1
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Wieczorek L, Chang D, Sanders-Buell E, Zemil M, Martinez E, Schoen J, Chenine AL, Molnar S, Barrows B, Poltavee K, Charurat ME, Abimiku A, Blattner W, Iroezindu M, Kokogho A, Michael NL, Crowell TA, Ake JA, Tovanabutra S, Polonis VR. Differences in neutralizing antibody sensitivities and envelope characteristics indicate distinct antigenic properties of Nigerian HIV-1 subtype G and CRF02_AG. Virol J 2024; 21:148. [PMID: 38951814 PMCID: PMC11218331 DOI: 10.1186/s12985-024-02394-y] [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: 02/23/2024] [Accepted: 05/19/2024] [Indexed: 07/03/2024] Open
Abstract
The magnitude of the HIV-1 epidemic in Nigeria is second only to the subtype C epidemic in South Africa, yet the subtypes prevalent in Nigeria require further characterization. A panel of 50 subtype G and 18 CRF02_AG Nigerian HIV-1 pseudoviruses (PSV) was developed and envelope coreceptor usage, neutralization sensitivity and cross-clade reactivity were characterized. These PSV were neutralized by some antibodies targeting major neutralizing determinants, but potentially important differences were observed in specific sensitivities (eg. to sCD4, MPER and V2/V3 monoclonal antibodies), as well as in properties such as variable loop lengths, number of potential N-linked glycans and charge, demonstrating distinct antigenic characteristics of CRF02_AG and subtype G. There was preferential neutralization of the matched CRF/subtype when PSV from subtype G or CRF02_AG were tested using pooled plasma. These novel Nigerian PSV will be useful to study HIV-1 CRF- or subtype-specific humoral immune responses for subtype G and CRF02_AG.
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Affiliation(s)
- Lindsay Wieczorek
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - David Chang
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Office of AIDS Research, National Institutes of Health, Rockville, MD, 20852, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth Martinez
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Jesse Schoen
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes-Laurence Chenine
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Integrated Biotherapeutics, Rockville, MD, 20850, USA
| | - Sebastian Molnar
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Brittani Barrows
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Lentigen Technology, Gaithersburg, MD, 20878, USA
| | - Kultida Poltavee
- SEARCH, Insititute of HIV Research and Innovation (IHRI), Bangkok, Thailand
| | - Man E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alash'le Abimiku
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William Blattner
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Afoke Kokogho
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Nelson L Michael
- Center for Infectious Disease Research, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Trevor A Crowell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA.
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2
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Marcelino R, Gramacho F, Martin F, Brogueira P, Janeiro N, Afonso C, Badura R, Valadas E, Mansinho K, Caldeira L, Taveira N, Marcelino JM. Antibody response against selected epitopes in the HIV-1 envelope gp41 ectodomain contributes to reduce viral burden in HIV-1 infected patients. Sci Rep 2021; 11:8993. [PMID: 33903642 PMCID: PMC8076315 DOI: 10.1038/s41598-021-88274-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/09/2021] [Indexed: 01/26/2023] Open
Abstract
The ectodomain of gp41 is the target of potent binding and neutralizing antibodies (NAbs) and is being explored in new strategies for antibody-based HIV vaccines. Previous studies have suggested that the W164A-3S (3S) and EC26-2A4 (EC26) peptides located in the gp41 ectodomain may be potential HIV vaccine candidates. We assessed 3S- and EC26-specific binding antibody responses and related neutralizing activity in a large panel of chronic HIV-1-infected Portuguese individuals on ART. A similar proportion of participants had antibodies binding to 3S (9.6%) and EC26 (9.9%) peptides but the level of reactivity against 3S was significantly higher compared to EC26, except in the rare patients with double peptide reactivity. The higher antigenicity of 3S was unrelated with disease stage, as assessed by CD4+ T cell counts, but it was directly related with plasma viral load. Most patients that were tested (89.9%, N = 268) showed tier 1 neutralizing activity, the potency being inversely associated with plasma viral load. In the subset of patients that were tested for neutralization of tier 2 isolates, neutralization breadth was inversely correlated with plasma viral load and directly correlated with CD4+ T cell counts. These results are consistent with a role for neutralizing antibodies in controlling viral replication and preventing the decline of CD4+ T lymphocytes. Importantly, in patients with 3S-specific antibodies, neutralizing titers were inversely correlated with viral RNA levels and proviral DNA levels. Moreover, patients with 3S and/or EC26-specific antibodies showed a 1.9-fold higher tier 2 neutralization score than patients without antibodies suggesting that 3S and/or EC26-specific antibodies contribute to neutralization breadth and potency in HIV-1 infected patients. Overall, these results suggest that antibodies targeting the S3 and EC26 epitopes may contribute to reduce viral burden and provide further support for the inclusion of 3S and EC26 epitopes in HIV-1 vaccine candidates.
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Affiliation(s)
- Rute Marcelino
- Global Health and Tropical Medicine-GHTM, Instituto de Higiene e Medicina Tropical-IHMT, Universidade Nova de Lisboa-UNL, 1349-008, Lisboa, Portugal.,Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, 1649-003, Lisboa, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Monte de Caparica, 2829-511, Monte de Caparica, Portugal
| | - Filipa Gramacho
- Hospital de Santa Maria-HSM, Centro Hospitalar Lisboa Norte-CHLN, E.P.E., Lisboa, 1649-028, Lisboa, Portugal
| | - Francisco Martin
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, 1649-003, Lisboa, Portugal
| | - Pedro Brogueira
- Serviço de Doenças Infeciosas, Hospital Egas Moniz-HEM, Centro Hospitalar Lisboa Ocidental-CHLO, E.P.E., Lisboa, 1349-019, Lisboa, Portugal
| | - Nuno Janeiro
- Hospital de Santa Maria-HSM, Centro Hospitalar Lisboa Norte-CHLN, E.P.E., Lisboa, 1649-028, Lisboa, Portugal.,Clínica Universitária de Doenças Infeciosas, Faculdade de Medicina, Universidade de Lisboa-UL, Lisboa, 1649-028, Lisboa, Portugal
| | - Claudia Afonso
- Hospital de Santa Maria-HSM, Centro Hospitalar Lisboa Norte-CHLN, E.P.E., Lisboa, 1649-028, Lisboa, Portugal.,Clínica Universitária de Doenças Infeciosas, Faculdade de Medicina, Universidade de Lisboa-UL, Lisboa, 1649-028, Lisboa, Portugal
| | - Robert Badura
- Hospital de Santa Maria-HSM, Centro Hospitalar Lisboa Norte-CHLN, E.P.E., Lisboa, 1649-028, Lisboa, Portugal.,Clínica Universitária de Doenças Infeciosas, Faculdade de Medicina, Universidade de Lisboa-UL, Lisboa, 1649-028, Lisboa, Portugal
| | - Emília Valadas
- Hospital de Santa Maria-HSM, Centro Hospitalar Lisboa Norte-CHLN, E.P.E., Lisboa, 1649-028, Lisboa, Portugal.,Clínica Universitária de Doenças Infeciosas, Faculdade de Medicina, Universidade de Lisboa-UL, Lisboa, 1649-028, Lisboa, Portugal
| | - Kamal Mansinho
- Serviço de Doenças Infeciosas, Hospital Egas Moniz-HEM, Centro Hospitalar Lisboa Ocidental-CHLO, E.P.E., Lisboa, 1349-019, Lisboa, Portugal
| | - Luís Caldeira
- Hospital de Santa Maria-HSM, Centro Hospitalar Lisboa Norte-CHLN, E.P.E., Lisboa, 1649-028, Lisboa, Portugal.,Clínica Universitária de Doenças Infeciosas, Faculdade de Medicina, Universidade de Lisboa-UL, Lisboa, 1649-028, Lisboa, Portugal
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, 1649-003, Lisboa, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Monte de Caparica, 2829-511, Monte de Caparica, Portugal
| | - José M Marcelino
- Global Health and Tropical Medicine-GHTM, Instituto de Higiene e Medicina Tropical-IHMT, Universidade Nova de Lisboa-UNL, 1349-008, Lisboa, Portugal. .,Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, 1649-003, Lisboa, Portugal. .,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Monte de Caparica, 2829-511, Monte de Caparica, Portugal.
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Vasylyeva TI, du Plessis L, Pineda-Peña AC, Kühnert D, Lemey P, Vandamme AM, Gomes P, Camacho RJ, Pybus OG, Abecasis AB, Faria NR. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. J Infect Dis 2020; 220:233-243. [PMID: 30805610 PMCID: PMC6581889 DOI: 10.1093/infdis/jiz085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. METHODS Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. RESULTS We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. CONCLUSIONS The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
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Affiliation(s)
- Tetyana I Vasylyeva
- Department of Zoology, University of Oxford, United Kingdom.,New College, University of Oxford, United Kingdom
| | | | - Andrea C Pineda-Peña
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia.,Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Anne-Mieke Vandamme
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Perpétua Gomes
- Laboratory of Molecular Biology, LMCBM, SPC, Hospital de Egas Moniz-Centro Hospitalar de Lisboa Ocidental, Lisbon.,Center for Interdisciplinary Research Egas Moniz, CiiEM, Almada, Portugal
| | - Ricardo J Camacho
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, United Kingdom
| | - Ana B Abecasis
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa
| | - Nuno R Faria
- Department of Zoology, University of Oxford, United Kingdom
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4
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Abstract
Background Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines. Methods Demographic, clinical and genomic data were collected from 3599 HIV-1 naive patients between 2001 and 2014. Sequences obtained from drug resistance testing were used for subtyping, TDR determination and transmission clusters (TC) analyses. Results In Portugal, transmission of subtype B was significantly associated with young males, while transmission of subtype G was associated with older heterosexuals. In Portuguese originated people, there was a decreasing trend both for prevalence of subtype G and for number of TCs in this subtype. The active TCs that were identified (i.e. clusters originated after 2008) were associated with subtype B-infected males residing in Lisbon. TDR was significantly different when comparing subtypes B (10.8% [9.5–12.2]) and G (7.6% [6.4–9.0]) (p = 0.001). Discussion TC analyses shows that, in Portugal, the subtype B epidemic is active and fueled by young male patients residing in Lisbon, while transmission of subtype G is decreasing. Despite similar treatment rates for both subtypes in Portugal, TDR is significantly different between subtypes.
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5
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Design and in vitro delivery of HIV-1 multi-epitope DNA and peptide constructs using novel cell-penetrating peptides. Biotechnol Lett 2019; 41:1283-1298. [PMID: 31531750 DOI: 10.1007/s10529-019-02734-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/15/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Developing an effective HIV vaccine that stimulates the humoral and cellular immune responses is still challenging because of the diversity of HIV-1 virus, polymorphism of human HLA and lack of a suitable delivery system. RESULTS Using bioinformatics tools, we designed a DNA construct encoding multiple epitopes. These epitopes were highly conserved within prevalent HIV-1 subtypes and interacted with prevalent class I and II HLAs in Iran and the world. The designed DNA construct included Nef60-84, Nef126-144, Vpr34-47, Vpr60-75, Gp16030-53, Gp160308-323 and P248-151 epitopes (i.e., nef-vpr-gp160-p24 DNA) which was cloned into pET-24a(+) and pEGFP-N1 vectors. The recombinant polyepitope peptide (rNef-Vpr-Gp160-P24; ~ 32 kDa) was successfully generated in E. coli expression system. The pEGFP-nef-vpr-gp160-p24 and rNef-Vpr-Gp160-P24 polyepitope peptide were delivered into HEK-293 T cells using cell-penetrating peptides (CPPs). The MPG and HR9 CPPs, as well as the novel LDP-NLS and CyLoP-1 CPPs, were utilized for DNA and peptide delivery into the cells, respectively. SEM results confirmed the formation of stable MPG/pEGFP-N1-nef-vpr-gp160-p24, HR9/pEGFP-N1-nef-vpr-gp160-p24, LDP-NLS/rNef-Vpr-Gp160-P24 and CyLoP-1/rNef-Vpr-Gp160-P24 nanoparticles with a diameter of < 200 nm through non-covalent bonds. MTT assay results indicated that these nanoparticles did not have any major toxicity in vitro. Fluorescence microscopy, flow cytometry and western blot data demonstrated that these CPPs could significantly deliver the DNA and peptide constructs into HEK-293 T cells. CONCLUSION The use of these CPPs can be considered as an approach in HIV vaccine development for in vitro and in vivo delivery of DNA and peptide constructs into mammalian cells.
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Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries. Sci Rep 2019; 9:7223. [PMID: 31076722 PMCID: PMC6510806 DOI: 10.1038/s41598-019-43420-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/12/2019] [Indexed: 11/10/2022] Open
Abstract
HIV-1 subtypes associate with differences in transmission and disease progression. Thus, the existence of geographic hotspots of subtype diversity deepens the complexity of HIV-1/AIDS control. The already high subtype diversity in Portugal seems to be increasing due to infections with sub-subtype A1 virus. We performed phylogenetic analysis of 65 A1 sequences newly obtained from 14 Portuguese hospitals and 425 closely related database sequences. 80% of the A1 Portuguese isolates gathered in a main phylogenetic clade (MA1). Six transmission clusters were identified in MA1, encompassing isolates from Portugal, Spain, France, and United Kingdom. The most common transmission route identified was men who have sex with men. The origin of the MA1 was linked to Greece, with the first introduction to Portugal dating back to 1996 (95% HPD: 1993.6–1999.2). Individuals infected with MA1 virus revealed lower viral loads and higher CD4+ T-cell counts in comparison with those infected by subtype B. The expanding A1 clusters in Portugal are connected to other European countries and share a recent common ancestor with the Greek A1 outbreak. The recent expansion of this HIV-1 subtype might be related to a slower disease progression leading to a population level delay in its diagnostic.
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7
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Delgado E, Benito S, Montero V, Cuevas MT, Fernández-García A, Sánchez-Martínez M, García-Bodas E, Díez-Fuertes F, Gil H, Cañada J, Carrera C, Martínez-López J, Sintes M, Pérez-Álvarez L, Thomson MM. Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain. Front Microbiol 2019; 10:655. [PMID: 31001231 PMCID: PMC6457325 DOI: 10.3389/fmicb.2019.00655] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Abstract
In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly comprising European individuals. Here we describe four large HIV-1 non-subtype B clusters spreading among MSM in Spain. Samples were collected in 9 regions. A pol fragment was amplified from plasma RNA or blood-extracted DNA. Phylogenetic analyses were performed via maximum likelihood, including database sequences of the same genetic forms as the identified clusters. Times and locations of the most recent common ancestors (MRCA) of clusters were estimated with a Bayesian method. Five large non-subtype B clusters associated with MSM were identified. The largest one, of F1 subtype, was reported previously. The other four were of CRF02_AG (CRF02_1; n = 115) and subtypes A1 (A1_1; n = 66), F1 (F1_3; n = 36), and C (C_7; n = 17). Most individuals belonging to them had been diagnosed of HIV-1 infection in the last 10 years. Each cluster comprised viruses from 3 to 8 Spanish regions and also comprised or was related to viruses from other countries: CRF02_1 comprised a Japanese subcluster and viruses from 8 other countries from Western Europe, Asia, and South America; A1_1 comprised viruses from Portugal, United Kingom, and United States, and was related to the A1 strain circulating in Greece, Albania and Cyprus; F1_3 was related to viruses from Romania; and C_7 comprised viruses from Portugal and was related to a virus from Mozambique. A subcluster within CRF02_1 was associated with heterosexual transmission. Near full-length genomes of each cluster were of uniform genetic form. Times of MRCAs of CRF02_1, A1_1, F1_3, and C_7 were estimated around 1986, 1989, 2013, and 1983, respectively. MRCA locations for CRF02_1 and A1_1 were uncertain (however initial expansions in Spain in Madrid and Vigo, respectively, were estimated) and were most probable in Bilbao, Spain, for F1_3 and Portugal for C_7. These results show that the HIV-1 epidemic among MSM in Spain is becoming increasingly diverse through the expansion of diverse non-subtype B clusters, comprising or related to viruses circulating in other countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Javier Cañada
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Martínez-López
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos Sintes
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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8
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Karamov E, Epremyan K, Siniavin A, Zhernov Y, Cuevas MT, Delgado E, Sánchez-Martínez M, Carrera C, Kornilaeva G, Turgiev A, Bacqué J, Pérez-Álvarez L, Thomson MM. HIV-1 Genetic Diversity in Recently Diagnosed Infections in Moscow: Predominance of A FSU, Frequent Branching in Clusters, and Circulation of the Iberian Subtype G Variant. AIDS Res Hum Retroviruses 2018; 34:629-634. [PMID: 29587492 DOI: 10.1089/aid.2018.0055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 protease-reverse transcriptase sequences from 62 HIV-1-infected individuals recently diagnosed in Moscow were analyzed. Subtype A former Soviet Union (FSU) (AFSU) variant was the predominant clade (62.9%), followed by subtype B (22.6%), unique recombinants (6.5%), subtype G (6.5%), and CRF01_AE (1.6%). AFSU predominated among people who inject drugs (88.9%) and heterosexually acquired infections (77.8%), while subtype B was the most prevalent genetic form among men who have sex with men (44%), although AFSU was also frequent in this population (36%). Forty-eight (77.4%) viruses branched within intrasubtype clusters, three of which, of subtype B, had a majority of viruses collected outside of FSU. The four subtype G viruses identified in this study belonged to the Portuguese-Spanish (Iberian) variant and, together with three from databases, formed a Russian cluster closely related to viruses from Denmark. This is the first report of the circulation of the Iberian subtype G variant in Russia.
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Affiliation(s)
- Eduard Karamov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Khoren Epremyan
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Andrei Siniavin
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Yury Zhernov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Galina Kornilaeva
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Ali Turgiev
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
- Immunomica LLC, Moscow, Russia
| | - Joan Bacqué
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Chow WZ, Bon AH, Keating S, Anderios F, Halim HA, Takebe Y, Kamarulzaman A, Busch MP, Tee KK. Extensive Genetic Diversity of HIV-1 in Incident and Prevalent Infections among Malaysian Blood Donors: Multiple Introductions of HIV-1 Genotypes from Highly Prevalent Countries. PLoS One 2016; 11:e0161853. [PMID: 27575746 PMCID: PMC5004849 DOI: 10.1371/journal.pone.0161853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/14/2016] [Indexed: 11/21/2022] Open
Abstract
Transfusion-transmissible infections including HIV-1 continue to pose major risks for unsafe blood transfusions due to both window phase infections and divergent viruses that may not be detected by donor screening assays. Given the recent emergence of several HIV-1 circulating recombinant forms (CRFs) in high-risk populations in the Southeast Asia region, we investigated the genetic diversity of HIV-1 among the blood donors in Kuala Lumpur, Malaysia. A total of 211 HIV-positive plasma samples detected among 730,188 donations to the National Blood Centre between 2013 and 2014 were provided (90.5% male, median age: 27.0 years old). Recent or long-term infection status at the time of donation was determined using a limiting antigen avidity enzyme immunoassay (LAg-Avidity EIA). HIV-1 gag-pol genes were amplified and sequenced from residual plasma for 149 cases followed by genotype determination using phylogenetic and recombination analyses. Transmitted antiretroviral resistance mutations were not observed among the blood donors, among which 22.7% were classified as recent or incident infections. Major circulating HIV-1 genotypes determined by neighbour-joining phylogenetic inference included CRF01_AE at 40.9% (61/149), CRF33_01B at 21.5% (32/149), and subtype B at 10.1% (15/149). Newly-described CRFs including CRF54_01B circulated at 4.0%, CRF74_01B at 2.0%, and CRF53_01B and CRF48_01B at 0.7% each. Interestingly, unique HIV-1 genotypes including African subtype G (8.7%), CRF45_cpx (1.3%), CRF02_AG (0.7%) and CRF07_BC (0.7%) from China were detected for the first time in the country. A cluster of subtype G sequences formed a distinct founder sub-lineage within the African strains. In addition, 8.7% (13/149) of HIV-infected donors had unique recombinant forms (URFs) including CRF01_AE/B' (4.7%), B'/C (2.7%) and B'/G (1.3%) recombinants. Detailed analysis identified similar recombinant structures with shared parental strains among the B'/C and B'/G URFs, some of which were sequenced from recently infected individuals, indicating the possible emergence and on-going spread of foreign clades of CRF candidates among the local population. The findings demonstrate extensive molecular complexity of HIV-1 among the infected blood donors in Malaysia, driven in part by the increased spread of recently described CRFs and multiple introductions of previously unreported genotypes from highly prevalent countries.
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Affiliation(s)
- Wei Zhen Chow
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Abdul Hamid Bon
- National Blood Centre of Kuala Lumpur (NBCKL), Kuala Lumpur, Malaysia
| | - Sheila Keating
- Blood Systems Research Institute (BSRI), San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco (UCSF), California, United States of America
| | - Fread Anderios
- National Blood Centre of Kuala Lumpur (NBCKL), Kuala Lumpur, Malaysia
| | | | - Yutaka Takebe
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Michael P. Busch
- Blood Systems Research Institute (BSRI), San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco (UCSF), California, United States of America
| | - Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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10
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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11
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Fernández-García A, Delgado E, Cuevas MT, Vega Y, Montero V, Sánchez M, Carrera C, López-Álvarez MJ, Miralles C, Pérez-Castro S, Cilla G, Hinojosa C, Pérez-Álvarez L, Thomson MM. Identification of an HIV-1 BG Intersubtype Recombinant Form (CRF73_BG), Partially Related to CRF14_BG, Which Is Circulating in Portugal and Spain. PLoS One 2016; 11:e0148549. [PMID: 26900693 PMCID: PMC4765764 DOI: 10.1371/journal.pone.0148549] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/19/2016] [Indexed: 02/06/2023] Open
Abstract
HIV-1 exhibits a characteristically high genetic diversity, with the M group, responsible for the pandemic, being classified into nine subtypes, 72 circulating recombinant forms (CRFs) and numerous unique recombinant forms (URFs). Here we characterize the near full-length genome sequence of an HIV-1 BG intersubtype recombinant virus (X3208) collected in Galicia (Northwest Spain) which exhibits a mosaic structure coincident with that of a previously characterized BG recombinant virus (9601_01), collected in Germany and epidemiologically linked to Portugal, and different from currently defined CRFs. Similar recombination patterns were found in partial genome sequences from three other BG recombinant viruses, one newly derived, from a virus collected in Spain, and two retrieved from databases, collected in France and Portugal, respectively. Breakpoint coincidence and clustering in phylogenetic trees of these epidemiologically-unlinked viruses allow to define a new HIV-1 CRF (CRF73_BG). CRF73_BG shares one breakpoint in the envelope with CRF14_BG, which circulates in Portugal and Spain, and groups with it in a subtype B envelope fragment, but the greatest part of its genome does not appear to derive from CRF14_BG, although both CRFs share as parental strain the subtype G variant circulating in the Iberian Peninsula. Phylogenetic clustering of partial pol and env segments from viruses collected in Portugal and Spain with X3208 and 9691_01 indicates that CRF73_BG is circulating in both countries, with proportions of around 2–3% Portuguese database HIV-1 isolates clustering with CRF73_BG. The fact that an HIV-1 recombinant virus characterized ten years ago as a URF has been shown to represent a CRF suggests that the number of HIV-1 CRFs may be much greater than currently known.
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Affiliation(s)
- Aurora Fernández-García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Elena Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María Teresa Cuevas
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Vanessa Montero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Celia Miralles
- Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | | | - Gustavo Cilla
- Hospital Universitario Donostia, San Sebastián, Spain
| | - Carmen Hinojosa
- Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Lucía Pérez-Álvarez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail:
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12
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Hait SH, Soares EA, Sprinz E, Arthos J, Machado ES, Soares MA. Worldwide Genetic Features of HIV-1 Env α4β7 Binding Motif: The Local Dissemination Impact of the LDI Tripeptide. J Acquir Immune Defic Syndr 2016; 70:463-71. [PMID: 26569174 DOI: 10.1097/qai.0000000000000802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND HIV-1 gp120 binds to integrin α4β7, a homing receptor of lymphocytes to gut-associated lymphoid tissues. This interaction is mediated by the LDI/V tripeptide encoded in the V2-loop. This tripeptide mimics similar motifs in mucosal addressin cellular adhesion molecule (MAdCAM) and vascular CAM (VCAM), the natural ligands of α4β7. In this study, we explored the association of V2-loop LDI/V mimotopes with transmission routes and patterns of disease progression in HIV-infected adult and pediatric patients. HIV-1 env sequences available in the Los Alamos HIV Sequence database were included in the analyses. METHODS HIV-1 V2-loop sequences generated from infected adults and infants from South and Southeast Brazil, and also retrieved from the Los Alamos database, were assessed for α4β7 binding tripeptide composition. Chi-Square/Fisher Exact test and Mann Whitney U test were used for tripeptide comparisons. Shannon entropy was assessed for conservancy of the α4β7 tripeptide mimotope. RESULTS We observed no association between the tripeptide composition or conservation and virus transmission route or disease progression. However, LDI was linked to successful epidemic dissemination of HIV-1 subtype C in South America, and further to other expanding non-B subtypes in Europe and Asia. In Africa, subtypes showing increased LDV prevalence evidenced an ongoing process of selection toward LDI expansion, an observation also extended to subtype B in the Americas and Western Europe. CONCLUSIONS The V2-loop LDI mimotope was conserved in HIV-1C from South America and other expanding subtypes across the globe, which suggests that LDI may promote successful dissemination of HIV at local geographic levels by means of increased transmission fitness.
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Affiliation(s)
- Sabrina H Hait
- *Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; †Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; ‡Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, Brazil; §Laboratory of Immune Regulation, National Institutes of Health, Bethesda, MD; and ‖Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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13
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de Pina-Araujo IIM, Delatorre E, Guimarães ML, Morgado MG, Bello G. Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal. PLoS One 2015; 10:e0127384. [PMID: 25993094 PMCID: PMC4439163 DOI: 10.1371/journal.pone.0127384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/15/2015] [Indexed: 01/04/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called GCV-PT). The GCV-PT clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the GCV-PT clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the GCV-PT clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the GCV-PT and CRF14_BG clades.
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Affiliation(s)
| | - Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Monick L. Guimarães
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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14
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Analysis of a local HIV-1 epidemic in portugal highlights established transmission of non-B and non-G subtypes. J Clin Microbiol 2015; 53:1506-14. [PMID: 25694526 DOI: 10.1128/jcm.03611-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/10/2015] [Indexed: 12/24/2022] Open
Abstract
The existing data support Portugal as the western European country with the highest HIV-1 subtype diversity. However, detailed phylogenetic studies of Portuguese HIV-1 epidemics are still scarce. Thus, our main goal was to analyze the phylodynamics of a local HIV-1 infection in the Portuguese region of Minho. Molecular epidemiological analysis was applied to data from 289 HIV-1-infected individuals followed at the reference hospital of the province of Minho, Portugal, at which isolated viruses had been sequenced between 2000 and 2012. Viruses of the G (29.1%) and B (27.0%) subtypes were the most frequent, followed by recombinant forms (17.6%) and the C (14.5%), F1 (7.3%), and A1 (4.2%) subtypes. Multinomial logistic regression revealed that the odds of being infected with the A1 and F1 subtypes increased over the years compared with those with B, G, or C subtypes or recombinant viruses. As expected, polyphyletic patterns suggesting multiple and old introductions of the B and G subtypes were found. However, transmission clusters of non-B and non-G viruses among native individuals were also found, with the dates of the most recent common ancestor estimated to be in the early 2000s. Our study supports that the HIV-1 subtype diversity in the Portuguese region of Minho is high and has been increasing in a manner that is apparently driven by factors other than immigration and international travel. Infections with A1 and F1 viruses in the region of Minho are becoming established and are mainly found in sexually transmitted clusters, reinforcing the need for more efficacious control measures targeting this infection route.
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15
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Delatorre E, Mir D, Bello G. Spatiotemporal dynamics of the HIV-1 subtype G epidemic in West and Central Africa. PLoS One 2014; 9:e98908. [PMID: 24918930 PMCID: PMC4053352 DOI: 10.1371/journal.pone.0098908] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/03/2014] [Indexed: 01/25/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the second most prevalent HIV-1 clade in West Africa, accounting for nearly 30% of infections in the region. There is no information about the spatiotemporal dynamics of dissemination of this HIV-1 clade in Africa. To this end, we analyzed a total of 305 HIV-1 subtype G pol sequences isolated from 11 different countries from West and Central Africa over a period of 20 years (1992 to 2011). Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method. Our analyses indicate that subtype G most probably emerged in Central Africa in 1968 (1956–1976). From Central Africa, the virus was disseminated to West and West Central Africa at multiple times from the middle 1970s onwards. Two subtype G strains probably introduced into Nigeria and Togo between the middle and the late 1970s were disseminated locally and to neighboring countries, leading to the origin of two major western African clades (GWA-I and GWA-II). Subtype G clades circulating in western and central African regions displayed an initial phase of exponential growth followed by a decline in growth rate since the early/middle 1990s; but the mean epidemic growth rate of GWA-I (0.75 year−1) and GWA-II (0.95 year−1) clades was about two times higher than that estimated for central African lineages (0.47 year−1). Notably, the overall evolutionary and demographic history of GWA-I and GWA-II clades was very similar to that estimated for the CRF06_cpx clade circulating in the same region. These results support the notion that the spatiotemporal dissemination dynamics of major HIV-1 clades circulating in western Africa have probably been shaped by the same ecological factors.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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16
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Gomes P, Carvalho AP, Diogo I, Gonçalves F, Costa I, Cabanas J, Camacho RJ. Comparison of the NucliSENS EasyQ HIV-1 v2.0 with Abbott m2000rt RealTime HIV-1 assay for plasma RNA quantitation in different HIV-1 subtypes. J Virol Methods 2013; 193:18-22. [DOI: 10.1016/j.jviromet.2013.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 04/18/2013] [Accepted: 05/08/2013] [Indexed: 01/22/2023]
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17
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Shankarappa R, Mullins JI. Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. J Virol Methods 2013; 194:169-77. [PMID: 23994080 DOI: 10.1016/j.jviromet.2013.08.012] [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: 03/22/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
Abstract
Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.
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Affiliation(s)
- Raj Shankarappa
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, United States
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18
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Pérez-Álvarez L, Delgado E, Vega Y, Montero V, Cuevas T, Fernández-García A, García-Riart B, Pérez-Castro S, Rodríguez-Real R, López-Álvarez MJ, Fernández-Rodríguez R, Lezaun MJ, Ordóñez P, Ramos C, Bereciartua E, Calleja S, Sánchez-García AM, Thomson MM. Predominance of CXCR4 tropism in HIV-1 CRF14_BG strains from newly diagnosed infections. J Antimicrob Chemother 2013; 69:246-53. [PMID: 23900735 DOI: 10.1093/jac/dkt305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES R5-tropic viruses are associated with HIV-1 transmission and predominate during the early stages of infection. X4-tropic populations have been detected in ~50% of patients with late-stage disease infected with subtype B viruses. In this study, we compared the frequency of X4 tropism in individuals infected with HIV-1 CRF14_BG viruses, which have a V3 loop of subtype B, with a control group of individuals infected with subtype B viruses. METHODS Sixty-three individuals infected with HIV-1 CRF14_BG (n = 31) or subtype B (n = 32) were studied. Similar proportions of newly diagnosed and chronically infected individuals were included in the subtype B and CRF14_BG groups. V3 sequences were obtained and coreceptor tropism was predicted using the Geno2pheno[coreceptor] algorithm. V3 net charge and 11/25 rules were also used for coreceptor prediction. RESULTS Overall, X4 tropism was more frequent among individuals infected with CRF14_BG viruses (87.1%) than subtype B viruses (34.3%), a difference that was statistically highly significant (P = 0.00001). Importantly, the frequencies among newly diagnosed individuals were 90% and 13.3%, respectively (P = 0.0007). Characteristic amino acids in the V3 loop (T13, M14, V19 and W20) were identified at higher frequencies in CRF14_BG viruses (54%) than subtype B viruses (0%; P < 0.000001). CONCLUSIONS CRF14_BG is the genetic form with the highest proportion of X4-tropic viruses reported to date in newly diagnosed and chronic infections. This suggests high pathogenicity for CRF14_BG viruses, potentially leading to rapid disease progression. CCR5 antagonists will be ineffective in most CRF14_BG-infected patients, even at early stages of infection.
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Affiliation(s)
- Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Freitas FB, Esteves A, Piedade J, Parreira R. Novel multiregion hybridization assay for the identification of the most prevalent genetic forms of the human immunodeficiency virus type 1 circulating in Portugal. AIDS Res Hum Retroviruses 2013; 29:318-28. [PMID: 22935093 DOI: 10.1089/aid.2012.0025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The most efficient method for HIV-1 genetic characterization involves full-genome sequencing, but the associated costs, technical features, and low throughput preclude it from being routinely used for the analysis of large numbers of viral strains. Multiregion hybridization assays (MHA) represent an alternative for a consistent genetic analysis of large numbers of viral strains. Classically, MHA rely on the amplification by real-time PCR of several regions scattered along the HIV-1 genome, and on their characterization with clade-specific TaqMan probes (also known as hydrolysis probes). In this context, the aim of our study was the development of a technical variant of an MHA (vMHA(B/G/02)) for genotyping the most prevalent genetic forms of HIV-1 circulating in Portugal. Different sets of primers were designed for universal and clade-specific amplifications of several sections of the viral genome: gag, pol(Pr), pol(RT), vpu, env(gp120), and env(gp41). vMHA(B/G/02) was implemented using a real-time PCR-based approach, with detection dependent on the use of SYBR Green I. As an alternative, a technically less demanding strategy based on conventional PCR and agarose gel analysis of the reaction products was also developed. This method performed with overall good sensitivity and specificity (>91%) when a convenience sample of 45 plasma-derived HIV-1 strains was analyzed. Apart from the detection of subtype B, G, CRF02_AG, and CRF14_BG viruses, several unique B/G recombinant were also detected. Curiously, recombinant viruses including CRF02_AG sequences were not detected in the group of samples analyzed.
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Affiliation(s)
- Ferdinando B. Freitas
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Aida Esteves
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - João Piedade
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ricardo Parreira
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
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Machado LY, Dubed M, Díaz H, Ruiz N, Romay D, Váldes N, Blanco M, Silva E. Transmitted HIV type 1 drug resistance in newly diagnosed Cuban patients. AIDS Res Hum Retroviruses 2013; 29:411-4. [PMID: 22985307 DOI: 10.1089/aid.2012.0183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Knowledge of the associated mutations to transmitted drug resistance (TDR) in strains of human immunodeficiency virus type 1 (HIV-1) constitutes a fundamental premise in epidemiological surveillance. In this present study, TDR from 200 Cuban patients who were diagnosed with HIV-1 between 2009 and 2011 was analyzed. By partial reverse transcriptase polymerase chain reaction (RT-PCR) and sequencing of the HIV pol gene, an HIV subtype and transmitted resistance profile were determined. The prevalence of associated mutations to the TDR in the individuals studied was 21.5%. In the region of the reverse transcriptase, the most common mutations were K103N and M184V, while in the region of the protease they were L33F and M46L. The results of this study provide evidence of TDR in the Cuban seropositive population and suggest the necessity of making resistance assays before beginning antiretroviral therapy in HIV-1-infected patients in Cuba.
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Affiliation(s)
- Liuber Y. Machado
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Marta Dubed
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Héctor Díaz
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Nancy Ruiz
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Dania Romay
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Neysi Váldes
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Madeline Blanco
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
| | - Eladio Silva
- AIDS Research Laboratory, Carretera Tapaste y Autopista Nacional, San José de las Lajas, Mayabeque, Cuba
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Bártolo I, Abecasis AB, Borrego P, Barroso H, McCutchan F, Gomes P, Camacho R, Taveira N. Origin and epidemiological history of HIV-1 CRF14_BG. PLoS One 2011; 6:e24130. [PMID: 21969855 PMCID: PMC3182163 DOI: 10.1371/journal.pone.0024130] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 08/05/2011] [Indexed: 01/03/2023] Open
Abstract
Background CRF14_BG isolates, originally found in Spain, are characterized by CXCR4 tropism and rapid disease progression. This study aimed to identify the origin of CRF14_BG and reconstruct its epidemiological history based on new isolates from Portugal. Methodology/Principal Findings C2V3C3 env gene sequences were obtained from 62 samples collected in 1993–1998 from Portuguese HIV-1 patients. Full-length genomic sequences were obtained from three patients. Viral subtypes, diversity, divergence rate and positive selection were investigated by phylogenetic analysis. The molecular structure of the genomes was determined by bootscanning. A relaxed molecular clock model was used to date the origin of CRF14_BG. Geno2pheno was used to predict viral tropism. Subtype B was the most prevalent subtype (45 sequences; 73%) followed by CRF14_BG (8; 13%), G (4; 6%), F1 (2; 3%), C (2; 3%) and CRF02_AG (1; 2%). Three CRF14_BG sequences were derived from 1993 samples. Near full-length genomic sequences were strongly related to the CRF14_BG isolates from Spain. Genetic diversity of the Portuguese isolates was significantly higher than the Spanish isolates (0.044 vs 0.014, P<0.0001). The mean date of origin of the CRF14_BG cluster was estimated to be 1992 (range, 1989 and 1996) based on the subtype G genomic region and 1989 (range, 1984–1993) based on the subtype B genomic region. Most CRF14_BG strains (78.9%) were predicted to be CXCR4. Finally, up to five amino acids were under selective pressure in subtype B V3 loop whereas only one was found in the CRF14_BG cluster. Conclusions CRF14_BG emerged in Portugal in the early 1990 s soon after the beginning of the HIV-1 epidemics, spread to Spain in late 1990 s as a consequence of IVDUs migration and then to the rest of Europe. CXCR4 tropism is a general characteristic of this CRF that may have been selected for by escape from neutralizing antibody response.
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Affiliation(s)
- Inês Bártolo
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
| | - Ana B. Abecasis
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
| | - Pedro Borrego
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
| | - Helena Barroso
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
| | - Francine McCutchan
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Perpétua Gomes
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
| | - Ricardo Camacho
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
| | - Nuno Taveira
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
- * E-mail:
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Revilla A, Delgado E, Christian EC, Dalrymple J, Vega Y, Carrera C, González-Galeano M, Ocampo A, de Castro RO, Lezaún MJ, Rodríguez R, Mariño A, Ordóñez P, Cilla G, Cisterna R, Santamaría JM, Prieto S, Rakhmanova A, Vinogradova A, Ríos M, Pérez-Álvarez L, Nájera R, Montefiori DC, Seaman MS, Thomson MM. Construction and phenotypic characterization of HIV type 1 functional envelope clones of subtypes G and F. AIDS Res Hum Retroviruses 2011; 27:889-901. [PMID: 21226626 DOI: 10.1089/aid.2010.0177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Subtype G has been estimated to represent the fourth most prevalent clade in the HIV-1 pandemic and subtype F is widely circulating in parts of South America (frequently within BF recombinant forms) and in Romania. However, functional envelope clones of these subtypes are lacking, which are needed for studies on antibody-mediated neutralization, coreceptor usage, and efficiency of viral entry inhibitor drugs. Here we report the construction, neutralization properties, and coreceptor usage of HIV-1 functional envelope clones of subtypes G (n = 15) and F (n = 7). These clones were obtained through RT-PCR amplification of HIV-1 gp160 from plasma RNA, and were used for pseudovirus production. All 15 subtype G-enveloped pseudoviruses were resistant to neutralization by gp120-targeted broadly neutralizing monoclonal antibodies (MAbs) b12 and 2G12, while a majority were neutralized by gp41-targeted MAbs 2F5 and 4E10. With regard to the subtype F envelopes, all seven pseudoviruses were resistant to 2F5 and b12, six were resistant to G12, and six were neutralized by 4E10. Coreceptor usage testing revealed that 21 of 22 envelopes were CCR5-tropic, including all 15 subtype G envelopes, seven of which were from patients with CD4(+) T cell counts <200/ml. These results confirm the broadly neutralizing activity of 4E10 on envelope clones across all tested group M clades, including subtypes G and F, reveal the resistance of most subtype F-enveloped pseudoviruses to broadly neutralizing MAbs b12, 2G12, and 2F5, and suggest that, similarly to subtype C, CXCR4 tropism is uncommon in subtype G, even at advanced stages of infection.
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Affiliation(s)
- Ana Revilla
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elizabeth C. Christian
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Justin Dalrymple
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Yolanda Vega
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María González-Galeano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Antonio Ocampo
- Complejo Hospitalario Xeral-Cíes, Vigo, Pontevedra, Spain
| | | | | | | | - Ana Mariño
- Hospital Arquitecto Marcide, Ferrol, A Coruña, Spain
| | | | | | | | | | | | - Aza Rakhmanova
- Botkin's Infectious Diseases Hospital, St. Petersburg, Russia
| | | | - Maritza Ríos
- National Reference Center of HIV/AIDS, Public Health Institute of Chile, Santiago, Chile
| | - Lucía Pérez-Álvarez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rafael Nájera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - David C. Montefiori
- Department of Surgery, Laboratory for AIDS Vaccine Research and Development, Duke University Medical Center, Durham, North Carolina
| | - Michael S. Seaman
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Evolutionary and structural features of the C2, V3 and C3 envelope regions underlying the differences in HIV-1 and HIV-2 biology and infection. PLoS One 2011; 6:e14548. [PMID: 21283793 PMCID: PMC3024314 DOI: 10.1371/journal.pone.0014548] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/10/2010] [Indexed: 11/21/2022] Open
Abstract
Background Unlike in HIV-1 infection, the majority of HIV-2 patients produce broadly reactive neutralizing antibodies, control viral replication and survive as elite controllers. The identification of the molecular, structural and evolutionary footprints underlying these very distinct immunological and clinical outcomes may lead to the development of new strategies for the prevention and treatment of HIV infection. Methodology/Principal Findings We performed a side-by-side molecular, evolutionary and structural comparison of the C2, V3 and C3 envelope regions from HIV-1 and HIV-2. These regions contain major antigenic targets and are important for receptor binding. In HIV-2, these regions also have immune modulatory properties. We found that these regions are significantly more variable in HIV-1 than in HIV-2. Within each virus, C3 is the most entropic region followed by either C2 (HIV-2) or V3 (HIV-1). The C3 region is well exposed in the HIV-2 envelope and is under strong diversifying selection suggesting that, like in HIV-1, it may harbour neutralizing epitopes. Notably, however, extreme diversification of C2 and C3 seems to be deleterious for HIV-2 and prevent its transmission. Computer modelling simulations showed that in HIV-2 the V3 loop is much less exposed than C2 and C3 and has a retractile conformation due to a physical interaction with both C2 and C3. The concealed and conserved nature of V3 in the HIV-2 is consistent with its lack of immunodominancy in vivo and with its role in preventing immune activation. In contrast, HIV-1 had an extended and accessible V3 loop that is consistent with its immunodominant and neutralizing nature. Conclusions/Significance We identify significant structural and functional constrains to the diversification and evolution of C2, V3 and C3 in the HIV-2 envelope but not in HIV-1. These studies highlight fundamental differences in the biology and infection of HIV-1 and HIV-2 and in their mode of interaction with the human immune system and may inform new vaccine and therapeutic interventions against these viruses.
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Abstract
BACKGROUND HIV-1 subtype B virus is the predominant subtype in HIV-infected individuals in the United States. However, increasing evidence suggests that prevalence of non-B subtypes may be on the rise in the West, and this may have implications for HIV-1 disease surveillance and treatment. The state of Maryland currently has the fourth highest AIDS case report rate in the United States. The goal of this study was to evaluate the prevalence of HIV-1 non-B subtypes in Maryland. The study population included individuals diagnosed with HIV in 2007 through the voluntary counseling and testing sites at the Maryland Department of Health and Mental Hygiene and HIV-infected patients who had genotyping performed at the University of Maryland Medical Center. RESULTS At the Department of Health and Mental Hygiene sites, 47 unique non-B subtype strains were identified representing a non-B prevalence of 12.9%. These non-B subtypes included CRF02_AG (n = 20), C (n = 11), A (n = 7), G (n = 5), D (n = 1), and unique recombinant forms (n = 3). The non-B patients were predominantly non-Hispanic black (95.7%) with 63.8% female. Although the majority of the HIV subtype B cases (65.3%) were identified from the Baltimore metropolitan area, most (80.9%) of the non-B cases were from the Maryland suburbs of Washington, DC. Among University of Maryland Medical Center patients, there were 30 non-B subtypes, representing a non-B prevalence of 1.9%. The non-B subtypes detected were CRF02_AG (n = 14), C (n = 6), A (n = 6), G (n = 2), D (n = 1), and unique recombinant forms (n = 1). Phylogenetic analysis of the non-B subtypes revealed that viral sequences from both sources were intermixed, confirming that both sampling frames were drawing from the same overall population. CONCLUSIONS Multiple HIV-1 subtypes exist in the Baltimore-Washington metropolitan area with a significant non-B-infected population in the Maryland suburbs of Washington, DC, suggesting 2 independent epidemics of HIV in Maryland. Population-based surveillance inclusive of groups at higher risk of non-B strains is essential to monitor the prevalence and variations of HIV subtypes in Maryland and the United States.
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Branco C, Esteves A, Piedade J, Parreira R. A new genotype 2 subcluster identified among GBV-C strains circulating in the Lisbon metropolitan area of Portugal. J Med Virol 2010; 82:452-9. [DOI: 10.1002/jmv.21703] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Pádua E, Parreira R, Tendeiro R, Nunes B, Castela J, Soares I, Mouzinho A, Reis E, Paixão MT. Potential impact of viral load and genetic makeup of HIV type 1 on mother-to-child transmission: characterization of env-C2V3C3 and nef sequences. AIDS Res Hum Retroviruses 2009; 25:1171-7. [PMID: 19886833 DOI: 10.1089/aid.2009.0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
HIV-1 mother-to-child transmission (MTCT) was evaluated in terms of the molecular characterization of the env and nef genomic regions and quantification of maternal RNA viral loads. Assignment of viral subtype was achieved by direct sequencing of PCR 1172 products amplified from proviral DNA in 45 HIV-1-nontransmitting mothers (NTM), along with 13 pairs of HIV-1-transmitting mothers (TM) and their infected children (C). Analysis of the env C2V3C3 and nef sequences revealed that subtypes G and B, and their genetic combinations (AG, BG), accounted for over 84.5% of all viruses identified. The genetic structure form envA-nefG was the most commonly observed, with a lower frequency in the NTM (13.3%) compared to the TM (23.1%) group. A greater number of genetic forms was observed among NTM, namely the presence of sequences assigned to subtypes D and F, as well as the intergenetic A/J, and C/U, recombinant forms, along with a mosaic provirus with a complex putative envA-nefEGE genetic structure. No significant differences were found when RNA viral loads were evaluated as a function of the viral subtypes. Nevertheless, a relatively high quantification of HIV-1 RNA was obtained in the NTM group, emphasizing the importance of the compliance and effectiveness of therapeutic schemes to control viral replication and reduce the risk of HIV vertical transmission. V3 sequences displaying features associated with the R5 phenotype dominated in both groups. Both C2V3C3 and Nef's functional domains were conserved during HIV-1 vertical transmission.
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Affiliation(s)
- Elizabeth Pádua
- Laboratório de Referência da SIDA, Instituto Nacional de Saúde, 1649-016 Lisboa, Portugal
| | - Ricardo Parreira
- Unidade de Virologia/UPMM, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal
| | - Rita Tendeiro
- Laboratório de Referência da SIDA, Instituto Nacional de Saúde, 1649-016 Lisboa, Portugal
| | - Baltazar Nunes
- Observatório Nacional de Saúde, Instituto Nacional de Saúde, 1649-016 Lisboa, Portugal
| | - João Castela
- Maternidade Alfredo da Costa, Rua Viriato, 1069-089 Lisboa, Portugal
| | - Isabel Soares
- Pediatria, Hospital Garcia de Orta, Pragal, 2801-951 Almada, Portugal
| | - Ana Mouzinho
- Infecto de Pediatria, Hospital Santa Maria, 1649-035 Lisboa, Portugal
| | - Eduarda Reis
- Neonatologia, Hospital S. Francisco Xavier, Estrada do Forte do Alto do Duque, 1495-005 Lisboa, Portugal
| | - Maria Teresa Paixão
- Núcleo de Vigilância Epidemiológica das Doenças Transmissíveis, Instituto Nacional de Saúde, 1649-016 Lisboa, Portugal
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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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Ramirez-Piedad MK, Lepej SZ, Yerly S, Begovac J. High prevalence of non-B HIV-1 subtypes in seamen and their sexual partners in Croatia. J Med Virol 2009; 81:573-7. [DOI: 10.1002/jmv.21433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Pádua E, Almeida C, Nunes B, Cortes Martins H, Castela J, Neves C, Paixão MT. Assessment of mother-to-child HIV-1 and HIV-2 transmission: an AIDS reference laboratory collaborative study. HIV Med 2009; 10:182-90. [PMID: 19207600 DOI: 10.1111/j.1468-1293.2008.00669.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE A prospective study was carried out to assess HIV-1 and HIV-2 mother-to-child transmission (MTCT) rates in Portugal between 1999 and 2005 by analysing the proportion of diagnosed infected children born to HIV-positive mothers. MATERIALS AND METHODS Serial blood samples were collected from 1315 children at risk of HIV-1 infection, 131 children at risk of HIV-2 infection and six children at risk of both HIV-1 and HIV-2 infections attending 25 Health Institutions. HIV proviral DNA was detected by nested polymerase chain reaction (PCR) and statistical analysis was performed using spss. RESULTS DNA PCR using HIV-1 and HIV-2 long terminal repeat (LTR) primers amplified 92.5% and 75% of maternal HIV infections, respectively. Overall, MTCT occurred in 3.4% [95% confidence interval (CI) 2.5-4.6%] of HIV-1 and 1.5% (95% CI 0.2-5.4%) of HIV-2 mother-child pairs. A significant decrease in HIV-1 MTCT was observed with time, from 7.0% (95% CI 2.6-14.6%) in 1999 to 0.5% (95% CI 0.0-2.5%) in 2005. HIV MTCT was associated with an absence of antiretroviral therapy in infected pregnant women (P<0.0001). Of the 48 infected children (46 with HIV-1 and two with HIV-2), the schedule of blood sample collection was followed for only 26 children. In 14 (53.8%) of those 26 children the infections were diagnosed in the first sample collected before they were 48 h old, suggesting in utero transmission. Despite the national recommendations for antenatal HIV testing, a high overall proportion (22.2% for HIV-1 and 44.3% for HIV-2) of mothers did not access any MTCT prevention measures, mostly because of late diagnosis in pregnancy. A small but significant proportion of HIV-2 infection was found in mothers with no identifiable link with West Africa. CONCLUSION HIV-2 transmission rates are low (1.5% in this study), and this may have led to a lower uptake of interventions, but in the absence of interventions transmission does occur. HIV-1 transmission was also associated with a lack of intervention, mostly as a result of late presentation. Use of primers restricted to a single sequence led to false-negative maternal results in a significant proportion of cases. In part this may have been attributable to very low HIV DNA loads as well as primer template mismatches. HIV infection was not documented in children born to mothers with negative HIV DNA PCR results.
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Affiliation(s)
- E Pádua
- AIDS Epidemic Reference Laboratory, National Institute of Health, Lisbon, Portugal
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Kousiappa I, van de Vijver DAMC, Demetriades I, Kostrikis LG. Genetic analysis of HIV type 1 strains from newly infected untreated patients in cyprus: high genetic diversity and low prevalence of drug resistance. AIDS Res Hum Retroviruses 2009; 25:23-35. [PMID: 19182918 DOI: 10.1089/aid.2008.0168] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract The molecular epidemiology of HIV-1 infection was first studied in Cyprus in the mid-1990s, but the extent of HIV-1 diversity and the prevalence of drug resistance have remained elusive. In an effort to address this issue, the present study examined HIV-1 strains isolated from 37 newly diagnosed untreated HIV-1 patients, representing 72% of the total number of newly diagnosed and drug-naive patients in the period 2003 to 2006. DNA sequences encoding the gag (p17, p24, p2, p7, p1, and p6), pol (protease and reverse transcriptase), and env (gp160) regions were amplified by RT-PCR from plasma HIV-1 RNA from all patients and sequenced using a newly designed methodology. All amplified products were studied according to established genetic methodologies to determine the genetic subtype and the prevalence of drug-resistance-associated mutations to currently available antiretroviral drugs. Analyses of the obtained viral sequences indicated that subtype A was the most common subtype present and accounted for 38% of the infections followed by subtype B (35%), subtype C (13%), CRF02_AG (8%), and subtypes D and CRF01_AE (3% each). One patient (2.7%) had an M41L/M and another patient (2.7%) an M184V amino acid substitution in the reverse transcriptase (RT) associated with high-level resistance to RT inhibitors. There were no patients with resistant mutations to protease inhibitors (PI). Additionally, one patient (2.7%) had an L44M amino acid substitution within the HR1 region of gp41 conferring resistance to the enfuvirtide (T20) fusion inhibitor. Similar to results of the 1994 molecular epidemiological study, these data demonstrate the extensive heterogeneity of HIV-1 infection in Cyprus and the low prevalence of transmitted resistance to current HIV-1 antiretroviral drugs. Taken together, these findings demonstrate that HIV-1 infection in Cyprus is being replenished by a continuous influx of new strains from many countries, establishing an ever-evolving and polyphyletic infection in the island.
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Affiliation(s)
- Ioanna Kousiappa
- Department of Biological Sciences, University of Cyprus , 1678 Nicosia, Cyprus
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Khamadi SA, Lihana RW, Mwaniki D, Kinyua J, Lagat N, Carter JY, Ichimura H, Oishi I, Okoth FA, Ochieng W. HIV type 1 genetic diversity in Moyale, Mandera, and Turkana based on env-C2-V3 sequences. AIDS Res Hum Retroviruses 2008; 24:1561-4. [PMID: 19102688 DOI: 10.1089/aid.2008.0085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genetic diversity of HIV-1 subtypes circulating in three districts of northern Kenya, i.e., Turkana, Mandera, and Moyale, was studied. DNA sequences encoding a portion of the env-C2-V3 region of the virus were amplified by PCR and sequenced directly. One hundred and fifty-nine samples were successfully sequenced in the env-C2-V3 region and analyzed. From the analysis, 57% were subtype A1, 27% were subtype C, 9% were subtype D, and the remaining 7% were unclassified. This study showed that HIV-1 subtype A1 was the dominant subtype in circulation in this region, though there was a significant percentage of HIV-1 subtype C in circulation there.
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Affiliation(s)
| | | | - D.L. Mwaniki
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Nancy Lagat
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Jane Y. Carter
- African Medical and Research Foundation Kenya, Nairobi, Kenya
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Yamaguchi J, Badreddine S, Swanson P, Bodelle P, Devare SG, Brennan CA. Identification of new CRF43_02G and CRF25_cpx in Saudi Arabia based on full genome sequence analysis of six HIV type 1 isolates. AIDS Res Hum Retroviruses 2008; 24:1327-35. [PMID: 18844465 DOI: 10.1089/aid.2008.0101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, we reported a high level of HIV-1 strain diversity in patients at the King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia. Based on phylogenetic analysis of gag p24, pol integrase, and env gp41 sequences, subtypes A, B, C, D, and G, and CRF02_AG, as well as unique recombinant forms were identified. Subtype G accounted for 25% of the infections in the Saudi population and this high prevalence was unexpected. Although subtype G is found in west central Africa, pure subtype G strains are uncommon. To further characterize the subtype G infections in Saudi Arabia, six strains that appeared to be pure subtype G were selected for full genome sequencing. Near full-length genomes were obtained using RT-PCR amplification to generate overlapping fragments from viral RNA extracted from plasma. The six strains are not subtype G throughout their entire genome. Four isolates have a recombinant structure composed of CRF02_AG and subtype G and share three identical breakpoints. This recombinant form defines a new CRF designated CRF43_02G. The remaining two isolates are CRF25_cpx, a circulating recombinant form identified in Cameroon composed of subtypes A and G and unclassified segments. Reanalysis of the previously reported Saudi HIV-1 partial genome sequences revealed additional isolates classified as CRF43_02G and CRF25_cpx and one isolate was reclassified to CRF22_01A. Identification of CRF43_02G in Saudi Arabia could indicate a transmission network within the country. Alternatively, the new CRF could have been introduced from an external source where this CRF is not yet recognized.
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Affiliation(s)
| | - Samar Badreddine
- King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
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Stebbing J, Powles T, Nelson M, Bower M. Significance of variation within HIV, EBV, and KSHV subtypes. ACTA ACUST UNITED AC 2008; 5:93-102. [PMID: 16928877 DOI: 10.1177/1545109706290171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Since their initial transmission to humans, viruses have diversified extensively through recombination and mutation. The presence of intra- and inter-individual viral diversity influences disease progression, drug resistance, and therapy and presumably explains the conflicting results in many studies, including the failure of peptide-based vaccination strategies. Although HIV is a small RNA virus, coinfection with large DNA viruses, notably the oncogenic gamma-herpesviridae human herpesvirus-8 and Epstein Barr virus, is common. This coinfection occurs secondary to immunosuppression and shared transmission routes with high-risk predisposing behavior. In addition, all 3 of these viruses can lead to chronic infections, long periods of latency, and reactivation characterized by pain and suffering. The efficient targeting of their genetic diversity represents one of the major challenges in their control, both in prophylactic and therapeutic strategies. An understanding of diversity will help delineate whether population-specific vaccine strategies are necessary.
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Affiliation(s)
- Justin Stebbing
- Department of HIV Medicine, The Chelsea and Westminster Hospital, 369 Fulham Road, London, United Kingdom
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34
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McConnell MJ, Docobo-Pérez F, Mata RC, Fernandez-Cuenca F, Viciana P, López-Cortés LF, Trastoy M, Pachón J, Pérez-Romero P. Molecular epidemiology of HIV type 1 in newly diagnosed patients in southern Spain. AIDS Res Hum Retroviruses 2008; 24:881-7. [PMID: 18572440 DOI: 10.1089/aid.2008.0051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prevalence of different HIV-1 subtypes in Spain varies by geographic region. In the present study isolates were collected from 72 newly diagnosed individuals in western Andalucia from 2004 to 2006. Viral sequences were amplified and the subtype diversity and prevalence of resistance mutations in the reverse transcriptase and protease genes were determined. The results presented here demonstrate that subtype B virus predominates in this region (88.9%), with the non-B subtypes CRF02_AG (9.7%) and B/G (1.4%) also present. Only two isolates (2.9%) carried resistance mutations in the reverse transcriptase gene and none of the isolates had major resistance mutations in the protease gene. Minor mutations in the protease gene were more prevalent with 86.1% of isolates containing at least one minor mutation. These results elucidate the subtype diversity present in this region and suggest that the transmission of highly resistant virus variants does not occur at a high frequency in this population.
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Affiliation(s)
- Michael J. McConnell
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
| | - Fernando Docobo-Pérez
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
| | - Rosario C. Mata
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
| | | | - Pompeyo Viciana
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
| | - Luis F. López-Cortés
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
| | - Mónica Trastoy
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
| | - Jerónimo Pachón
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
| | - Pilar Pérez-Romero
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocío, Seville, Spain
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35
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López-Vélez R, Beltrá MN, Jerez AH, del Amo Valero J. Infección por el VIH en inmigrantes. Enferm Infecc Microbiol Clin 2008; 26 Suppl 5:12-21. [DOI: 10.1157/13123263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Global molecular epidemiology of HIV: understanding the genesis of AIDS pandemic. ADVANCES IN PHARMACOLOGY 2008; 56:1-25. [PMID: 18086407 DOI: 10.1016/s1054-3589(07)56001-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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37
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Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D. Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol 2007; 81:13050-6. [PMID: 17898057 PMCID: PMC2169105 DOI: 10.1128/jvi.00889-07] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 09/17/2007] [Indexed: 11/20/2022] Open
Abstract
With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods.
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Affiliation(s)
- Robert J Gifford
- Department of Infection, University College London, London, United Kingdom.
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38
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Rouet F, Chaix ML, Nerrienet E, Ngo-Giang-Huong N, Plantier JC, Burgard M, Peeters M, Damond F, Ekouevi DK, Msellati P, Ferradini L, Rukobo S, Maréchal V, Schvachsa N, Wakrim L, Rafalimanana C, Rakotoambinina B, Viard JP, Seigneurin JM, Rouzioux C. Impact of HIV-1 genetic diversity on plasma HIV-1 RNA Quantification: usefulness of the Agence Nationale de Recherches sur le SIDA second-generation long terminal repeat-based real-time reverse transcriptase polymerase chain reaction test. J Acquir Immune Defic Syndr 2007; 45:380-8. [PMID: 17468666 DOI: 10.1097/qai.0b013e3180640cf5] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The high genetic diversity of HIV-1 has a major impact on the quantification of plasma HIV-1 RNA, representing an increasingly difficult challenge. A total of 898 plasma specimens positive for HIV-1 RNA by commercial assays (Amplicor v1.5; Roche Diagnostic Systems, Alameda, CA or Versant v3.0; Bayer Diagnostics, Emeryville, CA) were tested using the Agence Nationale de Recherches sur le SIDA second-generation (G2) real-time reverse transcriptase polymerase chain reaction (RT-PCR) test: 518 samples containing HIV-1 of known subtype, including 88 from 2 subtype panels and 430 harboring B (n = 266) and non-B (n = 164) group M HIV-1 subtypes from patients followed up in 2002 through 2005 at Necker Hospital (Paris, France), and 380 samples from 10 different countries (Argentina, Cambodia, Cameroon, Central African Republic, France, Ivory Coast, Madagascar, Morocco, Thailand, and Zimbabwe). HIV-1 RNA values obtained by G2 real-time PCR were highly correlated with those obtained by the Amplicor v1.5 for B and non-B subtypes (R = 0.892 and 0.892, respectively) and for samples from diverse countries (R = 0.867 and 0.893 for real-time PCR vs. Amplicor v1.5 and real-time PCR vs. Versant v3.0, respectively). Approximately 30% of specimens harboring non-B subtypes were underquantified by at least -0.51 log10 in Amplicor v1.5 versus 5% underquantified in G2 real-time PCR. Discrepant results were also obtained with subtype B samples (14% underquantified by Amplicor v1.5 vs. 7% by G2 real-time PCR). Similar percentages were observed when comparing results obtained with the G2 real-time PCR assay with those obtained using the Versant assay. Addressing HIV-1 diversity, continual monitoring of HIV-1 RNA assays, together with molecular epidemiology studies, is required to improve the accuracy of all HIV RNA assays.
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Affiliation(s)
- François Rouet
- Laboratoire de Virologie, Centre Muraz, BP 390 Bobo-Dioulasso 01, Burkina Faso.
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39
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Badreddine S, Smith K, van Zyl H, Bodelle P, Yamaguchi J, Swanson P, Devare SG, Brennan CA. Identification and characterization of HIV type 1 subtypes present in the Kingdom of Saudi Arabia: high level of genetic diversity found. AIDS Res Hum Retroviruses 2007; 23:667-74. [PMID: 17530991 DOI: 10.1089/aid.2007.0185] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Saudi Arabia has a very low prevalence of HIV infections and nothing is known about HIV strains present in the population. Here specimens were collected from 62 HIV-1-infected patients at the King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia. Viral sequences were PCR amplified using primers for HIV-1 group M in gag p24, pol integrase, and env gp41 and genetic subtype was determined by phylogenetic analysis. HIV-1 viral sequences were amplified from 56 of the 62 specimens. Based on phylogenetic analysis of viral sequences, subtype C was the most common subtype present and accounted for 39.3% of the infections followed by subtype G (25%), subtype B (17.9%), subtype D (3.6%), and subtypes A and CRF02_AG (1.8% each). In addition, for six specimens subtype classifications were discordant between gag, pol, and/or env; these intersubtype recombinant viruses account for 10.7% of the infections and consisted of recombinants of subtypes A/CRF01, A/CRF02, A/G, B/G, and D/CRF02. The high HIV-1 strain diversity suggests that there have been multiple introductions of HIV-1 into Saudi Arabia from several sources. Within the study population, there were five husband/wife pairs. For each pair, the viral sequences obtained were closely related to each other showing that heterosexual transmission occurred.
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Affiliation(s)
- Samar Badreddine
- King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
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40
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Toro C, Jiménez V, Rodríguez C, Del Romero J, Rodés B, Holguín A, Alvarez P, García-Campello M, Gómez-Hernando C, Guelar A, Sheldon J, de Mendoza C, Simón A, Soriano V. Molecular and epidemiological characteristics of blood-borne virus infections among recent immigrants in Spain. J Med Virol 2007; 78:1599-608. [PMID: 17063510 DOI: 10.1002/jmv.20744] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The increased immigration from developing regions to Western countries raises public health concerns related to blood-borne viruses. The prevalence of human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), and human T-lymphotropic virus (HTLV) infections among recent immigrants attending several Spanish diagnostic centers in years 2002 and 2003 was examined. Genetic characterization of viral subtypes and its relationship with distinct at-risk populations was carried out. A total of 1,303 immigrants were identified. They originated in Latin America (46.9%), Sub-Saharan Africa (23.7%), Eastern Europe (9.4%), and the Maghreb (9.2%). Seroprevalence rates were as follows: HIV-1 4.2%, HBV 4.1%, HCV 2.9%, and HTLV-1 0.8%. All patients with HIV-1 non-B subtypes, HBV genotypes E and A3, and HCV genotype 4 were sub-Saharan Africans, and had been infected mainly through heterosexual contacts. In contrast, Latin American homo/bisexual men carried HIV-1 subtype B most likely acquired after their arrival to Spain. In conclusion, while Sub-Saharan Africans carry wide diverse genetic variants of blood-borne viruses, the absence of high-risk practices in most cases could limit the spread of these variants. In contrast, Latin Americans with high-risk sexual practices may be a particularly vulnerable collective to acquire blood-borne viruses in the receptor country.
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Affiliation(s)
- Carlos Toro
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
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41
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Abstract
Human immunodeficiency virus (HIV) is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS). HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.
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Affiliation(s)
- Henry I Z Requejo
- Seção de Imunologia, Instituto Adolfo Lutz, Av. Dr. Arnaldo 351, 01246-902 São Paulo, SP, Brazil.
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42
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Babic DZ, Poljak M, Seme K, Tomazic J, Vidmar L. Molecular epidemiology of HIV-1 subtypes based on analysis ofpol sequences in Slovenia, 1996–2005. J Med Virol 2006; 78:997-1002. [PMID: 16789023 DOI: 10.1002/jmv.20654] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Various studies have demonstrated the increasing prevalence of non-B HIV-1 subtypes in Western Europe. In contrast, knowledge about the molecular epidemiology of HIV-1 in Central and Eastern Europe is limited. The objective of present study was to investigate the HIV-1 molecular diversity as well as time trends in HIV-1 subtype distribution in Slovenia. A retrospective molecular epidemiological survey was conducted on a cohort representing 88% (131/149) of all HIV-1 infected patients diagnosed between January 1996 and June 2005. The study revealed that subtype B is a predominant HIV-1 subtype in Slovenia (110/131; 84%), although a relatively high proportion (21/131; 16%) of non-B subtypes was found. Among them, a high proportion of recombinant (10/21; 48%) and different unclassified strains (8/21; 38%) were identified. Non-B subtype viruses were predominant among heterosexuals (19/21; 90%) and subtype B viruses among men who have sex with men (84/110; 76%). Importantly, 86% (18/21) of patients infected with non-B subtypes were of Slovenian nationality. In contrast to Western European countries, a significant increase (P = 0.015) in the proportion of men who have sex with men was observed recently among newly diagnosed HIV-1 infected patients in Slovenia.
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Affiliation(s)
- Dunja Z Babic
- Institute of Microbiology and Immunology, Medical Faculty, Ljubljana, Slovenia
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43
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Sengupta S, Jana S, Roy P, Sarkar K, Bhattacharya SK, Chakrabarti S. Phylogenetic analysis of the p24-p7 region of the human immunodeficiency virus type 1 gag gene to determine subtype distribution among female sex workers in Calcutta, India. J Clin Microbiol 2005; 43:5787-91. [PMID: 16272521 PMCID: PMC1287808 DOI: 10.1128/jcm.43.11.5787-5791.2005] [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] [Received: 05/13/2005] [Revised: 08/02/2005] [Accepted: 08/12/2005] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C, based on the envelope region, has been reported to be predominant in India. We sequenced the p24-p7 gag region from 51 HIV-1 seropositive female sex workers in Calcutta, India, for more-detailed molecular characterization. Subtype C was found to be prevalent, although no strong monophyletic cluster was observed.
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Affiliation(s)
- Satarupa Sengupta
- HIV/AIDS Laboratory, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Calcutta-700010, India
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44
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Shepherd BE, Rossini AJ, Soto RJ, De Rivera IL, Mullins JI. Sampling designs for HIV molecular epidemiology with application to Honduras. AIDS Res Hum Retroviruses 2005; 21:907-14. [PMID: 16386105 DOI: 10.1089/aid.2005.21.907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proper sampling is essential to characterize the molecular epidemiology of human immunodeficiency virus (HIV). HIV sampling frames are difficult to identify, so most studies use convenience samples. We discuss statistically valid and feasible sampling techniques that overcome some of the potential for bias due to convenience sampling and ensure better representation of the study population. We employ a sampling design called stratified cluster sampling. This first divides the population into geographical and/or social strata. Within each stratum, a population of clusters is chosen from groups, locations, or facilities where HIV-positive individuals might be found. Some clusters are randomly selected within strata and individuals are randomly selected within clusters. Variation and cost help determine the number of clusters and the number of individuals within clusters that are to be sampled. We illustrate the approach through a study designed to survey the heterogeneity of subtype B strains in Honduras.
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Affiliation(s)
- Bryan E Shepherd
- Department of Biostastics, Medical Education, University of Washington, Seattle, Washington 98195-7232, USA.
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45
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Achkar JM, Burda ST, Konings FAJ, Urbanski MM, Williams CAU, Seifen D, Kahirimbanyi MN, Vogler M, Parta M, Lupatkin HC, Zolla-Pazner S, Nyambi PN. Infection with HIV type 1 group M non-B subtypes in individuals living in New York City. J Acquir Immune Defic Syndr 2005; 36:835-44. [PMID: 15213568 DOI: 10.1097/00126334-200407010-00011] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To document infection with HIV type 1 (HIV-1) group M non-B subtypes in individuals living in New York City. DESIGN From October 1999 through April 2003, HIV-1-seropositive individuals were selected from 3 clinics in New York City based on having risk factors for infection with HIV-1 non-B subtypes. METHODS HIV-1 RNA was extracted from plasma samples, and partial gag, pol, or env genes were amplified by PCR analysis. The infecting HIV-1 group M subtype was determined based on results of either heteroduplex mobility assay or sequencing and phylogenetic analysis. RESULTS Ninety-seven subjects were enrolled in the study. Of the 97 subjects, 91 (94%) were selected based on having emigrated from a non-European country, while 6 (6%) were native United States citizens. Subtypes were successfully determined in 53 (55%) of the 97 plasma samples tested. The subtypes in 2 plasma samples were unclassifiable. HIV-1 infections were classified as those due to the following group M subtypes: A (n = 4; 7%), B (n = 12; 22%), C (n = 8; 15%), F (n = 2; 4%), CRF01_AE-like (n = 7; 13%), CRF02_AG-like (n = 19; 34%), an intersubtype recombinant form G/A (n = 1; 2%), and unclassifiable viruses (n = 2; 4%). CONCLUSION This study reveals infection with a broad variety of HIV-1 group M subtypes mostly in the immigrant population of New York City as well as how several non-B subtypes are being introduced into the United States.
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Affiliation(s)
- Jacqueline M Achkar
- Department of Medicine, New York University School of Medicine, NY 10010, USA.
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46
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Sengupta S, Jana S, Sarkar K, Bhattacharya SK, Chakrabarti S. Determination of gag subtypes of HIV type 1 detected among female sex workers in Calcutta, India. AIDS Res Hum Retroviruses 2005; 21:806-9. [PMID: 16218805 DOI: 10.1089/aid.2005.21.806] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 subtyping is important to study the changing scenario of genetic variation. The gag-based heteroduplex mobility assay (gag-HMA) was developed and evaluated as a powerful and reliable technique for identifying the HIV-1 group M subtypes A to H and the circulating recombinant forms (CRFs). To study the subtype distribution of HIV-1 strains from the eastern part of India, we used the gag-based HMA, followed by the sequencing and phylogenetic analysis. Blood samples from HIV-1-seropositive female sex workers in Calcutta were subjected to gag-HMA. The most prevalent subtype was found to be the C type, among which the C4 subsubtype was prevalent. However, a number of nontypable C strains were found in gag-HMA. Phylogenetic analysis revealed the discrete nature of the C strains and no monophyletic cluster was noticed. This result might indicate a growing tendency of variations among the HIV-1 type C strains circulating in eastern India.
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Affiliation(s)
- Satarupa Sengupta
- National Institute of Cholera and Enteric Diseases, ICMR, Calcutta-700010, India
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47
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Lospitao E, Alvarez A, Soriano V, Holguín A. HIV-1 subtypes in Spain: a retrospective analysis from 1995 to 2003. HIV Med 2005; 6:313-20. [PMID: 16156878 DOI: 10.1111/j.1468-1293.2005.00313.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVE To perform a retrospective analysis of all HIV-1 non-B variants circulating in Spain from 1995 to 2003 and extend their virological characterization. METHODS Samples from a total of 396 HIV-infected subjects with epidemiological suspicion of being infected with non-B clades were analysed during the study period. Subtyping was carried out on the protease (PR), reverse transcriptase (RT) and envelope (env) genes. RESULTS PR sequences belonging to non-B subtypes were recognized in 43.2% of cases (23 A, 13C, 6D, 3F, 118 G, 3H, 4 J and 1 U). Subtype G and AG recombinants were the most frequent variants (69%), and were found most often in subjects from West and Central Africa. Up to 70% of pol (PR, RT) sequences belonging to subtype G harboured env sequences belonging to clade A (55%), B (13.8%) or K (3.4%). Nearly half were mosaic GA viruses, and a few were CRF 14 BG viruses. Up to 14 new recombinant viruses, which could not be assigned to previously described circulating recombinant forms (CRFs), were found. CONCLUSIONS There is great diversity in the HIV-1 variants and recombinant viruses circulating in Spain. Non-B sequences may be underestimated if only the env region is examined in phylogenetic analyses. Drug resistance testing provides the advantage of pol subtyping, and its additional use for this purpose should be encouraged.
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Affiliation(s)
- E Lospitao
- Infectious Diseases Service, Hospital Carlos III, Madrid, Spain
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48
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Swanson P, de Mendoza C, Joshi Y, Golden A, Hodinka RL, Soriano V, Devare SG, Hackett J. Impact of human immunodeficiency virus type 1 (HIV-1) genetic diversity on performance of four commercial viral load assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT. J Clin Microbiol 2005; 43:3860-8. [PMID: 16081923 PMCID: PMC1233972 DOI: 10.1128/jcm.43.8.3860-3868.2005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Revised: 04/22/2005] [Accepted: 05/06/2005] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) evolution and changing strain distribution present a challenge to nucleic acid-based assays. Reliable patient monitoring of viral loads requires the detection and accurate quantification of genetically diverse HIV-1. A panel of 97 HIV-1-seropositive plasma samples collected from Cameroon, Brazil, and South Africa was used to compare the performance of four commercially available HIV RNA quantitative tests: Abbott LCx HIV RNA Quantitative assay (LCx), Bayer Versant HIV-1 RNA 3.0 (bDNA), Roche AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5), and bioMérieux NucliSens HIV-1 QT (NucliSens). The panel included group M, group O, and recombinant viruses based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified viral RNA in 97 (100%) of the samples. In comparison, bDNA, Monitor v1.5, and NucliSens quantified viral RNA in 96.9%, 94.8%, and 88.6% of the samples, respectively. The two group O specimens were quantified only by the LCx HIV assay. Analysis of nucleotide mismatches at the primer/probe binding sites for Monitor v1.5, NucliSens, and LCx assays revealed that performance characteristics reflected differences in the level of genetic conservation within the target regions.
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Affiliation(s)
- Priscilla Swanson
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Carmen de Mendoza
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Yagnya Joshi
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Alan Golden
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Richard L. Hodinka
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Vincent Soriano
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Sushil G. Devare
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - John Hackett
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
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49
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Harris B, von Truchsess I, Schätzl HM, Devare SG, Hackett J. Genomic characterization of a novel HIV type 1 B/G intersubtype recombinant strain from an injecting drug user in Germany. AIDS Res Hum Retroviruses 2005; 21:654-60. [PMID: 16060837 DOI: 10.1089/aid.2005.21.654] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recombinant forms of HIV-1 contribute significantly to the ongoing epidemic. In the present study we characterize the full-length genome of a novel B/G intersubtype recombinant strain from a patient with a history of injection drug use. This is the first evidence of a B/G recombinant among injecting drug users in Germany. Moreover, this genetically divergent strain has important clinical implications since it was undetectable in the NucliSens HIV-1 QT assay and significantly underquantified by the COBAS MONITOR version 1.5 test relative to the LCx HIV RNA Quantitative assay. Phylogenetic analysis revealed that this recombinant virus is ancestrally related to CRF14_BG, but carries two additional subtype B-derived segments within vif and pol integrase.
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Affiliation(s)
- Barbara Harris
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, USA
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50
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Holguín A, Alvarez A, Soriano V. Heterogeneous nature of HIV-1 recombinants spreading in Spain. J Med Virol 2005; 75:374-80. [PMID: 15648070 DOI: 10.1002/jmv.20280] [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: 01/03/2023]
Abstract
HIV-1 infections due to non-B subtypes are increasing rapidly in number and spreading across Europe. The genetic nature of HIV-1 non-B variants containing subtype G sequences at the protease (PR)-coding region are described from 48 unrelated subjects living in Spain. Phylogenetic analyses of the HIV-1 reverse transcriptase (RT) and envelope (env) genes (including the V3 loop) were performed. Up to 32 (66.6%) of samples carried inter-subtype recombinant viruses. Although double recombinants were found most frequently (G/A in 20; G/B in 8; G/K in 2), two individuals harbored triple recombinant viruses (GPR/BRT/Aenv and GPR/KRT/Aenv, respectively). Only 33 (68.7%) and 9 (18.7%) sequences clustered with clade G when examining the RT and env genes, respectively. Nearly 70% of samples with pol sequences (PR/RT) belonging to subtype G harbored env sequences ascribed to other clades: A (55.6%), B (11.1%), or K (3.7%). Of note, most recombinant viruses clustered with CRF02_AG, although CRF14_BG recombinants were also found. This study demonstrates that most viruses circulating in Spain with clade G sequences at the pol-coding region are in fact inter-subtype recombinants, with CRF02_AG being the most prevalent virus.
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Affiliation(s)
- Africa Holguín
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
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