nonsynonymous and synonymous mutations are consistent with the possibility of positive selection across geographic subpopulations within subtypes. CONCLUSION: We characterized systematic genotypic pol differences across geographic regions within subtypes that are not captured by the subtyping nomenclature. Awareness of such differences may improve the interpretation of future studies determining the phenotypic consequences of genetic backgrounds.
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Affiliation(s)
- Austin Huang
- Division of Infectious Diseases, Brown University, Providence, RI, USA
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13
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Genetic characterization of bluetongue virus serotype 9 isolates from India. Virus Genes 2012; 44:286-94. [DOI: 10.1007/s11262-011-0707-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
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14
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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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15
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Safiullah Sarker M, Rahman M, Urmi AZ, Al-Mamun F, Islam LN, Azim T. Detection of a Rare HIV Type 1 Strain CRF16_A2D in Bangladesh. AIDS Res Hum Retroviruses 2011; 27:435-8. [PMID: 20929347 DOI: 10.1089/aid.2010.0209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Circulating recombinant form (CRF) 16_A2D is a rare HIV strain among the most recently identified subsubtype A2. Samples taken from an HIV-seropositive married couple who attended a voluntary counseling and testing unit in Dhaka, Bangladesh showed two rare CRF16_A2D isolates. Further genetic analyses targeting three HIV genes (gag, pol, and env) showed that the two isolates from the couple were closely related making it likely that one of them acquired the virus and transferred it to the other. The husband admitted that he had contact with sex workers and both wife and husband had never traveled outside the country. This indicates that the husband might have acquired the virus from sex workers and that this rare strain is already circulating in the country. Detecting unusual isolates is important to determine the true diversity of HIV strains in the country. Monitoring of such strains will help in identifying transmission patterns and possible interventions to prevent the spread of HIV infection.
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Affiliation(s)
- M. Safiullah Sarker
- Virology Laboratory, ICDDR,B, Mohakhali, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | | | - Feroz Al-Mamun
- Virology Laboratory, ICDDR,B, Mohakhali, Dhaka, Bangladesh
| | - Laila N. Islam
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tasnim Azim
- Virology Laboratory, ICDDR,B, Mohakhali, Dhaka, Bangladesh
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HIV Genetic Diversity and Drug Resistance. Viruses 2010; 2:503-531. [PMID: 21994646 PMCID: PMC3185604 DOI: 10.3390/v2020503] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 12/11/2009] [Accepted: 02/01/2010] [Indexed: 02/07/2023] Open
Abstract
Most of the current knowledge on antiretroviral (ARV) drug development and resistance is based on the study of subtype B of HIV-1, which only accounts for 10% of the worldwide HIV infections. Cumulative evidence has emerged that different HIV types, groups and subtypes harbor distinct biological properties, including the response and susceptibility to ARV. Recent laboratory and clinical data highlighting such disparities are summarized in this review. Variations in drug susceptibility, in the emergence and selection of specific drug resistance mutations, in viral replicative capacity and in the dynamics of resistance acquisition under ARV selective pressure are discussed. Clinical responses to ARV therapy and associated confounding factors are also analyzed in the context of infections by distinct HIV genetic variants.
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Abstract
Background Human Immunodeficiency Virus type 1 (HIV-1), the causative agent of Acquired Immune Deficiency Syndrome (AIDS), exhibits very high genetic diversity with different variants or subtypes prevalent in different parts of the world. Proper classification of the HIV-1 subtypes, displaying differential infectivity, plays a major role in monitoring the epidemic and is also a critical component for effective treatment strategy. The existing methods to classify HIV-1 sequence subtypes, based on phylogenetic analysis focusing only on specific genes/regions, have shown inconsistencies as they lack the capability to analyse whole genome variations. Several isolates are left unclassified due to unresolved sub-typing. It is apparent that classification of subtypes based on complete genome sequences, rather than sub-genomic regions, is a more robust and comprehensive approach to address genome-wide heterogeneity. However, no simple methodology exists that directly computes HIV-1 subtype from the complete genome sequence. Results We use Chaos Game Representation (CGR) as an approach to identify the distinctive genomic signature associated with the DNA sequence organisation in different HIV-1 subtypes. We first analysed the effect of nucleotide word lengths (k = 2 to 8) on whole genomes of the HIV-1 M group sequences, and found the optimum word length of k = 6, that could classify HIV-1 subtypes based on a Test sequence set. Using the optimised word length, we then showed accurate classification of the HIV-1 subtypes from both the Reference Set sequences and from all available sequences in the database. Finally, we applied the approach to cluster the five unclassified HIV-1 sequences from Africa and Europe, and predict their possible subtypes. Conclusion We propose a genomic signature-based approach, using CGR with suitable word length optimisation, which can be applied to classify intra-species variations, and apply it to the complex problem of HIV-1 subtype classification. We demonstrate that CGR is a simple and computationally less intensive method that not only accurately segregates the HIV-1 subtype and sub-subtypes, but also aid in the classification of the unclassified sequences. We hope that it will be useful in subtype annotation of the newly sequenced HIV-1 genomes.
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Affiliation(s)
- Aridaman Pandit
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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18
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An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol 2009; 5:e1000581. [PMID: 19956739 PMCID: PMC2776870 DOI: 10.1371/journal.pcbi.1000581] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 10/28/2009] [Indexed: 11/19/2022] Open
Abstract
Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (≈5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate, robust and extensible subtyping procedures is clear. There are nine different subtypes of the main group of HIV-1, each originating as a distinct subepidemic of HIV-1. The distribution of subtypes is often unique to a given geographic region of the world and constitutes a useful epidemiological and surveillance resource. The effects of viral subtype on disease progression, treatment outcome and vaccine design are being actively researched, and the importance of accurate subtyping procedures is clear. In HIV-1, subtype assignment is complicated by frequent recombination among co-circulating strains, creating new genetic mosaics or recombinant forms: 43 have been characterized to date, and many more likely exist. We present an automated phylogenetic method (SCUEAL) to accurately characterize both simple and complex HIV-1 mosaics. Using computer simulations and biological data we demonstrate that SCUEAL performs very well under various conditions, especially when some of the existing classification procedures fail. Furthermore, we show that a small, but noticeable proportion of subtype characterization stored in public databases may be incomplete or incorrect. The computational technique introduced here should provide a much more accurate characterization of HIV-1 strains, especially novel recombinants, and lead to new insights into molecular history, epidemiology and geographical distribution of the virus.
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Huang DD, Foley BT, Tolzmann CA, Ouma A, Bremer JW. Complex mosaic composition of near full-length genomes of two NED (NIH-ENVA-DOD) subtype panel HIV type 1 strains, BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC). AIDS Res Hum Retroviruses 2009; 25:1039-43. [PMID: 19795987 DOI: 10.1089/aid.2009.0078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sequence characterization of the near full-length genomes of HIV-1 isolates BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC), was continued. These NED panel isolates, contributed by F. Brun-Vezinet (ENVA-France), were first identified as subtypes G and H, respectively. Our earlier analyses of portions of their pol genes showed that both were likely to be intersubtype recombinants of different composition. This study analyzed the remainder of each genome, confirming them to be complex recombinants. The BCF-Dioum genome resembles CRF06_cpx strains found in West Africa, composed of subtypes A/G/J/K. The BCF-Kita genome is a unique complex recombinant A-F-G-H-K-U strain. These data support previous observations of the complexity of strains originating from the DRC. BCF-Dioum may be a suitable strain for standards and reagents since it matches a defined circulating recombinant form. Studies and reagents made from BCF-Kita should take into account its complex genome.
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Affiliation(s)
- Diana D. Huang
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - Brian T. Foley
- HIV Sequence Database, Theoretical Biology and Biophysics Group (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Catlin A. Tolzmann
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - Annastasia Ouma
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - James W. Bremer
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
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20
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Kousiappa I, Van De Vijver DA, Kostrikis LG. Near full-length genetic analysis of HIV sequences derived from Cyprus: evidence of a highly polyphyletic and evolving infection. AIDS Res Hum Retroviruses 2009; 25:727-40. [PMID: 19619035 DOI: 10.1089/aid.2008.0239] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular epidemiology of HIV-1 infection was previously studied in Cyprus but the degree of HIV-1 diversity has remained indefinable. The main objective of the present study is to examine HIV-1 strains isolated from 77 HIV-1-infected individuals representing 38% of the known infected population in Cyprus in the period 1986 to 2006. DNA of the near full-length genome encoding gag, pol, vif, vpr, vpu, tat, rev, env, and 5'-end of nef was amplified by nested PCR/RT-PCR from all HIV-1 seropositives and sequenced using a newly designed assay. Detailed phylogenetic and bootscanning analyses were performed to determine phylogenetic associations and subtype assignments. Phylogenetic analyses of the obtained viral sequences indicated that subtype B was the dominant subtype (61%), followed by subtype A (23.3%), subtype C (5.2%), CRF02_AG (3.9%), and subtype D, CRF01_AE, and CRF04_cpx (1.3% each). Two HIV-1 isolates (2.6%), originating from the Democratic Republic of Congo (DRC), were not classified in any pure (sub)subtype or circulating recombinant form (CRF). Complete phylogenetic and bootscanning analyses revealed that one of these isolates had a new, unique recombinant pattern, comprising segments of subtypes D and G, and is distinct from any other CRFs or URFs reported so far. Detailed analyses of the sequence of the second isolate, which could not be classified, reveal that it is close to subtype K reference sequences but clusters near the root of the clade. At least two epidemiologically unrelated HIV-1 seropositives with an HIV-1 variant similar to this isolate are required to designate this variant as a novel HIV-1 subtype or subsubtype of subtype K. Analogous to results of the earlier epidemiological studies, these data exhibit the extensive heterogeneity of HIV-1 infection in Cyprus, which is being fueled by a continuous entry of new strains from other countries, creating an evolving and polyphyletic infection.
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Affiliation(s)
- Ioanna Kousiappa
- Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - David A.M.C. Van De Vijver
- Department of Virology, Erasmus MC, University Medical Centre Rotterdam, 3000 CA Rotterdam, The Netherlands
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Sanabani SS, Pastena ERDS, Kleine Neto W, Barreto CC, Ferrari KT, Kalmar EMN, Ferreira S, Sabino EC. Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in São Paulo, Brazil. Virol J 2009; 6:78. [PMID: 19531216 PMCID: PMC2704198 DOI: 10.1186/1743-422x-6-78] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 06/16/2009] [Indexed: 01/13/2023] Open
Abstract
Background The genetic diversity of the human immunodeficiency virus type 1 (HIV-1) is critical to lay the groundwork for the design of successful drugs or vaccine. In this study we aimed to characterize and define the molecular prevalence of HIV-1 subclade F1 currently circulating in São Paulo, Brazil. Methods A total of 36 samples were selected from 888 adult patients residing in São Paulo who had previously been diagnosed in two independent studies in our laboratory as being infected with subclade F1 based on pol subgenomic fragment sequencing. Proviral DNA was amplified from the purified genomic DNA of all 36 blood samples by 5 fragments overlapping PCR followed by direct sequencing. Sequence data were obtained from the 5 fragments of pure subclade F1 and phylogenetic trees were constructed and compared with previously published sequences. Subclades F1 that exhibited mosaic structure with other subtypes were omitted from any further analysis Results Our methods of fragment amplification and sequencing confirmed that only 5 sequences inferred from pol region as subclade F1 also holds true for the genome as a whole and, thus, estimated the true prevalence at 0.56%. The results also showed a single phylogenetic cluster of the Brazilian subclade F1 along with non-Brazilian South American isolates in both subgenomic and the full-length genomes analysis with an overall intrasubtype nucleotide divergence of 6.9%. The nucleotide differences within the South American and Central African F1 strains, in the C2-C3 env, were 8.5% and 12.3%, respectively. Conclusion All together, our findings showed a surprisingly low prevalence rate of subclade F1 in Brazil and suggest that these isolates originated in Central Africa and subsequently introduced to South America.
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Lemey P, Lott M, Martin DP, Moulton V. Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics 2009; 10:126. [PMID: 19397803 PMCID: PMC2684544 DOI: 10.1186/1471-2105-10-126] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 04/27/2009] [Indexed: 12/02/2022] Open
Abstract
Background Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences. Results Analysis of phylogenetic simulations reveal that identifying the descendents of relatively old recombination events is a challenging task for all methods available, and that quartet scanning performs relatively well compared to the triplet based methods. The use of quartet scanning is further demonstrated by analyzing both well-established and putative HIV-1 recombinant strains. In agreement with recent findings, we provide evidence that the presumed circulating recombinant CRF02_AG is a 'pure' lineage, whereas the presumed parental lineage subtype G has a recombinant origin. We also demonstrate HIV-1 intrasubtype recombination, confirm the hybrid origin of SIV in chimpanzees and further disentangle the recombinant history of SIV lineages in a primate immunodeficiency virus data set. Conclusion Quartet scanning makes a valuable addition to triplet-based methods for identifying recombinant sequences without prior specifications of either query and reference sequences. The new method is available in the VisRD v.3.0 package .
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Affiliation(s)
- Philippe Lemey
- Rega Institute, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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23
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Close phylogenetic relationship between Angolan and Romanian HIV-1 subtype F1 isolates. Retrovirology 2009; 6:39. [PMID: 19386115 PMCID: PMC2680801 DOI: 10.1186/1742-4690-6-39] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Accepted: 04/22/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Here, we investigated the phylogenetic relationships of the HIV-1 subtype F1 circulating in Angola with subtype F1 strains sampled worldwide and reconstructed the evolutionary history of this subtype in Central Africa. METHODS Forty-six HIV-1-positive samples were collected in Angola in 2006 and subtyped at the env-gp41 region. Partial env-gp120 and pol-RT sequences and near full-length genomes from those env-gp41 subtype F1 samples were further generated. Phylogenetic analyses of partial and full-length subtype F1 strains isolated worldwide were carried out. The onset date of the subtype F1 epidemic in Central Africa was estimated using a Bayesian Markov chain Monte Carlo approach. RESULTS Nine Angolan samples were classified as subtype F1 based on the analysis of the env-gp41 region. All nine Angolan sequences were also classified as subtype F1 in both env-gp120 and pol-RT genomic regions, and near full-length genome analysis of four of these samples confirmed their classification as "pure" subtype F1. Phylogenetic analyses of subtype F1 strains isolated worldwide revealed that isolates from the Democratic Republic of Congo (DRC) were the earliest branching lineages within the subtype F1 phylogeny. Most strains from Angola segregated in a monophyletic group together with Romanian sequences; whereas South American F1 sequences emerged as an independent cluster. The origin of the subtype F1 epidemic in Central African was estimated at 1958 (1934-1971). CONCLUSION "Pure" subtype F1 strains are common in Angola and seem to be the result of a single founder event. Subtype F1 sequences from Angola are closely related to those described in Romania, and only distantly related to the subtype F1 lineage circulating in South America. Original diversification of subtype F1 probably occurred within the DRC around the late 1950s.
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Drug resistance mutation profile and accumulation kinetics in human immunodeficiency virus-positive individuals infected with subtypes B and F failing highly active antiretroviral therapy are influenced by different viral codon usage patterns. Antimicrob Agents Chemother 2008; 52:4497-502. [PMID: 18838582 DOI: 10.1128/aac.00820-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major human immunodeficiency virus type 1 subtype circulating in Brazil is B, followed by F and C. We have genotyped 882 samples from Brazilian patients for whom highly active antiretroviral therapy failed, and we found subtype B and the unique recombinant B/F1 forms circulating. Due to codon usage variation, there is a significantly lower incidence of the substitutions L210W, Q151M, and F116Y in subtype F1 isolates than in the subtype B counterparts.
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Sylla M, Chamberland A, Boileau C, Traoré HA, Ag-Aboubacrine S, Cissé M, Koala S, Drabo J, Diallo I, Niamba P, Tremblay-Sher D, Machouf N, Rashed S, Nickle DC, Nguyen VK, Tremblay CL. Characterization of drug Resistance in Antiretroviral-Treated Patients Infected with HIV-1 CRF02_AG and AGK Subtypes in Mali and Burkina Faso. Antivir Ther 2008. [DOI: 10.1177/135965350801300116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background In a multicentred cohort of patients on antiretroviral therapy (ART) in Burkina Faso and Mali, we analysed the prevalence of HIV drug resistance mutations in patients failing a modified directly observed therapy (mDOT) protocol. Methods Patients on ART >6 months and with viral load (VL) >500 copies/ml were enrolled in a mDOT protocol. Genotypic resistance testing was performed on pre- and post-mDOT plasma samples of patients who still had VL >500 copies/ml after mDOT. Results Eight hundred and one patients from seven sites participated in the study. One hundred and thirteen patients (14.1%) had VL >500 copies/ml. Most patients were treated with lamivudine along with zidovudine or stavudine and efavirenz or nevirapine. Genotypes were available for 46 patients. The predominant HIV-1 subtypes were CRF02_AG in 26 (56.5%) and AGK/K/AK in 12 (26.1%) patients. The prevalence of drug resistance mutations by class were as follows for nucleoside reverse transcriptase inhibitors: 184I/V (82.6%), 215Y/F (32.6%), 219E/Q (19.6%), 70R (19.6%), 67N (21.7%), 41L (15.2%) and 151M(2.2%). For non-nucleoside reverse transcriptase inhibitors the prevalence was: 103N (50%) and 181C/I (19.6%). Phylogenetic analysis showed that, although the genetic distances were small among isolates, there was no clustering of a particular subtype in a specific region and that the high prevalence of AGK subtype in our drug-resistant population was not due to a circulating resistant strain. Conclusion Although CRF02_AG is the dominant clade in the Burkina Faso/Mali region, isolates with subtype K reverse transcriptase were frequent in our cohort. Drug resistance mutation pathways in subtype K reverse transcriptase need to be further evaluated in a larger cohort of non-B HIV-infected individuals.
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Affiliation(s)
| | - Mohamed Sylla
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
| | - Annie Chamberland
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
- Centre Hospitalier de l'Université de Montréal, Montréal, Canada
| | - Catherine Boileau
- Département de Médecine sociale et préventive, Université de Montréal, Montréal, Canada
| | | | | | | | | | - Joseph Drabo
- Centre hospitalier national Yalgado Ouédraogo, Ouagadougou, Burkina Faso
| | - Ismael Diallo
- Centre hospitalier national Yalgado Ouédraogo, Ouagadougou, Burkina Faso
| | - Pascal Niamba
- Centre hospitalier national Yalgado Ouédraogo, Ouagadougou, Burkina Faso
| | - Daniel Tremblay-Sher
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
| | - Nimâ Machouf
- Département de Médecine sociale et préventive, Université de Montréal, Montréal, Canada
- Clinique l'Actuel, Montréal, Canada
| | - Sélim Rashed
- Unité de Santé Internationale, Université de Montréal and Centre Hospitalier Maisonneuve-Rosemont, Montréal, Canada
| | - David C Nickle
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Vinh-Kim Nguyen
- Département de Médecine sociale et préventive, Université de Montréal, Montréal, Canada
- Clinique l'Actuel, Montréal, Canada
| | - Cécile L Tremblay
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
- Centre Hospitalier de l'Université de Montréal, Montréal, Canada
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Sacktor N, Nakasujja N, Robertson K, Clifford DB. HIV-associated cognitive impairment in sub-Saharan Africa--the potential effect of clade diversity. ACTA ACUST UNITED AC 2007; 3:436-43. [PMID: 17671521 DOI: 10.1038/ncpneuro0559] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 05/23/2007] [Indexed: 11/10/2022]
Abstract
In the US, HIV dementia occurs in 10-15% of HIV-positive individuals with advanced infection. The prevalence of HIV dementia in sub-Saharan countries, where the vast majority of individuals with HIV reside, is largely unknown. This Review will summarize our current understanding of HIV-associated cognitive impairment in resource-limited settings, focusing specifically on the countries of sub-Saharan Africa. We will describe the frequency of HIV dementia and HIV-associated cognitive impairment from several case series in the sub-Saharan region. We will then summarize recent studies from Uganda and Ethiopia that included detailed neuropsychological assessments. The potential influence of clade diversity on HIV-associated cognitive impairment will be discussed. Differences between the results of the studies in Uganda and in Ethiopia raise the possibility that HIV subtypes might have different biological properties with respect to their capacity to cause HIV-associated cognitive impairment. Further studies are needed to determine the true prevalence of HIV dementia in sub-Saharan Africa and to establish whether specific clade subtypes might influence the presentation of neurological complications.
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Affiliation(s)
- Ned Sacktor
- Department of Neurology, Johns Hopkins University School of Medicine, Johns Hopkins Bayview Medical Center, Baltimore, MD 21224, USA.
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27
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Sagoe KWC, Dwidar M, Lartey M, Boamah I, Agyei AA, Hayford AA, Mingle JAA, Arens MQ. Variability of the human immunodeficiency virus type 1 polymerase gene from treatment naïve patients in Accra, Ghana. J Clin Virol 2007; 40:163-7. [PMID: 17827059 DOI: 10.1016/j.jcv.2007.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 07/16/2007] [Accepted: 07/23/2007] [Indexed: 11/24/2022]
Abstract
BACKGROUND Little is known about the HIV-1 drug resistance mutations in Ghana. OBJECTIVES To determine the background protease (PR) and reverse transcriptase (RT) mutations of HIV-1 from treatment naïve patients in Ghana. STUDY DESIGN Twenty-five plasma samples randomly selected were analyzed for drug resistance mutations. The molecular phylogeny and recombinant patterns of the polymerase gene of HIV-1 were also analysed. RESULTS No major drug-resistance mutations were seen in protease or reverse transcriptase genes. The L10I, L10V, V11I and E35G minor mutations were seen in four patients, while the V179E was observed in a patient with subtype G. An insertion of lysine was found at codon 36 of the protease gene of one patient. The predominant subtype was the CRF02_AG strain (n=22), but 3 (13.6%) of these were recombinants with HIV-1 subtype K and/or A1. Two patients harboured unclassified/complex strains with D/CRF01_AE and G/CRFAG_02 subtypes for the PR and RT, respectively, using the Stanford Database. Viral loads (VL) ranged from 2290 to >1,500,000c/ml (mean=339,065c/ml). CONCLUSIONS Treatment naïve patients in Ghana before scale-up may have minor but not major PR mutations and high viral loads. The clinical effects of minor mutations/polymorphisms in the PR and RT genes and recombinants need to be investigated.
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Buonaguro L, Tornesello ML, Buonaguro FM. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol 2007; 81:10209-19. [PMID: 17634242 PMCID: PMC2045484 DOI: 10.1128/jvi.00872-07] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- L Buonaguro
- Laboratory of Viral Oncogenesis and Immunotherapy & AIDS Reference Center, Ist. Naz. Tumori Fond. G. Pascale, Via Mariano Semmola, 1, 80131 Naples, Italy.
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Sarrami-Forooshani R, Das SR, Sabahi F, Adeli A, Esmaeili R, Wahren B, Mohraz M, Haji-Abdolbaghi M, Rasoolinejad M, Jameel S, Mahboudi F. Molecular analysis and phylogenetic characterization of HIV in Iran. J Med Virol 2006; 78:853-63. [PMID: 16721846 DOI: 10.1002/jmv.20634] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the last few years. While the earliest cases were found in hemophiliacs, intravenous drug users are now fueling the outbreak. In this study, both the 122 clones of HIV-1 gag p17 and the 131 clones of env V1-V5 region were obtained from 61 HIV-1 seropositives belonging to these two groups in Iran. HIV-1 subtyping and phylogenetic analysis was done by heteroduplex mobility assays (HMA) and multiple clone sequencing. The result indicated all hemophiliacs are infected with HIV-1 subtype B and all intravenous drug users are infected with HIV-1 subtype A. Since intravenous drug abuse is the major transmission route in Iran, HIV-1 subtype A is likely to be the dominant viral subtype circulating in the country. The analysis of genetic distances showed subtype B viruses in Iran to be twice as heterogeneous as the subtype A viruses. In conclusion, this first molecular study of HIV-1 genotypes in Iran suggests two parallel outbreaks in distinct high-risk populations and may offer clues to the origin and spread of infection in Iran.
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30
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Visawapoka U, Tovanabutra S, Currier JR, Cox JH, Mason CJ, Wasunna M, Ponglikitmongkol M, Dowling WE, Robb ML, Birx DL, McCutchan FE. Circulating and unique recombinant forms of HIV type 1 containing subsubtype A2. AIDS Res Hum Retroviruses 2006; 22:695-702. [PMID: 16831094 DOI: 10.1089/aid.2006.22.695] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 strains containing subsubtype A2 are relatively rare in the pandemic but have been repeatedly identified in Kenya, where candidate vaccines based in part on subtype A, but not A2 strains, may be evaluated. Among the most recent is CRF16_A2D, a circulating recombinant form (CRF) whose prototypes are complete or partial HIV-1 sequences from Kenya, Korea, and Argentina. Using samples from blood bank discards in Kenya and complete genome sequencing, this report further documents CRF16_A2D and related recombinants and identifies a second CRF, CRF21_A2D. The two A2-containing CRFs, and two recombinants related to CRF16_A2D, share common structural elements but appear to have been independently derived. Concerted selection may have influenced the emergence and spread of certain A2-containing strains in Kenya. The second complete subtype C sequence from Kenya is also reported here. Monitoring of A2-containing recombinants and subtype C strains, both relatively rare in Kenya, may be informative in the course of cohort development and evaluation of candidate vaccines.
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Affiliation(s)
- Unchalee Visawapoka
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
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Lin HH, Gaschen BK, Collie M, El-Fishaway M, Chen Z, Korber BT, Beatrice ST, Zhang L. Genetic characterization of diverse HIV-1 strains in an immigrant population living in New York City. J Acquir Immune Defic Syndr 2006; 41:399-404. [PMID: 16652046 DOI: 10.1097/01.qai.0000200663.47838.f1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
New York City (NYC) is one of the original foci of the HIV-1 epidemic and has a greater number of AIDS cases than any other city in the United States. NYC also hosts the highest number of immigrants among the nation's cities: more than 2 million among a total population of 8 million. Such a high rate of immigration could act as a potential source for introducing and disseminating novel HIV-1 strains into the United States. Our current study focuses on the genetic characterization of HIV-1 strains circulating in an immigrant population in NYC. Of the 505 HIV-1-positive specimens obtained, 196 were available for viral sequencing from the C2 to V3 region of env. Phylogenetic analysis using maximum-likelihood and neighbor-joining methods demonstrated that non-B subtypes and circulating recombinant forms (CRFs) accounted for 43.4% (85 of 196 cases), whereas the remaining 56.6% (111 of 196) cases had viral variants similar to the typical North American subtype B virus. Of those non-B subtypes and CRFs, subtype A and CRF02 dominated (63.5% combined); other subtypes, including C, D, F1, G, CRF01_AE, and CRF06_cpx, were also detected. Two HIV-1 sequences do not cluster with any known subtypes or CRFs. Furthermore, the distribution of non-B subtypes and CRFs was consistent with the countries of origin, suggesting that many of the study subjects were likely infected in their home country before they entered the United States. Subtype B viruses identified in the immigrant population showed no significant differences from the typical North American B subtype, however, indicating that a significant proportion of the immigrants must have been infected after they came to the United States. Public health officials and physicians should be aware of the growing genetic diversity of HIV-1 in this country, particularly in areas with sizable immigrant populations.
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Affiliation(s)
- Hsi-Hsun Lin
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY 10016, USA
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Couto-Fernandez JC, Eyer-Silva WA, Guimarães ML, Chequer-Fernandez SL, Grinsztejn B, Delaporte E, Peeters M, Morgado MG. Phylogenetic analysis of Brazilian HIV type 1 subtype D strains: tracing the origin of this subtype in Brazil. AIDS Res Hum Retroviruses 2006; 22:207-11. [PMID: 16478405 DOI: 10.1089/aid.2006.22.207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
HIV-1 Subtype D occurs mainly in East and Central African countries, especially Uganda, where the prevalence of HIV-1 infection is among the highest in the world. We present the phylogenetic analysis of one nonautochthonous and four autochthonous (including a near full-length genome) Brazilian HIV-1 subtype D strains identified in Rio de Janeiro State, where subtypes B, F1, and BF1 recombinants predominate. Phylogenetic inferences using maximum likelihood were applied on a near-full length genome and on concatenated gag, protease, reverse transcriptase, integrase, C2V3/env, gp41, and nef segments. Sequences from an Angolan immigrant showed close genetic similarity with a strain described in Finland, from an HIV patient of African origin, whereas all four autochthonous Brazilian sequences clustered with South African strains, where subtype D occurs only in isolated cases. Our results suggest the successful introduction and circulation in Brazil of closely related HIV-1 subtype D strains, possibly of South African origin.
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Affiliation(s)
- José Carlos Couto-Fernandez
- Laboratório de AIDS & Imunologia Molecular, Departamento de Imunologia-ioc, Fundação Oswaldo Cruz, Av. Brasil 4365, Pavilhão Leônidas Deane, 413-415 Manguinhos, Rio de Janeiro-RJ, 21.045-900 Brazil.
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Yagyu F, Okitsu S, Tanamoto K, Ushijima H. Determination of HIV-1 subtypes (A-D, F, G, CRF01_AE) by PCR in the transmembrane region (gp41) with novel primers. J Med Virol 2005; 76:16-23. [PMID: 15778948 DOI: 10.1002/jmv.20318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HIV-1 has a huge genetic diversity. So far, nine subtypes have been isolated, namely, subtypes A, B, C, D, F, G, H, J, and K. Epidemiological study provides information which may help in the development of HIV-1 prevention programs or health policies. In the future, subtyping may also be critical for vaccine development, and an effective anti-viral drug will need to be effective for different subtypes of HIV virus. The analysis of the nucleotide sequence of the v3 region is considered the most reliable method for determining the HIV-1 subtype. However, the procedures for determining the v3 sequences are complicated and time consuming, requiring expensive reagents, equipment, and well-trained personnel. The polymerase chain reaction (PCR) method using subtype-specific primers for HIV-1 subtyping is easier and faster. The objective of this study was to develop subtype-specific primers for subtyping PCR. The specific primers were designed for subtypes A, B, C, D, F, G, and CRF01_AE, and these primers could be applied to assay for various HIV-1 subtypes in the clinical samples. The specific primers were designed for each subtypes in the gp41 region. The result of PCR was compared with the subtypes which was determined by the v3 sequence. The results of subtyping by PCR using the newly designed primers could detect 29 of 33 patients tested, and all matched those obtained by nucleotide sequencing of the env v3 region except for three subjects, which were differentiated as CRF02_AG. The newly designed primers functioned accurately and conclusively. In comparison with PCR as a method for the determination of subtypes, sequence analysis requires better-trained personnel, more expensive reagents, and more equipment and time.
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Affiliation(s)
- Fumihiro Yagyu
- Department of Developmental Medical Sciences, Institute of International Health, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Buckheit RW. Understanding HIV resistance, fitness, replication capacity and compensation: targeting viral fitness as a therapeutic strategy. Expert Opin Investig Drugs 2005; 13:933-58. [PMID: 15268633 DOI: 10.1517/13543784.13.8.933] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The increasingly prevalent emergence of drug-resistant virus strains in patients being treated with highly active antiretroviral regimens and the increasing rates of transmission of drug-resistant virus strains have focused attention on the critical need for additional antiretroviral agents with novel mechanisms of action and enhanced potency. Furthermore, novel means of employing highly active antiretroviral therapy are needed to reduce or eliminate the virological treatment failures that currently occur. Over the past several years, evidence has mounted supporting the fact that the emergence of resistant strains is associated with reductions in viral fitness, yielding decreases in plasma virus load in treated patients harbouring resistant populations of the virus. Additional mutations that serve to modify fitness (compensatory mutations) and mutations that impact the viral replication capacity also emerge under the selective pressure of drug treatment, and have both negative and positive effects on virus growth. Fitness is generally accepted to refer to the ability of HIV to replicate in a defined environment and thus is used to describe the viral replication potential in the absence of the drug. Although viral fitness and replication capacity are related in some ways, it is important to recognise that viral fitness is not the same as viral replication capacity. This review will assess the recent literature on antiviral drug resistance, viral fitness and viral replication capacity, and discuss means by which the adaptability of HIV to respond rapidly to antiviral treatment through mutation may be used against it. This would be done by treating patients with an aim to lock the deleterious mutations into the resistant virus genome, resulting in a positive therapeutic outcome despite the presence of resistance to the selecting agents. The review will specifically discuss the literature on nucleoside and non-nucleoside reverse transcriptase inhibitors, protease inhibitors, integrase inhibitors, fusion inhibitors, as well as other biological factors involved in viral fitness.
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Affiliation(s)
- Robert W Buckheit
- ImQuest BioSciences, Inc., 7340 Executive Way, Suite R, Frederick, Maryland 21704, USA.
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Travers SAA, O'Connell MJ, McCormack GP, McInerney JO. Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes. J Virol 2005; 79:1836-41. [PMID: 15650207 PMCID: PMC544114 DOI: 10.1128/jvi.79.3.1836-1841.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent studies have demonstrated the emergence of human immunodeficiency virus type 1 (HIV-1) subtypes with various levels of fitness. Using heterogeneous maximum-likelihood models of adaptive evolution implemented in the PAML software package, with env sequences representing each HIV-1 group M subtype, we examined the various intersubtype selective pressures operating across the env gene. We found heterogeneity of evolutionary mechanisms between the different subtypes with a category of amino acid sites observed that had undergone positive selection for subtypes C, F1, and G, while these sites had undergone purifying selection in all other subtypes. Also, amino acid sites within subtypes A and K that had undergone purifying selection were observed, while these sites had undergone positive selection in all other subtypes. The presence of such sites indicates heterogeneity of selective pressures within HIV-1 group M subtype evolution that may account for the various levels of fitness of the subtypes.
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Affiliation(s)
- Simon A A Travers
- Biology Department, National University of Ireland, Maynooth, County Kildare, Ireland
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Nukoolkarn S, Pongthapisith V, Panyim S, Leelamanit W. Sequence variability of the HIV type 1 protease gene in thai patients experienced with antiretroviral therapy. AIDS Res Hum Retroviruses 2004; 20:1368-72. [PMID: 15650431 DOI: 10.1089/aid.2004.20.1368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One hundred sequences of HIV-1 protease with the two flanking cleavage sites from 10 antiretroviral drug-treated Thai patients were examined for residue variability and for mutations at positions associated with the resistance to protease inhibitors. Seven patients were infected with CRF01_AE, two with subtype B, and one with a strain that did not belong to any of the currently identified subtypes or recombinant forms. A total of 46 out of the 99 positions (46%) in HIV-1 protease showed at least one amino acid change as compared with the HXB2 subtype B protease. Interestingly, 35% of these mutations were at positions associated with resistance to the PIs. The observation indicated that the viral protease is flexible in tolerating some degree of amino acid substitutions even in the critical regions under the selective pressure driven by antiretroviral drugs. The PR/RT cleavage site revealed conservation of the HXB2 sequence. Nevertheless, the p6*/PR cleavage site displayed variability, notably in the p6* region.
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Affiliation(s)
- Sarawut Nukoolkarn
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, 10400, Thailand
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Meloni ST, Kim B, Sankalé JL, Hamel DJ, Tovanabutra S, Mboup S, McCutchan FE, Kanki PJ. Distinct human immunodeficiency virus type 1 subtype A virus circulating in West Africa: sub-subtype A3. J Virol 2004; 78:12438-45. [PMID: 15507630 PMCID: PMC525043 DOI: 10.1128/jvi.78.22.12438-12445.2004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic analyses demonstrate significant diversity in worldwide circulating strains of human immunodeficiency virus type 1 (HIV-1). Detailed studies have revealed a complex pattern of intersubtype recombinations, as well as evidence of sub-subtypes circulating in various populations. In this study, we characterized an HIV-1 strain that had previously been identified as a distinct subcluster within the subtype A radiation based on partial sequence data. These viruses were of particular interest given that we recently found that their prevalence was significantly higher in dually infected individuals compared to women who were singly infected with HIV-1. Five viruses isolated from commercial sex workers in Dakar, Senegal, were full-length PCR amplified and sequenced. Phylogenetic analyses indicated that, whereas three of these viruses were closely related and clustered overall within the HIV-1 subtype A radiation, they were distinct from previously characterized sub-subtype A1 and A2 viruses. The clustering pattern was maintained in the individual gag, pol, and env regions of the genome. Distance calculations between these viruses, which we termed A3, and other reference sub-subtype A1 and A2 viruses fell in the range of distances between previously characterized sub-subtype groups. In addition, we found evidence of two A3-containing recombinants in our cohort. These recombinants are mosaics composed of sequence from both sub-subtype A3 and CRF02_AG, the major circulating recombinant form in this West African population. Based on phylogenetic analyses, we propose that the group of viruses found in the Dakar sex worker cohort, previously referred to as HIV-1 A subcluster 2, be referred to as HIV-1 sub-subtype A3.
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Affiliation(s)
- Seema Thakore Meloni
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Ave., Boston, MA 02115, USA
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Zetterberg V, Ustina V, Liitsola K, Zilmer K, Kalikova N, Sevastianova K, Brummer-Korvenkontio H, Leinikki P, Salminen MO. Two viral strains and a possible novel recombinant are responsible for the explosive injecting drug use-associated HIV type 1 epidemic in Estonia. AIDS Res Hum Retroviruses 2004; 20:1148-56. [PMID: 15588336 DOI: 10.1089/aid.2004.20.1148] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 infection has been rare in Estonia. In 2000, an explosive epidemic among injecting drug users was detected in the Eastern border region, resulting in 3603 newly reported cases by the end of 2003. The molecular epidemiology of the outbreak was studied to establish whether the Estonian epidemic is linked to the epidemics in Eastern Europe. Over 200 newly infected individuals were prospectively sampled from June 2000 to March 2002 in a geographically representative way, with known dates of diagnosis and information of probable route of transmission. Viral regions coding for two viral gene regions were directly sequenced from plasma viral RNA and phylogenetically analyzed. In addition, a larger region coding for the entire env gene was sequenced from one sample and studied for indications of possible recombinant structure. The Estonian HIV outbreak was found to be caused by simultaneous introduction of two strains: a minor subtype A strain very similar to the Eastern European subtype A strain (approximately 8% of cases), and a second major strain (77%) found to be most closely related to the CRF06-cpx strain, previously described only from African countries. The variability in the two clusters was very low, suggesting point source introductions. Ten percent of cases seemed to be newly generated recombinants of the A and CRF06-cpx strains. Analysis of viral diversification over time revealed a rate of change within the V3 region of 0.83%/year for the CRF06-cpx strain, consistent with findings from other subtypes. Due to the relatively frequently found novel recombinant forms, the Estonian HIV-1 epidemic may allow studies of coinfection and intersubtype recombination in detail.
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Affiliation(s)
- Veera Zetterberg
- HIV-Laboratory, Department of Infectious Disease Epidemiology, National Public Health Institute, Helsinki, Finland
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Buonaguro L, Tagliamonte M, Tornesello ML, Pilotti E, Casoli C, Lazzarin A, Tambussi G, Ciccozzi M, Rezza G, Buonaguro FM. Screening of HIV-1 Isolates by Reverse Heteroduplex Mobility Assay and Identification of Non-B Subtypes in Italy. J Acquir Immune Defic Syndr 2004; 37:1295-306. [PMID: 15385738 DOI: 10.1097/01.qai.0000123273.76723.04] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The increasing prevalence of HIV-1 transmission through heterosexual contacts and the growing number of immigrants from non-Western countries, where non-B subtypes and recombinant forms are prevalent, suggest the possible emergence in Italy of a new epidemic wave of HIV-1 non-B subtypes as well as recombinant forms. METHODS The distribution of HIV-1 subtypes has been evaluated in 63 seropositive individuals residing in Italy, most of whom were infected through a sexual route during the last 5 years. A modified heteroduplex mobility assay (HMA) strategy, reverse HMA (rHMA), has been developed in our laboratory, allowing rapid identification of divergent-from-B-subtype isolates, which have been subsequently characterized by detailed molecular and phylogenetic analyses. RESULTS Five samples show, on rHMA, an electrophoretic pattern compatible with a non-B subtype classification. Their phylogenetic analysis, performed on both env and gag regions, confirms the rHMA subtyping prediction, given that 3 samples fall into the "A-family" subtype and 2 into the G subtype. The 5 non-B-subtype HIV-1 isolates have been identified among 23 variants (prevalence, 21.74%) isolated during the 2000 to 2001 period in heterosexuals. In parallel, B-subtype isolates show high levels of intrasubtype nucleotide divergence, compatible with a constant HIV-1 molecular diversification. CONCLUSION The Italian HIV-1 epidemic is still mostly attributable to the B subtype, which shows an increasing nucleotide heterogeneity. Heterosexual transmission and the interracial blending, however, are slowly introducing novel HIV-1 subtypes, and the data indicate that rHMA represents a powerful tool for HIV-1 biomolecular screening in epidemics characterized by a mono-/dual-subtype predominance.
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Affiliation(s)
- Luigi Buonaguro
- Viral Oncology and AIDS Refer. Center, Ist. Naz. Tumori Fond. G. Pascale, Naples, Italy
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Abstract
Genetic diversity is a hallmark of HIV-1 infection with regard to the expansion of distinct viral subtypes (clades A, B, C, D, E, F, G, K, and O) in different geographical regions. Here, we discuss the issues of HIV-1 sensitivity to antiretroviral drugs and drug resistance in the context of HIV-1 subtype diversity. Virtually all available evidence suggests that all subtypes of HIV display similar sensitivity to antiviral drugs, but viruses from some subtypes or geographical regions may occasionally have a greater propensity to develop resistance against certain drugs than other viral variants. In some situations, the types of mutations associated with resistance may vary, as a result of subtle differences among subtypes with regard to the genetic code. This consideration notwithstanding, drug resistance is unlikely to become a more serious issue in developing than developed countries, and there is an urgency to make anti-HIV drugs available to all who are in need.
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Affiliation(s)
- Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada.
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Kantor R, Katzenstein D. Drug resistance in non-subtype B HIV-1. J Clin Virol 2004; 29:152-9. [PMID: 14962783 DOI: 10.1016/s1386-6532(03)00115-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2003] [Accepted: 04/04/2003] [Indexed: 10/27/2022]
Abstract
Treatment of HIV-1 with antiretroviral therapy may select mutations in the pol gene associated with resistance to reverse transcriptase inhibitors and protease inhibitors. To provide durable clinical benefit, emergence of drug resistance is countered by prescription of alternative drug regimens. Data on sequential treatments that are effective after virologic failure and the selection of drug resistance is largely confined to HIV-1 subtype B, the clade that has circulated in North America and Europe. However, HIV-1 subtype B currently accounts for only 12% of the estimated 40 million HIV infected individuals worldwide. The global HIV-1 epidemic includes infection with nine identified HIV-1 group M subtypes (A-K), as well as distinct sub-subtypes and numerous chimerical or recombinant forms. Increasing access to treatment of HIV-1 in the developing world and increasing non-subtype B infection through travel and migration pose new questions about the susceptibility and response of these diverse HIV-1 viruses to antiretroviral drugs. Here we review HIV diversity and the published literature on drug resistance, comparing the known resistance mutations in individuals infected with subtype B to the growing experience in the treatment of non-subtype B HIV-1 worldwide.
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Affiliation(s)
- Rami Kantor
- Division of Infectious Diseases, Center for AIDS Research, Stanford University Medical Center, 300 Pasteur Drive, room S-156, Stanford, CA 94305, USA.
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Papathanasopoulos MA, Hunt GM, Tiemessen CT. Evolution and diversity of HIV-1 in Africa--a review. Virus Genes 2003; 26:151-63. [PMID: 12803467 DOI: 10.1023/a:1023435429841] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The HIV/AIDS pandemic represents a major development crisis for the African continent, which is the worst affected region in the world. Currently, almost 30 of the 42 million people infected with HIV worldwide live in Africa. AIDS in humans is caused by two lentiviruses, HIV-1 and HIV-2, which entered the human population by zoonotic transmissions from at least two different African primate species. Extensive phylogenetic analyses of partial and full-length genome sequences have helped to gain insights into the evolutionary biology and population dynamics of HIV. One of the major characteristics of HIV is its rapid evolution, which has resulted in substantial genetic diversity amongst different isolates, the majority of which are represented in Africa. Genetic variability of HIV and any consequent phenotypic variation poses a significant challenge to disease control and surveillance in different geographic regions of Africa. This review focuses on the origins and evolution of HIV, current classification and diversity of HIV isolates in Africa and provides an extensive account of the geographic distribution of HIV types, groups, and subtypes in each of the 49 African countries. Numerous epidemiological studies have provided a picture of HIV distribution patterns in most countries in Africa, and these show increasing evidence of the importance of HIV-1 recombinants. In particular, this review highlights that our current understanding of HIV distribution in Africa is incomplete and inadequately represents the diversity of the virus, and underscores the need for ongoing surveillance.
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Affiliation(s)
- Maria A Papathanasopoulos
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Department of Virology, University of the Witwatersrand, Johannesburg, South Africa.
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Duque V, Holguín A, Silvestre M, González-Lahoz J, Soriano V. Human immunodeficiency virus type 1 recombinant B/G subtypes circulating in Coimbra, Portugal. Clin Microbiol Infect 2003; 9:422-5. [PMID: 12848757 DOI: 10.1046/j.1469-0691.2003.00541.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An increasing prevalence of HIV-1 non-B variants is being noticed in several European regions, particularly in countries such as Portugal, which have closer contacts with African endemic areas, where multiple HIV subtypes cocirculate. HIV-1 subtyping by phylogenetic analyses of reverse transcriptase, protease and env (C2-V3) genomic regions was carried out in plasma collected from 18 HIV-1-infected subjects living in Coimbra, Portugal, and suspected to be infected with non-B variants. Three (16.7%) subjects carried recombinant B/G viruses (BV3/BRT/Gpro; GV3/URT/Bpro; AV3/GRT/Bpro), whereas all the remaining individuals were infected with HIV-1 subtype B. This is the first report of recombinant B/G subtypes in Portugal.
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Affiliation(s)
- V Duque
- Department of Infectious Diseases, Hospitais da Universidade de Coimbra, Coimbra, Portugal
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45
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Zhong P, Burda S, Urbanski M, Kenfack H, Tongo M, Heyndrickx L, Nanfack A, Shang J, Agyingi L, Zolla-Pazner S, Zekeng L, Nyambi P. HIV type 1 group M clades infecting subjects from rural villages in equatorial rain forests of Cameroon. J Acquir Immune Defic Syndr 2002; 31:495-505. [PMID: 12473838 DOI: 10.1097/00126334-200212150-00007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Though the HIV-1 subtypes infecting patients living in urban and semi-urban areas in Cameroon have been reported, information on the subtypes infecting patients in rural villages is lacking. To begin to understand the diversity of the HIV-1 group M subtypes infecting persons living in rural villages in the equatorial rain forest regions of Cameroon, 49 plasma samples from 14 rural villages in four provinces of Cameroon were analyzed using heteroduplex mobility analysis (HMA), DNA sequencing, and phylogenetic tree analysis on the basis of env C2V5, gag, or pol regions. Sixty-one percent of the group M infections were clade A or CRF02_AG-like as subtyped by env and gag. Of the remaining group M infections, 12% were either A or CRF02_AG-like or CRF01_AE-like in recombination with other clades; 25% were infections that were entirely non-A or non-CRF02_AG-like; and 2% were CRF11_cpx. The HIV-1 group M clades identified included A, D, F (F2), G, and H. The CRF strains identified were CRF02_AG-like, CRF01_AE-like, and CRF11_cpx. Two new intersubtype recombinant infections, H/G and A/F2, were identified. This study suggests that the HIV-1 diversity in rural villages in the equatorial rain forest of Cameroon is at least as broad as has been observed in major cities of Cameroon and that multiple HIV-1 group M subtypes are infecting persons living in the countryside of Cameroon.
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Affiliation(s)
- Ping Zhong
- Department of Pathology, New York University School of Medicine, New York, NY, USA
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Guimarães ML, dos Santos Moreira A, Loureiro R, Galvão-Castro B, Morgado MG. High frequency of recombinant genomes in HIV type 1 samples from Brazilian southeastern and southern regions. AIDS Res Hum Retroviruses 2002; 18:1261-9. [PMID: 12487814 DOI: 10.1089/088922202320886307] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe the genetic variability of HIV-1 subtypes and recombinant genomes in samples from southeastern and southern Brazilian regions. Phylogenetic analysis of a subset of 34 samples (8F, 7B, 7C, 2D, 1A, and 9 B" variant) based on the DNA sequencing of the env gp120 and gp41, gag p17, and nef regions confirmed the presence of nine (26.5%) potentially HIV-1 recombinant genomes. From the eight C2-V3 gp120 subtype F samples, only two seem to be pure F. One of the samples, classified as B" in the C2-V3 gp120 and as B in gp41 had the gag and nef regions clustering with subtype C. Two of seven C2-V3 subtype C samples presented distinct recombinant patterns as Bgag/Cenv/Bnef and Bgag/Cenv/Cnef. Putative recombinant breakpoints were obtained for three samples presenting discordant subtypes (F/B) between gp120 and gp41 env fragments showing that similar breakpoints could be observed between two unlinked samples (95BRRJ014 and 96BRRJ101). A higher degree of polymorphism was verified in the analysis of a subtype A sample (98BRRS058) in the C2-V3/gp41 env fragment. The intrasubtype C distance was found to be lower than that found for the other subtypes for all genomic regions. These data confirm that distinct HIV-1 subtypes and recombinant forms are actively participating in the Brazilian AIDS epidemic, and that the subtype C was introduced more recently into southern Brazil.
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Chen MY, Wang WK, Lee MC, Twu SJ, Wu SI, Lee CN. Rapid detection of human immunodeficiency virus type 1 subtype e infection by PCR. J Clin Microbiol 2002; 40:3805-9. [PMID: 12354886 PMCID: PMC130852 DOI: 10.1128/jcm.40.10.3805-3809.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The CRF01_AE (subtype E) strain of human immunodeficiency virus type 1 (HIV-1), originally reported in Thailand, spread rapidly to and showed prevalence in several countries in Southeast Asia, including Taiwan. This strain was also found in other regions of the world. Based on sequence analysis of the vpu gene, a nested PCR assay including an outer primer pair and a subtype E-specific inner primer pair was developed in this study for rapid detection of subtype E viruses. It was tested with 397 HIV-1-positive samples of known subtypes. For these samples, the sensitivity of detection of subtype E viruses was 100% (127 of 127), and the specificity was 97.8% (264 of 270). Although six samples of either subtype A or G showed a positive PCR, most of the cross-reactivity could be reduced by raising the annealing temperature from 54 degrees C to 63 degrees C. When tested with 195 HIV-positive samples of unknown subtypes, the assay had a sensitivity of 98.0% and a specificity of 98.6%. This is a simple, convenient, and sensitive method for rapid detection of subtype E viruses, especially in regions in which viruses of subtypes B and E are predominant.
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Affiliation(s)
- Mao-Yuan Chen
- Department of Internal Medicine, College of Medicine, National Taiwan University, No. 1 Chang-Te Street, Taipei, Taiwan 100, Republic of China
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Dowling WE, Kim B, Mason CJ, Wasunna KM, Alam U, Elson L, Birx DL, Robb ML, McCutchan FE, Carr JK. Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants. AIDS 2002; 16:1809-20. [PMID: 12218394 DOI: 10.1097/00002030-200209060-00015] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To further define the genetic diversity of HIV-1 in Kenya using approaches that clearly distinguish subtypes from inter-subtype recombinants. DESIGN Near full genome sequencing and analysis were used, including sensitive new tools for detection and mapping of recombinants. METHODS Purified peripheral blood mononuclear cell DNA from 41 HIV-1 positive blood donations collected from six hospitals across southern Kenya was used to amplify near full-length genomes by nested PCR. These were sequenced on an ABI 3100 automated sequencer and analyzed phylogenetically. RESULTS Among 41 near full-length genomes, 25 were non-recombinant (61%) and 16 were recombinant (39%). Of the 25 pure subtypes, 23 were subtype A, one was subtype C and one was subtype D. Most recombinants consisted of subtype A and either subtype C or subtype D; a few contained A2, a recently identified sub-subtype. Two A2/D recombinants had identical breakpoints and may represent a circulating recombinant form. A third A2/D recombinant had the same structure as a previously described Korean isolate, and these may constitute a second A2-containing circulating recombinant form. CONCLUSIONS In Kenya, 93% of HIV-1 genomes were subtype A or A-containing recombinant strains. Almost 40% of all strains were recombinant. Vaccine candidates tested in Kenya should be based on subtype A strains, but the methods used for evaluation of breakthrough infections during future vaccine trials should be capable of identifying non-A subtypes, the A2 sub-subtype, and recombinants.
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Casper C, Fenyö EM. Mother-to-child transmission of HIV-1: the role of HIV-1 variability and the placental barrier. Acta Microbiol Immunol Hung 2002; 48:545-73. [PMID: 11791351 DOI: 10.1556/amicr.48.2001.3-4.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The acquired immunodeficiency syndrome (AIDS), which is caused by the human immunodeficiency virus (HIV), was first described in the United States of America in 1981 [1]. The worldwide spread of HIV has soon been recognized and AIDS has become one of the most alarming infectious diseases of our days. Its impact has been tremendous, high morbidity and mortality has caused a reversal of socioeconomic gains previously recorded in several developing countries, especially those in Sub-Saharan Africa [2]. Epidemiological data about the HIV and AIDS pandemic are updated by the Joint United Nation Programme on HIV/AIDS, UNAIDS (http://www.unaids.org). Their latest report from December 2000 states that in year 2000 approximately 5.3 million people have become newly infected with HIV, of which 2.2 were women and 600,000 children younger than 15 years of age. The estimated number of people living with HIV/AIDS globally is 36.1 million, of which 16.4 million are women and 1.4 million are children younger than 15 years of age. Approximately 25.3 million (70%) of these HIV infected people live in Sub-Saharan Africa, 5.8 million in South- and South-East Asia (15%), and 1.4 million in Latin-America (5%). During year 2000, 3 million people died of AIDS (1.3 million women and 500,000 children younger than 15 years of age). This means that an estimated total of 21.8 million persons have died of AIDS since the beginning of the epidemic, including 4.3 million children younger than 15 years of age.
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Affiliation(s)
- C Casper
- Microbiology and Tumorbiology Center, Department of Woman and Child Health, Karolinska Institutet, Stockholm, Sweden
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50
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Affiliation(s)
- I D Tatt
- Sexually Transmitted and Blood Borne Virus Laboratory, Central Public Health Laboratory, Public Health Laboratory Service, London, UK
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