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High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing. INFECTION GENETICS AND EVOLUTION 2020; 84:104365. [PMID: 32417307 DOI: 10.1016/j.meegid.2020.104365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
The HIV-1 epidemic in Belgium is primarily driven by MSM. In this patient population subtype B predominates but an increasing presence of non-B subtypes has been reported. We aimed to define to what extent the increasing subtype heterogeneity in a high at risk population induces the formation and spread of new recombinant forms. The study focused on transmission networks that reflect the local transmission to an important extent. One hundred and five HIV-1 transmission clusters were identified after phylogenetic analysis of 2849 HIV-1 pol sequences generated for the purpose of baseline drug resistance testing between 2013 and 2017. Of these 105 clusters, 62 extended in size during the last two years and were therefore considered as representing ongoing transmission. These 62 clusters included 774 patients in total. From each cluster between 1 and 3 representative patients were selected for near full-length viral genome sequencing. In total, the full genome sequence of 101 patients was generated. Indications for the presence of a new recombinant form were found for 10 clusters. These 10 clusters represented 105 patients or 13.6% of the patients covered by the study. The findings clearly show that new recombinant strains highly contribute to local transmission, even in an epidemic that is largely MSM and subtype B driven. This is an evolution that needs to be monitored as reshuffling of genome fragments through recombination may influence the transmissibility of the virus and the pathology of the infection. In addition, important changes in the sequence of the viral genome may challenge the performance of tests used for diagnosis, patient monitoring and drug resistance analysis.
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2
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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: 18] [Impact Index Per Article: 3.6] [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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Vinken L, Fransen K, Cuypers L, Alexiev I, Balotta C, Debaisieux L, Seguin-Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sönnerborg A, Vancutsem E, Vandamme AM, Van den Wijngaert S, Van Ranst M, Verhofstede C, Stadler T, Lemey P, Van Laethem K. Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium. Front Microbiol 2019; 10:613. [PMID: 30972053 PMCID: PMC6443750 DOI: 10.3389/fmicb.2019.00613] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/11/2019] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substantially, which prompted us to perform a detailed reconstruction of its epidemiological history. To this purpose, the Belgian AIDS Reference Laboratories collected HIV-1 pol sequences from all sub-subtype F1-infected patients for whom genotypic drug resistance testing was requested as part of routine clinical follow-up. This data was complemented with HIV-1 pol sequences from countries with a high burden of F1 infections or a potential role in the global origin of sub-subtype F1. The molecular epidemiology of the Belgian subtype F1 epidemic was investigated using Bayesian phylogenetic inference and transmission dynamics were characterized based on birth-death models. F1 sequences were retained from 297 patients diagnosed and linked to care in Belgium between 1988 and 2015. Phylogenetic inference indicated that among the 297 Belgian F1 sequences, 191 belonged to a monophyletic group that mainly contained sequences from people likely infected in Belgium (OR 26.67, 95% CI 9.59–74.15), diagnosed in Flanders (OR 7.28, 95% CI 4.23–12.53), diagnosed at a recent stage of infection (OR 7.19, 95% CI 2.88-17.95) or declared to be MSM (OR 34.8, 95% CI 16.0–75.6). Together with a Spanish clade, this Belgian clade was embedded in the genetic diversity of Brazilian subtype F1 strains and most probably emerged after one or only a few migration events from Brazil to the European continent before 2002. The origin of the Belgian outbreak was dated back to 2002 (95% higher posterior density 2000–2004) and birth-death models suggested that its extensive growth had been controlled (Re < 1) by 2012, coinciding with a time period where delay in antiretroviral treatment initiation substantially declined. In conclusion, phylogenetic reconstruction of the Belgian HIV-1 sub-subtype F1 epidemic illustrates the introduction and substantial dissemination of viral strains in a geographically restricted risk group that was most likely controlled by effective treatment as prevention.
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Affiliation(s)
- Lore Vinken
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Katrien Fransen
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ivailo Alexiev
- National Reference Confirmatory Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Claudia Balotta
- Infectious Diseases and Immunopathology Section, 'L. Sacco' Department of Biomedical and Clinical Sciences, 'L. Sacco' Hospital, University of Milan, Milan, Italy
| | - Laurent Debaisieux
- AIDS Reference Laboratory, CUB-Hopital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Sergio García Ribas
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Perpétua Gomes
- Serviço de Patologia Clínica, Laboratorio de Biologia Molecular, LMCBM, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | | | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jean Ruelle
- Unit of Medical Microbiology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Murat Sayan
- PCR Unit, Clinical Laboratory, Kocaeli University, İzmit, Turkey.,Research Center of Experimental Health Sciences, Near East University, Nicosia, Cyprus
| | - Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases 'Matei Bals', Bucharest, Romania
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Martine Peeters
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ellen Vancutsem
- AIDS Reference Laboratory, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Anne-Mieke Vandamme
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Unidade de Microbiologia, Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sigi Van den Wijngaert
- AIDS Reference Laboratory, Department of Microbiology, Saint-Pierre University Hospital, Brussels, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
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Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities. INFECTION GENETICS AND EVOLUTION 2018. [PMID: 29522828 DOI: 10.1016/j.meegid.2018.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To improve insight in the drivers of local HIV-1 transmission in Belgium, phylogenetic, demographic, epidemiological and laboratory data from patients newly diagnosed between 2013 and 2015 were combined and analyzed. Characteristics of clustered patients, paired patients and patients on isolated branches in the phylogenetic tree were compared. The results revealed an overall high level of clustering despite the short time frame of sampling, with 47.6% of all patients having at least one close genetic counterpart and 36.6% belonging to a cluster of 3 or more individuals. Compared to patients on isolated branches, patients in clusters more frequently reported being infected in Belgium (95.1% vs. 47.6%; p < 0.001), were more frequently men having sex with men (MSM) (77.9% vs. 42.8%; p < 0.001), of Belgian origin (68.2% vs. 32.9%; p < 0.001), male gender (92.6% vs. 65.8%; p < 0.001), infected with subtype B or F (87.8% vs. 43.4%; p < 0.001) and diagnosed early after infection (55.4% vs. 29.0%; p < 0.001). Strikingly, Sub-Saharan Africans (SSA), overall representing 27.1% of the population were significantly less frequently found in clusters than on individual branches (6.0% vs. 41.8%; p < 0.001). Of the SSA that participated in clustered transmission, 66.7% were MSM and this contrasts sharply with the overall 12.0% of SSA reporting MSM. Transmission clusters with SSA were more frequently non-B clusters than transmission clusters without SSA (44.4% versus 18.2%). MSM-driven clusters with patients of mixed origin may account, at least in part, for the increasing spread of non-B subtypes to the native MSM population, a cross-over that has been particularly successful for subtype F and CRF02_AG. The main conclusions from this study are that clustered transmission in Belgium remains almost exclusively MSM-driven with very limited contribution of SSA. There were no indications for local ongoing clustered transmission of HIV-1 among SSA.
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Beloukas A, Psarris A, Giannelou P, Kostaki E, Hatzakis A, Paraskevis D. Molecular epidemiology of HIV-1 infection in Europe: An overview. INFECTION GENETICS AND EVOLUTION 2016; 46:180-189. [PMID: 27321440 DOI: 10.1016/j.meegid.2016.06.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) is characterised by vast genetic diversity. Globally circulating HIV-1 viruses are classified into distinct phylogenetic strains (subtypes, sub-subtypes) and several recombinant forms. Here we describe the characteristics and evolution of European HIV-1 epidemic over time through a review of published literature and updated queries of existing HIV-1 sequence databases. HIV-1 in Western and Central Europe was introduced in the early-1980s in the form of subtype B, which is still the predominant clade. However, in Eastern Europe (Former Soviet Union (FSU) countries and Russia) the predominant strain, introduced into Ukraine in the mid-1990s, is subtype A (AFSU) with transmission mostly occurring in People Who Inject Drugs (PWID). In recent years, the epidemic is evolving towards a complex tapestry with an increase in the prevalence of non-B subtypes and recombinants in Western and Central Europe. Non-B epidemics are mainly associated with immigrants, heterosexuals and females but more recently, non-B clades have also spread amongst groups where non-B strains were previously absent - non-immigrant European populations and amongst men having sex with men (MSM). In some countries, non-B clades have spread amongst the native population, for example subtype G in Portugal and subtype A in Greece, Albania and Cyprus. Romania provides a unique case where sub-subtype F1 has predominated throughout the epidemic. In contrast, HIV-1 epidemic in FSU countries remains more homogeneous with AFSU clade predominating in all countries. The differences between the evolution of the Western epidemic and the Eastern epidemic may be attributable to differences in transmission risk behaviours, lifestyle and the patterns of human mobility. The study of HIV-1 epidemic diversity provides a useful tool by which we can understand the history of the pandemic in addition to allowing us to monitor the spread and growth of the epidemic over time.
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Affiliation(s)
- Apostolos Beloukas
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alexandros Psarris
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Polina Giannelou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- 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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Chalmet K, Staelens D, Blot S, Dinakis S, Pelgrom J, Plum J, Vogelaers D, Vandekerckhove L, Verhofstede C. Epidemiological study of phylogenetic transmission clusters in a local HIV-1 epidemic reveals distinct differences between subtype B and non-B infections. BMC Infect Dis 2010; 10:262. [PMID: 20822507 PMCID: PMC2940905 DOI: 10.1186/1471-2334-10-262] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 09/07/2010] [Indexed: 11/20/2022] Open
Abstract
Background The number of HIV-1 infected individuals in the Western world continues to rise. More in-depth understanding of regional HIV-1 epidemics is necessary for the optimal design and adequate use of future prevention strategies. The use of a combination of phylogenetic analysis of HIV sequences, with data on patients' demographics, infection route, clinical information and laboratory results, will allow a better characterization of individuals responsible for local transmission. Methods Baseline HIV-1 pol sequences, obtained through routine drug-resistance testing, from 506 patients, newly diagnosed between 2001 and 2009, were used to construct phylogenetic trees and identify transmission-clusters. Patients' demographics, laboratory and clinical data, were retrieved anonymously. Statistical analysis was performed to identify subtype-specific and transmission-cluster-specific characteristics. Results Multivariate analysis showed significant differences between the 59.7% of individuals with subtype B infection and the 40.3% non-B infected individuals, with regard to route of transmission, origin, infection with Chlamydia (p = 0.01) and infection with Hepatitis C virus (p = 0.017). More and larger transmission-clusters were identified among the subtype B infections (p < 0.001). Overall, in multivariate analysis, clustering was significantly associated with Caucasian origin, infection through homosexual contact and younger age (all p < 0.001). Bivariate analysis additionally showed a correlation between clustering and syphilis (p < 0.001), higher CD4 counts (p = 0.002), Chlamydia infection (p = 0.013) and primary HIV (p = 0.017). Conclusions Combination of phylogenetics with demographic information, laboratory and clinical data, revealed that HIV-1 subtype B infected Caucasian men-who-have-sex-with-men with high prevalence of sexually transmitted diseases, account for the majority of local HIV-transmissions. This finding elucidates observed epidemiological trends through molecular analysis, and justifies sustained focus in prevention on this high risk group.
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Giuliani M, Montieri S, Palamara G, Latini A, Alteri C, Perno C, Santoro M, Rezza G, Ciccozzi M. Non-B HIV type 1 subtypes among men who have sex with men in Rome, Italy. AIDS Res Hum Retroviruses 2009; 25:157-64. [PMID: 19108689 DOI: 10.1089/aid.2008.0175] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
An increase in the circulation of HIV-1 non-B subtypes has been observed in recent years in Western European countries. Due to the lack of data on the circulation of HIV-1 non-B subtypes among European HIV-1-infected men who have sex with men (MSM), a biomolecular study was conducted in Rome, Italy. HIV-1 partial pol gene sequences from 111 MSM individuals (76 drug naive and 35 drug experienced) were collected during the years 2004-2006. All these sequences were analyzed using the REGA HIV-1 Subtyping Tool, and aligned using CLUSTAL X followed by manual editing using the Bioedit software. A BLAST search for non-B subtype sequences was also performed. Twenty-six (23.4%) MSM were not Italians. Eight individuals (7.2%) were diagnosed as HIV infected before 1991, 20 (18.0%) between 1991 and 1999, and 83 (74.8%) from 2000 to 2006. Fifteen (15/111, 13.5%) individuals were infected with the non-B subtype. The percentage of infection with HIV-1 non-B subtypes was 8.2% (7/85) among Italian MSM and 30.8% (8/26) among the non-Italians (OR = 4.95 95% IC: 1.40-17.87). Individuals infected with the non-B subtype were significantly younger than those infected with the HIV-1 B subtype (28 years vs. 34 years, p = 0.003). The CRFs were more prevalent (8.1%) than pure subtypes (5.4%), which were distributed as follows: subtype C (2.6%), subtype A1 (1.7%), and subtype F1 (0.9%). Major mutations conferring resistance to antiretroviral drugs (ARV) were not found among HIV-1 non-B subtype drug-naive patients but were found in two ARV-experienced individuals. The data show that viral diversity is likely increasing in a population group that had been previously characterized by the circulation of HIV-1 subtype B.
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Affiliation(s)
- M. Giuliani
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - S. Montieri
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
| | - G. Palamara
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - A. Latini
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - C. Alteri
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - C.F. Perno
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - M.M. Santoro
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - G. Rezza
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
| | - M. Ciccozzi
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
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Buonaguro L, Petrizzo A, Tagliamonte M, Vitone F, Re MC, Pilotti E, Casoli C, Sbreglia C, Perrella O, Tornesello ML, Buonaguro FM. Molecular and phylogenetic analysis of HIV-1 variants circulating in Italy. Infect Agent Cancer 2008; 3:13. [PMID: 18847472 PMCID: PMC2586622 DOI: 10.1186/1750-9378-3-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 10/10/2008] [Indexed: 01/09/2023] Open
Abstract
Objective The continuous identification of HIV-1 non-B subtypes and recombinant forms in Italy indicates the need of constant molecular epidemiology survey of genetic forms circulating and transmitted in the resident population. Methods The distribution of HIV-1 subtypes has been evaluated in 25 seropositive individuals residing in Italy, most of whom were infected through a sexual route during the 1995–2005 period. Each sample has been characterized by detailed molecular and phylogenetic analyses. Results 18 of the 25 samples were positive at HIV-1 PCR amplification. Three samples showed a nucleotide divergence compatible with a non-B subtype classification. The phylogenetic analysis, performed on both HIV-1 env and gag regions, confirms the molecular sub-typing prediction, given that 1 sample falls into the C subtype and 2 into the G subtype. The B subtype isolates show high levels of intra-subtype nucleotide divergence, compatible with a long-lasting epidemic and a progressive HIV-1 molecular diversification. Conclusion The Italian HIV-1 epidemic is still mostly attributable to the B subtype, regardless the transmission route, which shows an increasing nucleotide heterogeneity. Heterosexual transmission and the interracial blending, however, are slowly introducing novel HIV-1 subtypes. Therefore, a molecular monitoring is needed to follow the constant evolution of the HIV-1 epidemic.
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Affiliation(s)
- Luigi Buonaguro
- Laboratory of Molecular Biology and Viral Oncogenesis & AIDS Reference Center, Istituto Nazionale Tumori Fondazione Giovanni Pascale, Naples, Italy.
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9
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Buonaguro L, Tagliamonte M, Tornesello ML, Buonaguro FM. Genetic and phylogenetic evolution of HIV-1 in a low subtype heterogeneity epidemic: the Italian example. Retrovirology 2007; 4:34. [PMID: 17517125 PMCID: PMC1892567 DOI: 10.1186/1742-4690-4-34] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 05/21/2007] [Indexed: 11/10/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) is classified into genetic groups, subtypes and sub-subtypes which show a specific geographic distribution pattern. The HIV-1 epidemic in Italy, as in most of the Western Countries, has traditionally affected the Intra-venous drug user (IDU) and Homosexual (Homo) risk groups and has been sustained by the genetic B subtype. In the last years, however, the HIV-1 transmission rate among heterosexuals has dramatically increased, becoming the prevalent transmission route. In fact, while the traditional risk groups have high levels of knowledge and avoid high-risk practices, the heterosexuals do not sufficiently perceive the risk of HIV-1 infection. This misperception, linked to the growing number of immigrants from non-Western Countries, where non-B clades and circulating recombinant forms (CRFs) are prevalent, is progressively introducing HIV-1 variants of non-B subtype in the Italian epidemic. This is in agreement with reports from other Western European Countries. In this context, the Italian HIV-1 epidemic is still characterized by low subtype heterogeneity and represents a paradigmatic example of the European situation. The continuous molecular evolution of the B subtype HIV-1 isolates, characteristic of a long-lasting epidemic, together with the introduction of new subtypes as well as recombinant forms may have significant implications for diagnostic, treatment, and vaccine development. The study and monitoring of the genetic evolution of the HIV-1 represent, therefore, an essential strategy for controlling the local as well as global HIV-1 epidemic and for developing efficient preventive and therapeutic strategies.
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Affiliation(s)
- Luigi Buonaguro
- Lab of Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples, Italy
| | - Maria Tagliamonte
- Lab of Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples, Italy
| | - Maria Lina Tornesello
- Lab of Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples, Italy
| | - Franco M Buonaguro
- Lab of Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples, Italy
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10
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Lin HH, Gaschen BK, Collie M, El-Fishaway M, Chen Z, Korber BT, Beatrice ST, Zhang L. Genetic characterization of diverse HIV-1 strains in an immigrant population living in New York City. J Acquir Immune Defic Syndr 2006; 41:399-404. [PMID: 16652046 DOI: 10.1097/01.qai.0000200663.47838.f1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
New York City (NYC) is one of the original foci of the HIV-1 epidemic and has a greater number of AIDS cases than any other city in the United States. NYC also hosts the highest number of immigrants among the nation's cities: more than 2 million among a total population of 8 million. Such a high rate of immigration could act as a potential source for introducing and disseminating novel HIV-1 strains into the United States. Our current study focuses on the genetic characterization of HIV-1 strains circulating in an immigrant population in NYC. Of the 505 HIV-1-positive specimens obtained, 196 were available for viral sequencing from the C2 to V3 region of env. Phylogenetic analysis using maximum-likelihood and neighbor-joining methods demonstrated that non-B subtypes and circulating recombinant forms (CRFs) accounted for 43.4% (85 of 196 cases), whereas the remaining 56.6% (111 of 196) cases had viral variants similar to the typical North American subtype B virus. Of those non-B subtypes and CRFs, subtype A and CRF02 dominated (63.5% combined); other subtypes, including C, D, F1, G, CRF01_AE, and CRF06_cpx, were also detected. Two HIV-1 sequences do not cluster with any known subtypes or CRFs. Furthermore, the distribution of non-B subtypes and CRFs was consistent with the countries of origin, suggesting that many of the study subjects were likely infected in their home country before they entered the United States. Subtype B viruses identified in the immigrant population showed no significant differences from the typical North American B subtype, however, indicating that a significant proportion of the immigrants must have been infected after they came to the United States. Public health officials and physicians should be aware of the growing genetic diversity of HIV-1 in this country, particularly in areas with sizable immigrant populations.
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Affiliation(s)
- Hsi-Hsun Lin
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY 10016, USA
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11
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Aggarwal I, Smith M, Tatt ID, Murad S, Osner N, Geretti AM, Easterbrook PJ. Evidence for onward transmission of HIV-1 non-B subtype strains in the United Kingdom. J Acquir Immune Defic Syndr 2006; 41:201-9. [PMID: 16394853 DOI: 10.1097/01.qai.0000179430.34660.11] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An increasing proportion of new HIV diagnoses in the United Kingdom and other European countries are attributable to non-B subtype infections, mainly among black Africans with infections heterosexually acquired in sub-Saharan Africa. We examined whether there was evidence for onward transmission of non-B subtypes within an ethnically diverse HIV-1-infected cohort in South London. Three hundred eighty-four HIV-1-infected patients attending Kings College Hospital were subtyped using an in-house enzyme-linked immunoassay and env sequencing. Epidemiologic data were obtained from medical chart review and the patients' physician and were used to establish the most likely source and country of infection. Overall, 344 patients (154 black African, 148 white UK-born, and 42 black Caribbean) had an identifiable subtype. The prevalence of non-B subtypes among the black African, white, and black Caribbean patients was 96.8%, 14.2%, and 31%, respectively. Most non-B subtype infections were identified in black Africans (149 of 183 cases) and were mainly acquired in sub-Saharan Africa, but 22.9% (42 of 183 cases) of all non-B infections were probably acquired in the United Kingdom. Among the 21 white UK-born patients infected with a non-B subtype, 15 probably acquired the infection in the United Kingdom and only 6 of these patients reported a source sexual partner from an HIV endemic area. All 13 black Caribbean patients with a non-B infection most likely acquired their infection in the United Kingdom, most of whom (8 of 13 patients) were probably infected by a partner from an HIV endemic area. Potential acquisition of HIV infection in the United Kingdom was lowest among black African patients with a non-B infection, and most of these infections were probably acquired from a partner originating from an HIV endemic area. This study provides the first evidence for onward transmission of non-B subtypes in the United Kingdom, particularly among the black Caribbean population.
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Affiliation(s)
- Ila Aggarwal
- Department of HIV/GU Medicine, Kings College London School of Medicine at Guy's, Kings College and St. Thomas' Hospitals, West Education Centre, London, UK
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12
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Abstract
PURPOSE OF REVIEW Recent progress in the identification of leukemia antigens has stimulated the development of vaccines to treat hematological malignancies. Here we review the identification and characterization of the myeloid leukemia-specific antigens proteinase 3 and neutrophil elastase found in the primary (azurophil) granule proteins of granulocytes and their precursors. A peptide 'PR1' derived from these proteins induces powerful HLA-A0201-restricted CD8 T-cell proliferation. PR1-specific T cells are cytotoxic to leukemia and myelodysplastic syndrome progenitors, and occur at low frequencies in normal individuals. Frequencies are higher in patients with myeloid leukemias, and highest in patients with chronic myeloid leukemia entering molecular remission after allogeneic stem cell transplantation. RECENT FINDINGS These observations, together with the known association of autoimmunity to proteinase 3 and neutrophil elastase in Wegener's granulomatosis, support the concept that there is a natural immunity to primary granule proteins which can be boosted to enhance immunity to leukemia. Preliminary reports indicate that PR1 peptide vaccination induces significant increases in PR1-specific cytotoxic T cells with rapid and durable remissions in some patients with advanced myeloid leukemias. SUMMARY These promising developments in antileukemia vaccines have stimulated research to optimize vaccine delivery and modify regulation of natural T-cell immunity to primary granule proteins to improve treatment of otherwise refractory myeloid leukemias and myelodysplastic syndrome.
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Affiliation(s)
- John Barrett
- Hematology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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Akouamba BS, Viel J, Charest H, Merindol N, Samson J, Lapointe N, Brenner BG, Lalonde R, Harrigan PR, Boucher M, Soudeyns H. HIV-1 genetic diversity in antenatal cohort, Canada. Emerg Infect Dis 2005; 11:1230-4. [PMID: 16102312 PMCID: PMC3320510 DOI: 10.3201/eid1108.040877] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003. Clade assignments were derived by phylogenetic analysis of amplified pol sequences. Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%) with nonclade B viruses, including subtypes A, C, D, F, G, and H. Four sequences remained unassigned. Forty-three of 44 women infected with non-clade B viruses were newcomers from sub-Saharan Africa, and subtype identity was consistent with those circulating in their countries of origin. These results highlight the epidemiologic importance of non-B HIV-1 in antenatal populations in a large North American urban center, underscore the influence of population movements on clade intermixing, and identify a group of patients who could be targeted for surveillance and drug therapy followup.
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Affiliation(s)
- Bertine S. Akouamba
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Janique Viel
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
| | - Hugues Charest
- Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Natacha Merindol
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | | | - Normand Lapointe
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Bluma G. Brenner
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| | | | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marc Boucher
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Hugo Soudeyns
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
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14
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Best SJ, Dax EM. Assays for HIV with improved sensitivity and specificity. Expert Opin Investig Drugs 2005; 6:965-83. [PMID: 15989656 DOI: 10.1517/13543784.6.8.965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Increased knowledge of the human immunodeficiency virus (HIV) and the infection it causes in humans has resulted in an enormous expansion in the understanding of viral parameters and host changes. HIV is a virus which mutates readily and rapidly, presenting many challenges to assay developers, and monitors of therapy and drug-resistance. Prolific viral replication at all the stages of the disease means that an accurate assessment of viral burden, viral load and changes to immune system markers is essential for effective clinical management and treatment. In the present review we have summarised current opinion on the kinetics of HIV infection and the pathogenesis of the disease it causes, and have provided a background to the evolution of HIV assays. Sensitivities and specificities of assays used for anti-HIV and HIV detection have improved, and new assays have been developed employing novel molecular techniques, which are being applied to meet continually evolving demands for more sensitive measurement of an increasing number of parameters. The future of HIV testing is also considered in the light of new knowledge concerning virus dynamics in vivo, the likelihood of the emergence of new subtypes and the changing approach to therapy. Assays will be, on the whole, used to quantify virus and to measure the host reactions to infection, often in the presence of antivirals. Thus, extreme sensitivity and specificity will be required.
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Affiliation(s)
- S J Best
- National Serology Reference Laboratory at Fairfield Hospital, Yarra Bend Road, Fairfield 3078, Australia.
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15
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Buonaguro L, Tagliamonte M, Tornesello ML, Buonaguro FM. Evaluation of a modified version of Heteroduplex Mobility Assay for rapid screening of HIV-1 isolates in epidemics characterized by mono/dual clade predominance. J Virol Methods 2005; 124:123-34. [PMID: 15664060 DOI: 10.1016/j.jviromet.2004.11.014] [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: 08/09/2004] [Revised: 11/11/2004] [Accepted: 11/15/2004] [Indexed: 11/24/2022]
Abstract
The geographical distribution of human immunodeficiency virus type 1 (HIV-1) subtypes show, with the exception of some African Countries, a specific pattern. However, the significant phenomenon of migration to Western Countries, coupled to inter-ethnic blending, may result in a constant introduction and spread of novel subtypes and/or recombinant forms in previously homogeneous HIV-1 epidemics. The need to identify and trace these events prompted the development of a rapid and specific bio-molecular tool for the HIV-1 screening, based on the well-established Heteroduplex Mobility Assay (HMA). This modified version of HMA (rHMA) has been designed to detect, by a short electrophoretic analysis, HIV-1 isolates remarkably divergent form the local predominant clade, for subsequent more accurate genetic and phylogenetic analyses. The method has been validated for both C2-V5 region of env gene and the p24-p7 region of the gag gene, by proof-of-concept experiments performed on a panel of reference standards representing the globally most prevalent HIV-1 subtypes, and applied to screen Italian and Ugandan field isolates. The rHMA experimental conditions identified in this study have been shown to be specific and reliable for both sub-genomic regions of each subtype used. In the context of nationwide monitoring programs, the rHMA may represent a powerful tool for the HIV-1 molecular surveillance in both developed and developing countries, particularly those characterized by mono/dual-clade HIV-1 epidemic, which is relevant for epidemiological studies and for the development of preventive and therapeutic strategies.
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Affiliation(s)
- Luigi Buonaguro
- Lab. Viral Oncology, AIDS Refer. Center, Ist. Naz. Tumori Fond. G. Pascale, Cappella dei Cangiani, 80131 Naples, Italy.
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16
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Buonaguro L, Tagliamonte M, Tornesello ML, Pilotti E, Casoli C, Lazzarin A, Tambussi G, Ciccozzi M, Rezza G, Buonaguro FM. Screening of HIV-1 Isolates by Reverse Heteroduplex Mobility Assay and Identification of Non-B Subtypes in Italy. J Acquir Immune Defic Syndr 2004; 37:1295-306. [PMID: 15385738 DOI: 10.1097/01.qai.0000123273.76723.04] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The increasing prevalence of HIV-1 transmission through heterosexual contacts and the growing number of immigrants from non-Western countries, where non-B subtypes and recombinant forms are prevalent, suggest the possible emergence in Italy of a new epidemic wave of HIV-1 non-B subtypes as well as recombinant forms. METHODS The distribution of HIV-1 subtypes has been evaluated in 63 seropositive individuals residing in Italy, most of whom were infected through a sexual route during the last 5 years. A modified heteroduplex mobility assay (HMA) strategy, reverse HMA (rHMA), has been developed in our laboratory, allowing rapid identification of divergent-from-B-subtype isolates, which have been subsequently characterized by detailed molecular and phylogenetic analyses. RESULTS Five samples show, on rHMA, an electrophoretic pattern compatible with a non-B subtype classification. Their phylogenetic analysis, performed on both env and gag regions, confirms the rHMA subtyping prediction, given that 3 samples fall into the "A-family" subtype and 2 into the G subtype. The 5 non-B-subtype HIV-1 isolates have been identified among 23 variants (prevalence, 21.74%) isolated during the 2000 to 2001 period in heterosexuals. In parallel, B-subtype isolates show high levels of intrasubtype nucleotide divergence, compatible with a constant HIV-1 molecular diversification. CONCLUSION The Italian HIV-1 epidemic is still mostly attributable to the B subtype, which shows an increasing nucleotide heterogeneity. Heterosexual transmission and the interracial blending, however, are slowly introducing novel HIV-1 subtypes, and the data indicate that rHMA represents a powerful tool for HIV-1 biomolecular screening in epidemics characterized by a mono-/dual-subtype predominance.
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Affiliation(s)
- Luigi Buonaguro
- Viral Oncology and AIDS Refer. Center, Ist. Naz. Tumori Fond. G. Pascale, Naples, Italy
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17
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Vandamme AM, Sönnerborg A, Ait-Khaled M, Albert J, Asjo B, Bacheler L, Banhegyi D, Boucher C, Brun-Vézinet F, Camacho R, Clevenbergh P, Clumeck N, Dedes N, Luca AD, Doerr HW, Faudon JL, Gatti G, Gerstoft J, Hall WW, Hatzakis A, Hellmann N, Horban A, Lundgren JD, Kempf D, Miller M, Miller V, Myers TW, Nielsen C, Opravil M, Palmisano L, Perno CF, Phillips A, Pillay D, Pumarola T, Ruiz L, Salminen M, Schapiro J, Schmidt B, Schmit JC, Schuurman R, Shulse E, Soriano V, Staszewski S, Vella S, Youle M, Ziermann R, Perrin L. Updated European Recommendations for the Clinical Use of HIV Drug Resistance Testing. Antivir Ther 2004. [DOI: 10.1177/135965350400900619] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In most European countries, HIV drug resistance testing has become a routine clinical tool. However, its practical implementation in a clinical context is demanding. The European HIV Drug Resistance Panel was established to make recommendations to clinicians and virologists on this topic and to propose quality control measures. The panel recommends resistance testing for the following indications: i) drug-naive patients with acute or recent infection; ii) therapy failure, including suboptimal treatment response, when treatment change is considered; iii) pregnant HIV-1-infected women and paediatric patients with detectable viral load when treatment initiation or change is considered; and iv) genotype source patient when post-exposure prophylaxis is considered. In addition, for drug-naive patients with chronic infection in whom treatment is to be started, the panel suggests that resistance testing should be strongly considered and recommends testing the earliest sample for drug resistance if suspicion of resistance is high or prevalence of resistance in this population exceeds 10%. The panel does not favour genotyping over phenotype, however it is anticipated that genotyping will be used more often because of its greater accessibility, lower cost and faster turnaround time. For the interpretation of resistance data, clinically validated systems should be used to the greatest extent possible. It is mandatory that laboratories performing HIV resistance tests take regular part in quality assurance programs. Similarly, it is necessary that HIV clinicians and virologists take part in continuous education and meet regularly to discuss problematic clinical cases. Indeed, resistance test results should be used in the context of all other clinically relevant information for predicting therapy response. The panel also encourages the timely collection of epidemiological information to estimate the impact of transmission of resistant HIV and the prevalence of HIV-1 non-B subtypes in the different European countries.
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Affiliation(s)
- A-M Vandamme
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - A Sönnerborg
- Divisions of Infectious Diseases and Clinical Virology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - M Ait-Khaled
- GlaxoSmithKline, HIV Medicines Development Centre Europe, Greenford, UK
| | - J Albert
- Dept of Virology, Swedish Institute for Infectious Diease Control and Microbiology and Tumourbiology Center, Karolinska Institutet, Solna, Sweden
| | - B Asjo
- Centre for Research in Virology, Gade Institute, University of Bergen, Bergen, Norway
| | | | - D Banhegyi
- 5th Department of Medicine, Saint Laszlo Hospital, Budapest, Hungary
| | - C Boucher
- University Medical Centre Utrecht, Utrecht, The Netherlands
| | - F Brun-Vézinet
- Department of Virology, Hôpital Bichat Claude Bernard, Paris, France
| | - R Camacho
- Hospital Egas Moniz, Serviço de Imuno-Hemoterapia, Lisboa, Portugal
| | - P Clevenbergh
- Service de Médecine Interne A, Hôpital Lariboisiere, Paris, France
| | - N Clumeck
- Department of Infectious Diseases, CHU Saint-Pierre, Brussels, Belgium
| | | | - A De Luca
- Istituto di Clinica delle Malattie Infettive, Università Cattolica del Sacro Cuore, Rome, Italy
| | - HW Doerr
- Institute for Medical Virology, University Clinic Frankfurt, Frankfurt, Germany
| | | | - G Gatti
- Vertex Pharmaceuticals, Genova, Italy
| | - J Gerstoft
- Rigshospitalet Department of Infectious Diseases, University of Copenhagen, Copenhagen, Denmark
| | - WW Hall
- University College Dublin, Department Medical Microbiology, Dublin, Ireland
| | - A Hatzakis
- National Retrovirus Reference Centre, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
| | - N Hellmann
- ViroLogic, Inc., South San Francisco, Calif., USA
| | - A Horban
- Hospital of Infectious Diseases, AIDS Diagnosis and Therapy Centre, Warsaw, Poland
| | - JD Lundgren
- Copenhagen HIV Programme (CHIP) - Section 044, Hvidovre University Hospital, Hvidovre, Denmark
| | - D Kempf
- Abbott Laboratories, Abbott Park, Ill., USA
| | - M Miller
- Gilead Sciences, Foster City, Calif., USA
| | - V Miller
- Forum for Collaborative HIV Research, George Washington University, Washington DC, USA
| | - TW Myers
- Roche Molecular Systems, Alameda, Calif., USA
| | - C Nielsen
- Department of Virology, Statens Serum Institut, Copenhagen S, Denmark
| | - M Opravil
- Department of Medicine, University Hospital Zurich, Zurich, Switzerland
| | | | - CF Perno
- University of Rome Tor Vergata and INMI L. Spallanzani, Rome, Italy
| | - A Phillips
- Royal Free Centre for HIV Medicine and Department of Primary Care & Population Sciences, Royal Free and University College Medical School, London, UK
| | - D Pillay
- Royal Free and University College Medical School, University College London, London, UK
| | - T Pumarola
- Servicio de Microbiología, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - L Ruiz
- Retrovirology Lab, IRSICAIXA Foundation, Barcelona, Spain
| | - M Salminen
- Department of Infectious Disease Epidemiology, National Public Health Institute, Helsinki, Finland
| | | | - B Schmidt
- Institute of Clinical and Molecular Virology, German National Reference Centre for Retroviruses, Erlangen, Germany
| | - J-C Schmit
- National Service of Infectious Diseases, Retrovirology Laboratory Luxembourg, Centre Hospitalier de Luxembourg, Luxembourg
| | - R Schuurman
- University Medical Centre Utrecht, Department of Virology, Utrecht, The Netherlands
| | - E Shulse
- Celera Diagnostics, Alameda, Calif., USA
| | - V Soriano
- Department of Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | | | - S Vella
- Istituto Superiore di Sanità, Rome, Italy
| | - M Youle
- Royal Free and University College Medical School, London, UK
| | - R Ziermann
- Bayer HealthCare – Diagnostics, Medical and Scientific Affairs, Berkeley, Calif., USA
| | - L Perrin
- Laboratoire de Virologie, Geneva University Hospital, Geneva, Switzerland
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Vachot L, Ataman-Onal Y, Terrat C, Durand PY, Ponceau B, Biron F, Verrier B. Short communication: retrospective study to time the introduction of HIV type 1 non-B subtypes in Lyon, France, using env genes obtained from primary infection samples. AIDS Res Hum Retroviruses 2004; 20:687-91. [PMID: 15307910 DOI: 10.1089/0889222041524607] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using blood samples from primary HIV-1 infection (PHI) patients obtained in Lyon, France, we characterized the newly transmitted HIV-1 variants in this area during the 1992-1996 period. As PHI samples allowed the precise timing of the transmission event, we were able to date the introduction of non-B subtypes or recombinant forms of the virus in Lyon. Genomic DNA from 18 HIV-1-positive patients at primary infection was used to amplify the full-length env gene by nested PCR; after cloning, the gene was sequenced for subsequent phylogenetic analysis. Several non-B subtypes and recombinant forms of HIV-1 were identified among the 18 patients studied (1 subtype F1, 1 CRF01-AE, 2 subtype G and 2 CRF02-AG). We also found a new J/K recombinant form transmitted in 1995 and never described until now. The introduction of CRF02-AG in Lyon, France, occurred prior to 1992 and six transmission events including non-B subtypes were documented in the following 4 years. Heterosexual contacts appeared as the main introduction pathway for non-B subtypes or recombinant forms. Nevertheless, as transmission of these viruses occurred not only during travel to endemic regions, but also in France or Germany, we conclude that non-B strains entered Europe before the studied period. This retrospective study showed that even if subtype B remained prevalent in the spreading HIV-1 infection in Lyon between 1992 and 1996, non-B subtypes and circulating recombinant forms represented a significantly growing part.
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Snoeck J, Van Laethem K, Hermans P, Van Wijngaerden E, Derdelinckx I, Schrooten Y, van de Vijver DAMC, De Wit S, Clumeck N, Vandamme AM. Rising Prevalence of HIV-1 Non-B Subtypes in Belgium: 1983???2001. J Acquir Immune Defic Syndr 2004; 35:279-85. [PMID: 15076243 DOI: 10.1097/00126334-200403010-00009] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This study documented the HIV-1 subtype distribution in 2 Belgian hospitals and determined predictive demographics for non-B subtypes. Overall, subtype B was the most prevalent subtype in this population, followed by subtypes A and C. Several recombinants were detected, circulating recombinants as well as new ones. We found a rise in non-B subtypes from 0% in 1983 to 57% in 2001. The Cochran-Armitage trend test (P < 0.001) as well as the correlation analysis (R = 0.71, P = 0.0006) was highly significant. Recombinants were also increasing in this patient population from 0% in 1983 to 10% in 2001, with good support from the statistical analyses (trend test P < 0.001; correlation analysis R = 0.67, P = 0.0016). Heterosexual route of infection, black African race, African origin of the virus, and year of diagnosis were predictors for infection with non-B subtypes in multivariate analysis. This analysis indicates that the prevalence of non-B subtypes and recombinants in this patient population is high and increasing. Gathering demographic and sequence information from newly diagnosed patients could be useful to further follow the spread of non-B subtypes in Belgium and Europe, but subtyping based on sequence information still remains the most reliable method.
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Affiliation(s)
- Joke Snoeck
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
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20
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Derdelinckx I, Van Laethem K, Maes B, Schrooten Y, De Schouwer K, De Wit S, Fransen K, García Ribas S, Moutschen M, Vaira D, Zissis G, Van Ranst M, Van Wijngaerden E, Vandamme AM. Performance of the VERSANT HIV-1 resistance assays (LiPA) for detecting drug resistance in therapy-naive patients infected with different HIV-1 subtypes. ACTA ACUST UNITED AC 2004; 39:119-24. [PMID: 14625094 DOI: 10.1016/s0928-8244(03)00240-2] [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: 11/24/2022]
Abstract
In this study we evaluated the performance of the VERSANT HIV-1 Resistance Assays (LiPA) in detecting drug resistance in therapy-naive HIV-infected patients diagnosed in Belgium in 2000. We compared the results with population sequencing and found concordance to be in line with previous studies in treatment-experienced patients (86.87% for reverse transcriptase (RT); 92.77% for protease (PRO)). Discordance was mainly due to indeterminate reactions on LiPA (8.45% for RT; 6.85% for PRO) and minor discordances (4.13% for RT; 0.25% for PRO). Major discordances were rare (0.46% for RT; 0.12% for PRO). Indeterminate reactions were significantly associated with strains belonging to non-B subtypes.
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Affiliation(s)
- Inge Derdelinckx
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
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21
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Machuca A, Hewlett I. [Residual risk of human immunodeficiency virus infection in blood banks. Impact of screening with nucleic acid tests]. Med Clin (Barc) 2004; 121:418-25. [PMID: 14563274 DOI: 10.1016/s0025-7753(03)73974-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In most developed countries of the world, the risk of human immunodeficiency virus (HIV) transmission by transfusion of blood and blood products is extraordinarily small. This level of blood safety has been accomplished by successive refinement in donor screening and testing procedures for the detection and inactivation of different infectious agents in blood and blood products. In USA, the recent introduction of nucleic acid techniques (NAT) in blood banks for the detection of HIV and hepatitis C virus (HCV) has meant a great advance in decreasing the residual risk of HIV/HCV transmission by blood transfusion. In general, after analyzing the first four-years of NATs experience in US blood banks, the introduction of NATs in European blood centers could be considered, since this technique has shown improved output to detect donations from individuals in the very early stages of infection before detectable serologic response has been developed.
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Affiliation(s)
- Ana Machuca
- Laboratorio de Virología Molecular, CBER/FDA, Bethesda, Maryland 20892, USA.
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Perrin L, Kaiser L, Yerly S. Travel and the spread of HIV-1 genetic variants. THE LANCET. INFECTIOUS DISEASES 2003; 3:22-7. [PMID: 12505029 DOI: 10.1016/s1473-3099(03)00484-5] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
HIV-1 comprises three groups, the main (M group), O (outlier) and N (non-M, non-O). The M group, divided into 11 subtypes, is responsible for the global HIV-1 pandemic. Recombination between M subtypes has resulted in the generation of multiple circulating recombinant forms (CRFs) consisting of mosaic lineages. Most subtypes and CRFs are represented in Africa, whereas predominance of one or a few subtypes was reported initially elsewhere. This finding reflects the African origin of the epidemic. In western countries, where the B subtype is predominant, there is a steep increase in non B-subtypes and CRFs, while new recombinants emerge worldwide. Travellers contribute to the spread of HIV-1 genetic diversity worldwide, and in the developing world migration of rural populations and civil war are additional contributing factors. The spreading of HIV-1 variants has implications for diagnostic, treatment, and vaccine development.
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Affiliation(s)
- Luc Perrin
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva, Switzerland.
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Amendola A, Bordi L, Angeletti C, Visco-Comandini U, Abbate I, Cappiello G, Budabbus MA, Eljhawi OA, Mehabresh MI, Girardi E, Antinori A, Ippolito G, Capobianchi MR. Underevaluation of HIV-1 plasma viral load by a commercially available assay in a cluster of patients infected with HIV-1 A/G circulating recombinant form (CRF02). J Acquir Immune Defic Syndr 2002; 31:488-94. [PMID: 12473837 DOI: 10.1097/00126334-200212150-00006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The authors studied the correlation and agreement of commercially available assays in detection and quantification of the HIV-1 intersubtype A/G circulating recombinant form CRF02. The assays under comparison were Bayer Versant HIV-1 RNA, version 3.0; Roche Amplicor HIV-1 Monitor, version 1.5 (standard procedure); and Organon Teknika NucliSens HIV-1 RNA QT. Plasma samples from 114 patients infected with CRF02 were tested by the three assays under standard conditions. Although correlation among the assays was high and statistically significant for subtype B and CRF02, in the latter instance, NucliSens measured average viral load values (3.29 +/- 0.71 log(10) copies/mL) about 4 and >8 times lower than those obtained by Versant (3.90 +/- 0.90 log(10) copies/mL) and Amplicor (4.22 +/- 1.05 log(10) copies/mL), respectively. Furthermore, in a statistically significant percentage of CRF02-harboring samples, NucliSens produced viral load values undetectable or 1 log(10) lower than those obtained in Versant and Amplicor assays. Altogether, these data underline a low performance of NucliSens in detecting and quantifying viremia in plasma samples harboring the CRF02. These results are potentially important as global distribution of new HIV-1 subtypes is expanding, and recombinant strains, particularly CRF02, are emerging and becoming highly prevalent.
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Affiliation(s)
- Alessandra Amendola
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy
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24
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Molldrem JJ, Kant S, Jiang W, Lu S. The basis of T-cell-mediated immunity to chronic myelogenous leukemia. Oncogene 2002; 21:8668-73. [PMID: 12476312 DOI: 10.1038/sj.onc.1206093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Jeffrey J Molldrem
- Transplantation Immunology Section, Department of Blood and Marrow Transplantation, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA.
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25
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Molldrem JJ, Komanduri K, Wieder E. Overexpressed differentiation antigens as targets of graft-versus-leukemia reactions. Curr Opin Hematol 2002; 9:503-8. [PMID: 12394172 DOI: 10.1097/00062752-200211000-00006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The graft-versus-leukemia (GVL) effect associated with allogeneic blood and marrow transplantation has largely been a clinically described phenomenon until recently. We are beginning to understand the cellular and molecular nature of GVL, and in this review the authors highlight the potential for self-antigen-specific T lymphocytes to contribute to GVL. The authors focus on myeloid tissue-restricted proteins as GVL target antigens in CML and AML, and in particular on proteinase 3 and other azurophil granule proteins as targets for both autologous and allogeneic T-cell responses. Finally, the authors discuss myeloid self-antigen-directed alloreactivity in the context of our evolving understanding of the critical molecular determinants of allogeneic T-cell recognition. By altering T-cell receptor affinity, peptide specificity can be maintained and the potency of immunity can be enhanced in the MHC-mismatched setting.
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Affiliation(s)
- Jeffrey J Molldrem
- Transplantation Immunology Section, Department of Blood and Marrow Transplantation, University of Texas M.D. Anderson Cancer Center, Houston, 77030, USA.
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26
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Holguín A, Alvarez A, Soriano V. High prevalence of HIV-1 subtype G and natural polymorphisms at the protease gene among HIV-infected immigrants in Madrid. AIDS 2002; 16:1163-70. [PMID: 12004275 DOI: 10.1097/00002030-200205240-00010] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Genetic characterization of HIV-1 subtypes among immigrants and natives infected overseas. METHODS Phylogenetic analysis of HIV-1 protease sequences obtained from 109 foreigners (mainly Africans) and 32 native individuals infected overseas attending a reference HIV/AIDS centre located in Madrid, Spain. RESULTS The overall rate of infection with HIV-1 non-B subtypes was 50.3% (71/141). Whereas 94.3% (67/71) belonged to immigrants (mostly Africans, 60/67), only 5.6% (4/71) were from native individuals (P < 0.05). The distribution of non-B subtypes was: 49 G, eight C, six A, four D, two F and two H. The high prevalence of subtype G was mainly related to individuals from west-central Africa. Interestingly, substitutions at three or more positions associated with protease inhibitor (PI) resistance were recognized in 52.6% of naive subjects carrying non-B subtypes, but only in 8% of those infected with B viruses (P < 0.05). The genotypes most frequently recognized among non-B and B subtypes occurred, respectively, at positions 36 (100 versus 12%), 20 (77.2 versus 0%), 63 (40.3 versus 64%), 82 (17.5 versus 0%), 10 (14 versus 12%), 77 (3.5 versus 34%), and 71 (0 versus 2%). Accordingly, changes I-36 and I-20 may be considered specific genetic markers for non-B, group M variants and subtype G infections, respectively. CONCLUSION Nearly two-thirds of foreigners with HIV-1 infection in Madrid carry non-B subtypes, subtype G (protease) being the most common among west-central African immigrants. The high rate of natural polymorphisms at the protease gene in non-B viruses may compromise the response to PI. Therefore, HIV subtyping should be considered in treatment guidelines.
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Affiliation(s)
- Africa Holguín
- Service of Infectious Diseases, Hospital Carlos III, Instituto de Salud Carlos III, Madrid, Spain
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27
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Snoeck J, Van Dooren S, Van Laethem K, Derdelinckx I, Van Wijngaerden E, De Clercq E, Vandamme AM. Prevalence and origin of HIV-1 group M subtypes among patients attending a Belgian hospital in 1999. Virus Res 2002; 85:95-107. [PMID: 11955642 DOI: 10.1016/s0168-1702(02)00021-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
HIV-1 group M strains are usually subtyped based on gag and/or env gene sequences. In our lab, part of the pol gene sequence was available in order to determine the genotypic anti-HIV drug resistance profile. To estimate the prevalence of the different HIV-1 subtypes in patients visiting the University Hospitals in Leuven in 1999 and for whom a genotypic drug resistance test was needed, we tried to use the pol sequence for subtyping. Recombination was investigated by similarity plots and bootscanning and subtyping was performed by phylogenetic analysis. The overall region spanning the entire protease and 747 nucleotides of the reverse transcriptase proved very suitable for subtyping, although there was a low phylogenetic signal at the beginning of the reverse transcriptase (nucleotides 0-250), as we demonstrated by likelihood mapping. Of the 41 samples analyzed, 21 belonged to subtype B. Of the other 20 non-B strains, 9 belonged to subtype C, 2 to subtype D and 1 to subtype A, G, H and J, respectively, 3 were CRF_02 (Circulating Recombinant Form), 1 was recombinant with a novel breakpoint and 1 sample was untypable. Although subtype B is still the most prevalent subtype in Belgium, it seems to be responsible for only half of the infections in this study. We could also document that the prevalence of subtype C is high in the Belgian native patients, especially among the heterosexually infected population. This could possibly be an indication for an epidemic spread of HIV-1 subtype C in Belgium, as for one third of these patients, no link to an endemic region could be found. The other non-B subtypes and the recombinants are mainly introduced by immigrants or by Belgian citizens traveling abroad.
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Affiliation(s)
- Joke Snoeck
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000, Belgium
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28
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Caride E, Hertogs K, Larder B, Dehertogh P, Brindeiro R, Machado E, de Sá CA, Eyer-Silva WA, Sion FS, Passioni LF, Menezes JA, Calazans AR, Tanuri A. Genotypic and phenotypic evidence of different drug-resistance mutation patterns between B and non-B subtype isolates of human immunodeficiency virus type 1 found in Brazilian patients failing HAART. Virus Genes 2002; 23:193-202. [PMID: 11724274 DOI: 10.1023/a:1011812810397] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have investigated the phenotypic and genotypic susceptibility of 14 HIV-1 strains isolated from individuals failing HAART therapy to protease inhibitors (PI). Proviral and plasma viral pol gene fragment were amplified, sequenced and subtyped. Nine samples clustered with protease subtype B reference strains and the remaining samples were classified as non-B subtype corresponding to subtype F (n = 4) and subtype A (n = 1). Although all patients were treated with similar P1 drug regimen, the non-B subtype isolates did not present the L90M and 184V mutations and used mainly G48V and V82A/F to achieve drug resistance. A strong cross-resistance phenotype among all four PI was associated with the mutation L90M in the subtype-B isolates, and with G48V and V82A/F in the non-B counterparts. This observation revealed that the non-B viruses tested had specific genotypic characteristics contrasting with the subtype-B isolates.
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Affiliation(s)
- E Caride
- Genetic Department, UFRJ, Rio de Janeiro, Brazil
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29
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Delgado E, Thomson MM, Villahermosa ML, Sierra M, Ocampo A, Miralles C, Rodríguez-Pérez R, Diz-Aren J, Ojea-de Castro R, Losada E, Cuevas MT, Vázquez-de Parga E, Carmona R, Pérez-Alvarez L, Medrano L, Cuevas L, Taboada JA, Nájera R. Identification of a newly characterized HIV-1 BG intersubtype circulating recombinant form in Galicia, Spain, which exhibits a pseudotype-like virion structure. J Acquir Immune Defic Syndr 2002; 29:536-43. [PMID: 11981372 DOI: 10.1097/00126334-200204150-00016] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We recently reported the finding of phylogenetically related HIV-1 BG intersubtype recombinant and G subtype nonrecombinant viruses circulating among injecting drug users in the region of Galicia in northwestern Spain. Here, we report the characterization of near full-length genome sequences of nine of these viruses (seven BG recombinant and two of nonrecombinant G subtype), obtained from epidemiologically unlinked individuals. Bootscan analysis reveals that six recombinant viruses share an identical mosaic structure, with two intersubtype breakpoints delimiting a B subtype segment comprising most of Env gp120 and the external portion of Env gp41, with the remaining portions of the genome being of subtype G, thus mimicking a pseudotype virion structure. The seventh BG recombinant virus exhibits breakpoints in env coincident with the other BG viruses but contains additional B subtype segments in gag and pol. In phylogenetic trees of complete genomes and of the B subtype segment of env, all seven BG viruses group in a monophyletic cluster. G subtype portions of the BG viruses group uniformly with the newly derived nonrecombinant G subtype viruses of Galicia in bootscan analysis, which points to the locally circulating G subtype strain as parental of the recombinants. These results allow us to define a new HIV-1 circulating recombinant form (CRF14_BG), the first reported to originate in Western Europe.
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Affiliation(s)
- Elena Delgado
- Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain
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30
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Elbeik T, Alvord WG, Trichavaroj R, de Souza M, Dewar R, Brown A, Chernoff D, Michael NL, Nassos P, Hadley K, Ng VL. Comparative analysis of HIV-1 viral load assays on subtype quantification: Bayer Versant HIV-1 RNA 3.0 versus Roche Amplicor HIV-1 Monitor version 1.5. J Acquir Immune Defic Syndr 2002; 29:330-9. [PMID: 11917236 DOI: 10.1097/00126334-200204010-00002] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Quantification of HIV-1 subtypes is essential for appropriate clinical management. Whereas viral load assays were initially developed to accurately quantify subtype B, the recent worldwide spread of non-B subtypes and the introduction of treatment programs in regions with non-B subtypes have prompted adaptations of these assays. The Bayer Versant HIV-1 RNA 3.0 Assay (branched DNA [bDNA] 3.0) and the Roche Amplicor HIV-1 Monitor version 1.5 (Amplicor 1.5) assays are reported to quantify all subtypes in group M; however, evaluation of performance characteristics remains limited. In this study, we evaluated the accuracy and reliability of bDNA 3.0 and Amplicor 1.5 on multiple serially diluted viral isolates from HIV-1 group M, subtypes A through F. Testing was conducted on both assay systems in two independent laboratories. Comparative pansubtype quantification from regression analysis showed that quantification by bDNA 3.0 was approximately 0.3 log-fold lower than that by Amplicor 1.5. Comparative pansubtype accuracy analysis showed data points more closely distributed about their respective regression lines and thus showing greater reliability by bDNA 3.0 than by Amplicor 1.5.
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Affiliation(s)
- Tarek Elbeik
- Department of Laboratory Medicine, University of California at San Francisco and Clinical Laboratories at San Francisco General Hospital, San Francisco, California 94110, USA.
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31
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Machuca R, Bøgh M, Salminen M, Gerstoft J, Kvinesdal B, Pedersen C, Obel N, Nielsen H, Nielsen C. HIV-1 subtypes in Denmark. SCANDINAVIAN JOURNAL OF INFECTIOUS DISEASES 2002; 33:697-701. [PMID: 11669229 DOI: 10.1080/00365540110026863] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The objective of this study was to investigate the presence of non-subtype B HIV-1 in Denmark. The C2-V3-C3 region of the env gene from proviral DNA obtained from patients suspected of being infected with non-subtype B virus was PCR-amplified and directly sequenced. The DNA sequences were aligned with full-length HIV-1 reference strains from each subtype and analysed using the phylogenetic package PHYLIP 3.1. The neighbour-joining method was used with 100 bootstraps. Of the 144 patients included in this study C2-V3-C3 sequences were obtained from 129 patients (90%). The phylogenetic analyses showed that virus from 49 patients (38%) was subtype A, 39 (30%) subtype C, 9 (7%) subtype D, 14 (11%) subtype CRF01_AE, 16 (12%) subtype B, 1 (1%) subtype F and 1 (1%) subtype J. This study demonstrates that almost all subtypes can be detected in Denmark; all non-subtype B infections could be traced to countries with a high prevalence of non-subtype B virus.
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Affiliation(s)
- R Machuca
- Department of Virology, Statens Serum Institut, Copenhagen, Denmark
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García-Albert L, Ortiz M, García-Saiz A. HIV type 1 non-B subtype prevalence in Spain, 1997-1998. AIDS Res Hum Retroviruses 2001; 17:1317-20. [PMID: 11602041 DOI: 10.1089/08892220152596560] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have evaluated the prevalence of HIV-1 non-B subtypes in Spain by means of an enzyme immunoassay (EIA) for discrimination between B and non-B subtypes. Samples were obtained from newly diagnosed patients attended at internal medicine outpatient clinics between October 1997 and October 1998. Discrimination between HIV-1 B and non-B subtypes was carried out by means of the EIA, with V3 synthetic peptides specific to the different subtypes. Non-B-serotyped samples were genetically analyzed in the gp41 region from the original sera. During the study period, 909 samples were collected from 21 medical units located in various Spanish geographical regions. Serotyping was possible in 885 cases, of which 791 were assigned as B serotype (89.38%), 70 showed no reactivity to any of the peptides (7.91%), and the remaining samples displayed other reaction patterns (2.72%). Of the 94 non-B-assigned samples, 65 were genetically characterized in the gp41 region of the env gene: 55 were B subtype, 5 were A subtype (4 clustered with CRF02AG reference strains), 3 were C subtype, and 2 were G subtype. The prevalence rate for non-B subtypes in Spain was established at 1.13% (95% CI, 0.59-2.21). Although the B subtype is predominant in the Spanish population, other subtypes have been detected.
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Affiliation(s)
- L García-Albert
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
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33
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Thomson MM, Nájera R. Travel and the introduction of human immunodeficiency virus type 1 non-B subtype genetic forms into Western countries. Clin Infect Dis 2001; 32:1732-7. [PMID: 11360216 DOI: 10.1086/320764] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2000] [Revised: 02/09/2001] [Indexed: 11/03/2022] Open
Abstract
Both high mutation rates and recombination contribute to the genetic diversity of human immunodeficiency virus type 1 (HIV-1). Among viruses of the main group, which are responsible for the HIV-1 pandemic, 21 circulating genetic forms have been reported, 11 of which are recombinant between > or = 2 subtypes. In Western Europe and the Americas, the HIV-1 epidemic is largely dominated by B subtype viruses; however, infections with diverse non-B subtype genetic forms are increasingly being recognized. In Western Europe and North America, most of them have been identified in immigrants or travelers returning from areas with high HIV-1 prevalence, mainly from sub-Saharan Africa and Southeast Asia, where non-B subtype genetic forms predominate, but propagation within other groups has been reported in some Western countries. This may have implications for prophylactic and therapeutic strategies and, by bringing in contact different genetic forms, may favor the generation of novel recombinant viruses. Travelers from different categories--including immigrants, military personnel, seamen, tourists, expatriates, diplomats, and businessmen--may be at risk of transporting HIV non-B subtype genetic forms to Western countries.
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Affiliation(s)
- M M Thomson
- Area de Patogenia Viral, Centro Nacional de Biología Fundamental, Instituto de Salud Carlos III, Madrid, Spain
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Parry JV, Murphy G, Barlow KL, Lewis K, Rogers PA, Belda FJ, Nicoll A, McGarrigle C, Cliffe S, Mortimer PP, Clewley JP. National surveillance of HIV-1 subtypes for England and Wales: design, methods, and initial findings. J Acquir Immune Defic Syndr 2001; 26:381-8. [PMID: 11317083 DOI: 10.1097/00126334-200104010-00017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The HIV-1 infections detected in an ongoing national unlinked anonymous HIV surveillance program were subtyped and analyzed according to demographic and risk characteristics. Of the 893 anti--HIV-1--positive specimens allocated to an exposure group, 70% could be subtyped. Almost 25% of infections subtyped were non-B, mostly subtypes A, C, and D. Non-B infections were rare in homosexual and bisexual men and in drug injectors. Forty percent of infections in heterosexual men attending genitourinary medicine clinics were non-B subtypes; of these, 25% were subtype A infections and 59% were subtype C infections. For female clinic attendees, 61% were non-B subtype infections, of which 48% were subtype A infections and 42% were subtype C infections. Of the clinic attendees born in the United Kingdom and Europe, 14% of the men and 35% of the women were infected with non-B subtypes. In contrast, 78% of infections in antenatal patients were non-B subtypes, of which 61% were subtype A and 29% were subtype C. Extrapolation to the estimated 29,700 prevalent adult infections in the United Kingdom indicates that approximately 8,100 (27%) such infections are non-B subtypes and that these are found almost entirely in heterosexuals. The findings suggest spread of infection of non-B subtypes to heterosexuals born in the United Kingdom from individuals infected in regions of high prevalence.
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Affiliation(s)
- J V Parry
- Sexually Transmitted and Blood Borne Virus Laboratory, Central Public Health Laboratory, London, United Kingdom
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36
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Liitsola K, Holmström P, Laukkanen T, Brummer-Korvenkontio H, Leinikki P, Salminen MO. Analysis of HIV-1 genetic subtypes in Finland reveals good correlation between molecular and epidemiological data. SCANDINAVIAN JOURNAL OF INFECTIOUS DISEASES 2001; 32:475-80. [PMID: 11055649 DOI: 10.1080/003655400458721] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The molecular epidemiology of HIV-1 genetic subtypes was studied in a cross-sectional sample collected from HIV-infected individuals living in Finland between 1988 and 1994 and compared with independently collected epidemiological data. Subtypes were determined by sequencing and phylogenetic analysis of the gag NCp7 and the env coding regions of PBMC provirus. Finnish viruses belonging to 7 subtypes were found. Two thirds (n = 70) of the sequences could be classified as subtype B, while others belonged to subtypes A, C, D, F and G and the circulating recombinant form AE(CM240) (n = 25). There were significant differences in gender distribution and mode-of-transmission between B-type infections and infections with the other subtypes. Most subtype B strains in Finland were associated with homosexual transmission and about half of these were acquired in Finland, while most individuals harbouring non-B infections indicated heterosexual transmission and direct or indirect contact with Africa or Southeast Asia. The heterogeneity of genetic subtypes in the country was in good agreement with the epidemiological data suggesting that a significant proportion of infections were imported. HIV-1 subtype determination may prove to be a valuable tool for providing objective epidemiological data.
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Affiliation(s)
- K Liitsola
- National Public Health Institute, Department of Infectious Disease Epidemiology, HIV Laboratory, Helsinki, Finland
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37
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Thomson MM, Delgado E, Manjón N, Ocampo A, Villahermosa ML, Mariño A, Herrero I, Cuevas MT, Vázquez-de Parga E, Pérez-Alvarez L, Medrano L, Taboada JA, Nájera R. HIV-1 genetic diversity in Galicia Spain: BG intersubtype recombinant viruses circulating among injecting drug users. AIDS 2001; 15:509-16. [PMID: 11242148 DOI: 10.1097/00002030-200103090-00010] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND The HIV-1 epidemics in Western Europe are dominated by B subtype viruses. Non-B subtype is largely restricted to individuals infected outside of Europe and to their direct contacts and is generally acquired by the heterosexual route. METHODS Protease and a segment of reverse transcriptase were amplified and sequenced from plasma RNA in 451 individuals from seven cities of Galicia, north-western Spain. Subtype sequence homologies were determined using the BLAST algorithm. Non-B sequences were examined by phylogenetic analysis and intersubtype recombination by bootscanning. The env V3 region was analysed in all non-B and in 38 B subtype viruses. RESULTS Ten different non-B genetic forms were identified in 20 (4.4%) individuals. Subtypes were concordant between pol and V3 in five viruses; 14 (70%) infections were with intersubtype recombinant viruses, and one individual had a dual B+G infection. Seven recombinant viruses were phylogenetically related to five reported recombinant forms. Three non-recombinant G and six recombinant BG viruses formed a monophyletic cluster for pol. All but three individuals with non-B infections were native Spanish. Only 6 of 16 individuals referred to sexual contacts with sub-Saharan Africans. Twelve (60%) non-B subtype infections, including all with G and BG viruses, were in injecting drug users (IDU). CONCLUSIONS Non-B subtype viruses were identified in 4.4%, with a high diversity of genetic forms, including 70% infections with intersubtype recombinant viruses. The majority of individuals with non-B infections were IDU, most of them without known contacts with non-European sources, and among whom BG recombinant viruses are circulating.
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Affiliation(s)
- M M Thomson
- Area de Patogenia Viral, Centro Nacional de Biología Fundamental, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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38
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de Oliveira CF, Diaz RS, Machado DM, Sullivan MT, Finlayson T, Gwinn M, Lackritz EM, Williams AE, Kessler D, Operskalski EA, Mosley JW, Busch MP. Surveillance of HIV-1 genetic subtypesand diversity in the US blood supply. Transfusion 2000; 40:1399-406. [PMID: 11099672 DOI: 10.1046/j.1537-2995.2000.40111399.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Recent reports of variant (non-subtype B) HIV infections in US populations have raised concerns about the sensitivity of subtype B virus-based donor screening and diagnostic assays. This study was designed to determine the prevalence and genetic diversity of HIV subtypes in US blood donors over the last two decades. STUDY DESIGN AND METHODS Three groups were studied: hemophiliacs infected by clotting factor concentrates in the early 1980s (n = 49), blood donors retrospectively identified as being seropositive in 1985 (n = 97), and blood donors identified as seropositive between 1993 and 1996 (n = 405). Subtype assignment was based primarily on heteroduplex mobility analysis (HMA) of HIV-1 env, with DNA sequence confirmation of selected specimens. HIV peptide-based EIA serotyping was used to rule out HIV-2 and group O infections and to serotype HMA-refractory specimens. RESULTS Of 551 specimens, 535 (97%) were assigned subtypes; 532 (99%) of these were subtype B. Three postscreening donations (1%) were assigned non-B subtypes (2 A, 1 C). Two of these three donors were born in Africa; the third was born in the United States and reported no risk factors other than heterosexual activity. HMA distribution plots showed an increase in env diversity among HIV-1 group B strains over time. CONCLUSION The results support the need for continued surveillance of HIV subtype diversity and ongoing validation of the sensitivity of HIV diagnostic assays to non-B subtype infections.
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Affiliation(s)
- C F de Oliveira
- Blood Centers of the Pacific/Irwin Center, San Francisco, CA 94118, USA
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Quiñones-Mateu ME, Ball SC, Marozsan AJ, Torre VS, Albright JL, Vanham G, van Der Groen G, Colebunders RL, Arts EJ. A dual infection/competition assay shows a correlation between ex vivo human immunodeficiency virus type 1 fitness and disease progression. J Virol 2000; 74:9222-33. [PMID: 10982369 PMCID: PMC102121 DOI: 10.1128/jvi.74.19.9222-9233.2000] [Citation(s) in RCA: 194] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study was designed to examine the impact of human immunodeficiency virus type 1 (HIV-1) fitness on disease progression through the use of a dual competition/heteroduplex tracking assay (HTA). Despite numerous studies on the impact of HIV-1 diversity and HIV-specific immune response on disease progression, we still do not have a firm understanding of the long-term pathogenesis of this virus. Strong and early CD8-positive cytotoxic T-cell and CD4-positive T-helper cell responses directed toward HIV-infected cells appear to curb HIV pathogenesis. However, the rate at which the virus infects the CD4(+) T-cell population and possibly destroys the HIV-specific immune response may also alter the rate of disease progression. For HIV-1 fitness studies, we established conditions for dual HIV-1 infections of peripheral blood mononuclear cells (PBMC) and a sensitive HTA to measure relative virus production. A pairwise comparison was then performed to estimate the relative fitness of various non-syncytium-inducing/CCR5-tropic (NSI/R5) and syncytium-inducing/CXCR4-tropic (SI/X4) HIV-1 isolates. Four HIV-1 strains (two NSI/R5 and two SI/X4) with moderate ex vivo fitness were then selected as controls and competed against primary HIV-1 isolates from an HIV-infected Belgian cohort. HIV-1 isolates from long-term survivors (LTS) were outcompeted by control strains and were significantly less fit than HIV-1 isolates from patients with accelerated progression to AIDS (PRO). In addition, NSI/R5 HIV-1 isolates from PRO overgrew control SI/X4 strains, suggesting that not all SI/X4 HIV-1 isolates replicate more efficiently than all NSI/R5 isolates. Finally, there were strong, independent correlations between viral load and the total relative fitness values of HIV-1 isolates from PRO (r = 0.84, P = 0.033) and LTS (r = 0.86, P = 0.028). Separation of the PRO and LTS plots suggest that HIV-1 fitness together with viral load may be a strong predictor for the rate of disease progression.
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Affiliation(s)
- M E Quiñones-Mateu
- Department of Medicine, Division of Infectious Diseases, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Caride E, Brindeiro R, Hertogs K, Larder B, Dehertogh P, Machado E, de Sá CA, Eyer-Silva WA, Sion FS, Passioni LF, Menezes JA, Calazans AR, Tanuri A. Drug-resistant reverse transcriptase genotyping and phenotyping of B and non-B subtypes (F and A) of human immunodeficiency virus type I found in Brazilian patients failing HAART. Virology 2000; 275:107-15. [PMID: 11017792 DOI: 10.1006/viro.2000.0487] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Development of drug resistance is the inevitable consequence of incomplete suppression of virus plasma levels in HIV-1-infected patients treated with highly active antiretroviral therapy. Resistance mutations previously characterized have been found in B subtype viruses of developed countries. Moreover, mutation profiles for non-B and more divergent B subtype viruses found in developing countries shall be analyzed together with their ex vivo phenotyping in order to establish an exact correlation between the genotyping data and the clinical management counseling for those uncommon virus subtypes. In the present study, we evaluated the mutation profile for individuals infected with B subtype and non-B subtype viruses. Viral DNA fragments corresponding to the RT gene were amplified, sequenced, and subtyped. Phenotyping analysis for reverse transcriptase nucleoside (NRTI) and nonnucleoside inhibitor susceptibility was performed using the recombinant virus assay technology. Brazilian non-B subtypes (subtype F, n = 4, and subtype A, n = 1) isolates showed essentially the same B subtype mutation profile, presenting an NRTI drug resistance with similar MIC50% and MIC90% values for all drugs analyzed regardless of their subtypes. A strong cross-resistance phenotype among AZT, 3TC, and abacavir could be seen in all isolates analyzed. A novel result was that some RT sequences not only revealed the presence of G333D/E mutations but also correlated to the presence of mutation T386I that could abrogate the M184V-surpassing effect of L210W or L210W plus G333D/E. These findings suggest that Brazilian non-B subtype HIV-1 strains use an identical RT drug resistance mutation pattern when compared to B isolates and will contribute to the validation of the genotypic and phenotypic tests in these predominant worldwide-spread viral variants.
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Affiliation(s)
- E Caride
- Laboratory of Molecular Virology, Genetic Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, Brazil
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Swanson P, Harris BJ, Holzmayer V, Devare SG, Schochetman G, Hackett J. Quantification of HIV-1 group M (subtypes A-G) and group O by the LCx HIV RNA quantitative assay. J Virol Methods 2000; 89:97-108. [PMID: 10996643 DOI: 10.1016/s0166-0934(00)00205-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) genetic diversity presents a challenge to nucleic acid-based assays with regard to sensitivity of detection and accuracy of quantification. The Abbott LCx HIV RNA Quantitative assay (LCx(R) HIV assay), a competitive RT-PCR targeting the pol integrase region, was evaluated using a panel of 297 HIV-1 seropositive plasma samples from Cameroon, Uganda, Brazil, Thailand, Spain, Argentina and South Africa. The panel included group M subtypes A-G, mosaics, and group O based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified 290 (97.6%) of the samples, including all the group O samples tested. In comparison, the Roche AMPLICOR HIV-1 MONITOR test versions 1.0 and 1.5 quantified 67.3 and 94.6% of the samples, respectively. No group O specimens were quantified by either version of AMPLICOR HIV-1 MONITOR. Seven specimens were below the detectable limits of all the three assays. The LCx HIV assay had fewer nucleotide mismatches at primer/probe binding sites as compared with both AMPLICOR HIV-1 MONITOR tests. The high degree of nucleotide conservation within the pol target region enables the LCx HIV assay to efficiently quantify the HIV-1 subtypes A-G and the most genetically diverse HIV-1, group O.
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Affiliation(s)
- P Swanson
- AIDS Research and Retrovirus Discovery, Abbott Laboratories, D-9NG, Bldg. AP20, 100 Abbott Park Road, Abbott Park, IL 60064-6015, USA
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Janssens W, Salminen MO, Laukkanen T, Heyndrickx L, Colebunders R, McCutchan FE, van der Groen G. Near full-length genome analysis of HIV type 1 CRF02.AG subtype C and CRF02.AG subtype G recombinants. AIDS Res Hum Retroviruses 2000; 16:1183-9. [PMID: 10954895 DOI: 10.1089/088922200415045] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 CRF02.AG strains are prevalent in west and west-central Africa, suggesting a longstanding presence of these subtype A/G recombinants in the global epidemic. Cocirculation of CRF02.AG strains with other group M subtypes may give rise to HIV-1 recombinants constituting a mosaic genome comprising fragments of three different subtypes. We report on the genetic analysis of the near-full-length genomes of such recombinants (VI1035 and VI1197) as well as CRF02.AG strains in Belgian individuals. VI1035 and VI1197 may be the result of successful "second-generation" recombinations of HIV-1 strains CRF02.AG with, respectively, subtype C (VI1035) and G (VI1197) strains in a dually infected individual.
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Affiliation(s)
- W Janssens
- Department of Microbiology, Institute of Tropical Medicine, Antwerp, Belgium.
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Janssens W, Laukkanen T, Salminen MO, Carr JK, Van der Auwera G, Heyndrickx L, van der Groen G, McCutchan FE. HIV-1 subtype H near-full length genome reference strains and analysis of subtype-H-containing inter-subtype recombinants. AIDS 2000; 14:1533-43. [PMID: 10983640 DOI: 10.1097/00002030-200007280-00009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To characterize near-full-length genomes of two HIV-1 subtype H strains. To extend sequence data to include full env and gag, and analyse and redefine, previously documented subtype H strains. DESIGN Near-full-length genomes of HIV-1 env subtype H strains VI991 and VI997 were amplified, cloned, sequenced, phylogenetically analysed and compared with a panel of 23 HIV-1 group M reference isolates. The mosaic nature of previously published subtype H strains VI557 and CA13 was reanalysed. MATERIALS AND METHODS Peripheral blood mononuclear cells (PBMC) from individuals harbouring strains VI991 and VI997 were co-cultivated with PHA stimulated donor PBMC. Near-full-length genomes of VI991 and VI997, and gag and env genes of CA13 and VI557, were amplified by polymerase chain reaction, cloned and sequenced. Intersubtype recombination analyses were performed by similarity plot, bootscanning and phylogenetic analysis. RESULTS Near-full-length clones of HIV-1 VI991 and VI997 are representative of subtype H. They form a phylogenetic cluster with the only previously described subtype H representative HIV-1 90CF056.1, regardless of the genome region analysed. VI557 is redefined as a gag and env subtype H mosaic virus containing unclassified fragments. CA13 is a complex intersubtype recombinant between subtypes A, H and unclassified strains CONCLUSION Near-full-length genome analysis identified HIV-1 VI991 and VI997 as two new subtype H representatives. These reagents will allow defining and classifying non-recombinant as well as recombinant HIV-1, eventually helping to solve the puzzle of HIV-1 subtypes.
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Affiliation(s)
- W Janssens
- Department of Microbiology, Institute of Tropical Medicine, Antwerp, Belgium.
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Op de Coul E, van der Schoot A, Goudsmit J, van den Burg R, Janssens W, Heyndrickx L, van der Groen G, Cornelissen M. Independent introduction of transmissible F/D recombinant HIV-1 from Africa into Belgium and The Netherlands. Virology 2000; 270:267-77. [PMID: 10792985 DOI: 10.1006/viro.2000.0247] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Most HIV-1 subtype F viruses described so far have been isolated from individuals originating in South America, Romania, or Central Africa. Previous studies have shown that subtype F viruses from these three areas can be distinguished by phylogenetic tree analysis of various parts of the HIV genome. Subtype F strains circulating in Central Africa and classified as subgroup F2 and F3 have relatively large nucleotide distances from strains of subgroup F1, which includes some African strains, along with strains from Romania and South America. Subtype F strains have now appeared in Europe. In this study, we analyzed the complete gag gene and a large fragment of the pol gene of seven strains of African origin that represent the three F subgroups. At least five of the seven strains appear to be intersubtype recombinants. Of four strains circulating in Belgium and the Netherlands, three were F/D mosaics and the fourth harboured a G(gag)/GH(pol)/F3(env) recombinant structure. Two of the three F/D mosaics showed identical breakpoints and were independently introduced in Belgium and the Netherlands. At least two of the mosaics were further transmitted. The remaining three strains of the seven we studied were isolated from individuals in Cameroon. Two included large or smaller F1 fragments in gag and pol. The third strain was subtype D along the entire gag and pol fragment. A parental African subtype F that showed no evidence for recombination was not found.
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Affiliation(s)
- E Op de Coul
- Division of Public Health and Environment, Municipal Health Service, Nieuwe Achtergracht 100, Amsterdam, 1018 WT, the Netherlands.
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Couturier E, Damond F, Roques P, Fleury H, Barin F, Brunet JB, Brun-Vézinet F, Simon F. HIV-1 diversity in France, 1996-1998. The AC 11 laboratory network. AIDS 2000; 14:289-96. [PMID: 10716505 DOI: 10.1097/00002030-200002180-00011] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To study the distribution of HIV-1 subtypes in France and to describe the characteristics of patients infected with non-B subtypes. METHODS All adults who tested HIV-1 positive on Western blot for the first time in one of the participating laboratories between September 1996 and March 1998 were eligible, whether or not they had been diagnosed previously elsewhere. Data on age, sex, country of birth, HIV-transmission group, dates of the last negative and first positive HIV test and clinical stage were collected. Serotyping was performed with a peptide subtype-specific enzyme immunoassay on each plasma sample and genotyping with heteroduplex mobility assay on each non-B serotype-infected patient. Patients characteristics were compared in B and non-B subtypes. RESULTS Of the 2168 HIV-positive patients included by 32 laboratories, subtype,results were available for 2042. Among those, 73.4% were men, 12.2% born in sub-Saharan Africa, 41.5% infected through heterosexual contact and 67.6% in CDC stage A. Among the 2042 patients, 1 725 (84.5%) were infected with B subtype. Among the 317 non-B subtypes, subtype A was predominant (66.9%); all other subtypes (C, D, E, F, G, H, O) were present. Factors independently associated with a non-B subtype were to be included in the Paris area [adjusted odds ratio (aOR), 1.6; 95% confidence interval (CI), 1.1-2.3], to be born in sub-Saharan Africa (aOR, 26.0; 95% CI, 17.5-37.8) and to be infected through heterosexual contact (aOR, 4.2; 95% CI, 2.8-6.4). CONCLUSIONS In France, although B subtype is still predominant, all non-B subtypes are now present. The diversity of HIV strains may affect diagnostic tests and clinical practice, especially viral load measurements. Moreover, the decreased susceptibility of non-B subtypes to antiretroviral drugs emphasizes the importance of surveillance of HIV diversity.
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Affiliation(s)
- E Couturier
- European Centre for the Epidemiological Monitoring of AIDS, Hôpital National de Saint-Maurice, France
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Cornelissen M, van Den Burg R, Zorgdrager F, Goudsmit J. Spread of distinct human immunodeficiency virus type 1 AG recombinant lineages in Africa. J Gen Virol 2000; 81:515-23. [PMID: 10644851 DOI: 10.1099/0022-1317-81-2-515] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To identify new subtype G human immunodeficiency virus type 1 (HIV-1) strains and AG recombinant forms, we collected 28 serum samples from immigrants to the Netherlands from 12 countries throughout Africa. Based on the gag sequences 22 isolates were identified as subtype A or G. Phylogenetic analysis of discontinuous regions of the gag (726 nt), pol (1176 nt) and env (276 nt) genes revealed 13 AG recombinants with the mosaic structure A(gag)/G(pol)/A(env), three with A(gag)/G(pol)/G(env) and one other with A(gag) /G(pol)/G(env), in addition to 'pure' subtypes A(gag)/A(pol)/A(env) (n=1) and G(gag)/G(pol)/G(env) (n=4). To analyse the crossover points in more detail, a new RT-PCR was developed resulting in a large contiguous sequence of 2600 nt from the gag region to half the pol region. All the 13 A(gag)/G(pol)/A(env) recombinants appeared to belong to the circulating recombinant form (CRF) AG (IbNG). The three A(gag)/G(pol) /G(env) recombinants differed from the CRF AG (IbNG) subtype, suggesting the identification of a new CRF subtype. The recovery of AG recombinants from African countries a thousand miles apart indicates the active spread of new recombinants.
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Affiliation(s)
- M Cornelissen
- Department of Human Retrovirology, Academic Medical Centre, University of Amsterdam, Meibergdreef 45, 1105BA Amsterdam, The Netherlands.
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Busch MP, Kleinman SH, Jackson B, Stramer SL, Hewlett I, Preston S. Committee report. Nucleic acid amplification testing of blood donors for transfusion-transmitted infectious diseases: Report of the Interorganizational Task Force on Nucleic Acid Amplification Testing of Blood Donors. Transfusion 2000; 40:143-59. [PMID: 10685998 DOI: 10.1046/j.1537-2995.2000.40020143.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Stoeckli TC, Steffen-Klopfstein I, Erb P, Brown TM, Kalish ML. Molecular epidemiology of HIV-1 in Switzerland: evidence for a silent mutation in the C2V3 region distinguishing intravenous drug users from homosexual men. Swiss HIV Cohort Study. J Acquir Immune Defic Syndr 2000; 23:58-67. [PMID: 10708057 DOI: 10.1097/00126334-200001010-00008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To study the molecular epidemiology of HIV-1 strains found in Switzerland and to determine possible genetic linkages among strains sorted by risk group or geographic region. DESIGN A cross-sectional, clinic-based survey of HIV-1 molecular sequences and linked patient history from Swiss people. METHODS Specimens were collected from 215 HIV-1-infected people in HIV outpatient clinics of four tertiary referral centers (Lausanne, St. Gallen, Zurich, and Basel) between May and August 1996, mainly from homosexual men, injecting drug users (IDU), and heterosexually infected people. In addition, specimens collected between 1991 and 1995 in the HIV outpatient clinic at University of Geneva were included into this survey. These specimens were collected primarily for an ongoing, prospective cohort (Swiss HIV Cohort Study). Direct C2V3C3 sequences of the env gene were determined from 158 samples of peripheral blood mononuclear cells. Genetic data were analyzed with the available patient history on each specimen. RESULTS As found in other previous studies in Europe, primarily subtype B viruses were identified, whereas seven (4%) of 158 were non-subtype B: one subtype D, four subtype A, and two subtype E. Five of seven non-B subtypes occurred in immigrants from African or Asian countries and all seven were found exclusively in individuals who had been infected by heterosexual contact. No significant clustering of strains within different study sites or risk groups was found. A silent mutation (LAI env 834) occurred significantly more often in IDU than in homosexual men (p<.001). CONCLUSIONS Although the lack of significant clustering of strains by risk group or geographic region may result from early introduction of subtype B viruses in Switzerland, the strong association of a silent mutation with IDU suggests that, early in the epidemic, there was a unique founder virus among IDUs. The HIV epidemic in Switzerland is still predominantly caused by subtype B viruses.
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Affiliation(s)
- T C Stoeckli
- Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Molecular Epidemiology of HIV-1 in Switzerland: Evidence for a Silent Mutation in the C2V3 Region Distinguishing Intravenous Drug Users From Homosexual Men. J Acquir Immune Defic Syndr 2000. [DOI: 10.1097/00042560-200001010-00008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hu DJ, Buvé A, Baggs J, van der Groen G, Dondero TJ. What role does HIV-1 subtype play in transmission and pathogenesis? An epidemiological perspective. AIDS 1999; 13:873-81. [PMID: 10475680 DOI: 10.1097/00002030-199905280-00002] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- D J Hu
- Division of HIV/AIDS Prevention, National Center for HIV, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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