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Obeng BM, Bonney EY, Asamoah-Akuoko L, Nii-Trebi NI, Mawuli G, Abana CZY, Sagoe KWC. Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana. Virol J 2020; 17:114. [PMID: 32709248 PMCID: PMC7378406 DOI: 10.1186/s12985-020-01386-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Background Detection of HIV-1 transmitted drug resistance (TDR) and subtype diversity (SD) are public health strategies to assess current HIV-1 regimen and ensure effective therapeutic outcomes of antiretroviral therapy (ART) among HIV-1 patients. Globally, limited data exist on TDR and SD among blood donors. In this study, drug resistance mutations (DRMs) and SD amongst HIV-1 sero-positive blood donors in Accra, Ghana were characterized. Methods Purposive sampling method was used to collect 81 HIV sero-positive blood samples from the Southern Area Blood Center and confirmed by INNO-LIA as HIV-1 and/or HIV-2. Viral RNA was only extracted from plasma samples confirmed as HIV-1 positive. Complementary DNA (cDNA) was synthesized using the RNA as a template and subsequently amplified by nested PCR with specific primers. The expected products were verified, purified and sequenced. Neighbour-joining tree with the Kimura’s 2-parameter distances was generated with the RT sequences using Molecular Evolutionary Genetic Analysis version 6.0 (MEGA 6.0). Results Out of the 81 plasma samples, 60 (74%) were confirmed as HIV-1 sero-positive by INNO-LIA HIVI/II Score kit with no HIV-2 and dual HIV-1/2 infections. The remaining samples, 21 (26%) were confirmed as HIV sero-negative. Of the 60 confirmed positive samples, (32) 53% and (28) 47% were successfully amplified in the RT and PR genes respectively. Nucleotide sequencing of amplified samples revealed the presence of major drug resistance mutations in two (2) samples; E138A in one sample and another with K65R. HIV-1 Subtypes including subtypes A, B, CRF02_AG and CRF09_cpx were found. Conclusion This study found major drug resistance mutations, E138A and K65R in the RT gene that confer high level resistance to most NNRTIs and NRTI respectively. CRF02_AG was most predominant, the recorded percentage of subtype B and the evolutionary relationship inferred by phylogenetic analysis may suggest possible subtype importation. However, a more prospective and detailed analysis is needed to establish this phenomenon. The data obtained would inform the selection of drugs for ART initiation to maximize therapeutic options in drug-naïve HIV-1 patients in Ghana.
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Affiliation(s)
- Billal Musah Obeng
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana. .,Department of Medical Microbiology, School of Medicine and Dentistry, University of Ghana, Accra, Ghana.
| | - Evelyn Yayra Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana
| | | | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Gifty Mawuli
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana
| | - Christopher Zaab-Yen Abana
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra, Ghana
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Sanarico N, D’Amato S, Bruni R, Rovetto C, Salvi E, Di Zeo P, Chionne P, Madonna E, Pisani G, Costantino A, Equestre M, Tosti ME, Cenci A, Maggiorella MT, Sernicola L, Pontali E, Pansera A, Quattrocchi R, Carbonara S, Signorile F, Surace LA, Federzoni G, Garlassi E, Starnini G, Monarca R, Babudieri S, Rapicetta M, Pompa MG, Caraglia A, Ensoli B, Ciccaglione AR, Buttò S. Correlates of infection and molecular characterization of blood-borne HIV, HCV, and HBV infections in HIV-1 infected inmates in Italy: An observational cross-sectional study. Medicine (Baltimore) 2016; 95:e5257. [PMID: 27858889 PMCID: PMC5591137 DOI: 10.1097/md.0000000000005257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coinfection of blood-borne hepatitis B and hepatitis C viruses (HBV and HCV, respectively) in human immunodeficiency virus type 1 (HIV-1)-positive individuals frequently occurs in inmate population and peculiar viral strains and patterns of virological markers may be observed.Plasma from 69 HIV-1-positive inmates was obtained from 7 clinical centers connected with correctional centers in different towns in Italy. HIV, HBV, and HCV markers were tested by commercial assays. Virus genotyping was carried out by sequencing the protease and reverse transcriptase-encoding region (PR-RT region) for HIV and a region encompassing the NS5B gene for HCV and subsequent phylogenetic analysis.Twelve over 14 HIV-subtyped inmates were infected with HIV-1 subtype B strains. The 2 non-B strains belonged to subtype G and CRF02_AG, in an Italian and a Gambian patient, respectively. Variants carrying the K103N and Y181C resistance mutations to non-nucleoside reverse transcriptase inhibitors (NNRTIs) were found in 2 out of 9 patients naive for combined antiretroviral therapy (cART) (22.2%). Most HIV-positive patients (92.8%) showed evidence of past or present HBV and/or HCV infection. Prevalence of HBV and HCV was 81.2% for both viruses, whereas prevalence of HBV/HCV coinfection was 69.6%. A significantly higher presence of HCV infection was found in Italians [odds ratio (OR) 11.0; interval 1.7-80.9] and in drug users (OR 27.8; interval 4.9-186.0). HCV subtypes were determined in 42 HCV or HBV/HCV-coinfected individuals. HCV subtypes 1a, 3a, 4d, and 1b were found in 42.9%, 40.5%, 14.3%, and 2.4% of inmates, respectively. Low titers of HBV DNA in HBV DNA positive subjects precluded HBV subtyping.The high prevalence of HBV and HCV coinfections in HIV-infected inmates, as well as the heterogeneity of HIV and HCV subtypes suggest the need to adopt systematic controls in prisons to monitor both the burden and the genetic forms of blood-borne viral infections, in order to apply targeted therapeutic interventions.
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Affiliation(s)
| | | | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | - Emanuela Salvi
- National AIDS Center, Istituto Superiore di Sanità, Rome
| | | | - Paola Chionne
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | - Giulio Pisani
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | - Angela Costantino
- National AIDS Center, Istituto Superiore di Sanità, Rome
- Italian Ministry of Health, Rome
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | - Michele Equestre
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | - Maria E. Tosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | | | | | - Emanuele Pontali
- ASL 3 Genovese and Department of Infectious Diseases, Galliera Hospital, Genova
| | | | | | | | | | - Lorenzo Antonio Surace
- Centro Medicina del Viaggiatore e delle Migrazioni, Presidio Ospedaliero di Lamezia Terme, Giovanni Paolo II Hospital, Lamezia Terme
| | | | | | | | | | | | - Maria Rapicetta
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | | | - Barbara Ensoli
- National AIDS Center, Istituto Superiore di Sanità, Rome
| | | | - Stefano Buttò
- National AIDS Center, Istituto Superiore di Sanità, Rome
- Correspondence: Stefano Buttò, National AIDS Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy (e-mail: )
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Jongwe TI, Chapman R, Douglass N, Chetty S, Chege G, Williamson AL. HIV-1 Subtype C Mosaic Gag Expressed by BCG and MVA Elicits Persistent Effector T Cell Responses in a Prime-Boost Regimen in Mice. PLoS One 2016; 11:e0159141. [PMID: 27427967 PMCID: PMC4948879 DOI: 10.1371/journal.pone.0159141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/28/2016] [Indexed: 11/18/2022] Open
Abstract
Over 90% of HIV/AIDS positive individuals in sub-Saharan Africa are infected with highly heterogeneous HIV-1 subtype C (HIV-1C) viruses. One of the best ways to reduce the burden of this disease is the development of an affordable and effective prophylactic vaccine. Mosaic immunogens are computationally designed to overcome the hurdle of HIV diversity by maximizing the expression of potential T cell epitopes. Mycobacterium bovis BCG ΔpanCD auxotroph and modified vaccinia Ankara (MVA) vaccines expressing HIV-1C mosaic Gag (GagM) were tested in a prime-boost regimen to demonstrate immunogenicity in a mouse study. The BCG-GagM vaccine was stable and persisted 11.5 weeks post vaccination in BALB/c mice. Priming with BCG-GagM and boosting with MVA-GagM elicited higher Gag-specific IFN-γ ELISPOT responses than the BCG-GagM only and MVA-GagM only homologous vaccination regimens. The heterologous vaccination also generated a more balanced and persistent CD4+ and CD8+ T cell Gag-specific IFN-γ ELISPOT response with a predominant effector memory phenotype. A Th1 bias was induced by the vaccines as determined by the predominant secretion of IFN-γ, TNF-α, and IL-2. This study shows that a low dose of MVA (104 pfu) can effectively boost a BCG prime expressing the same mosaic immunogen, generating strong, cellular immune responses against Gag in mice. Our data warrants further evaluation in non-human primates. A low dose vaccine would be an advantage in the resource limited countries of sub-Saharan Africa and India (where the predominating virus is HIV-1 subtype C).
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Affiliation(s)
- Tsungai Ivai Jongwe
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicola Douglass
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shivan Chetty
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gerald Chege
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
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4
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Davanos N, Panos G, Gogos CA, Mouzaki A. HIV-1 subtype characteristics of infected persons living in southwestern Greece. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2015; 7:277-83. [PMID: 26715861 PMCID: PMC4686321 DOI: 10.2147/hiv.s90755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background The rapid replication rate of HIV-1, coupled with a high mutation rate and recombination, is the underlying force driving its genetic diversity. In the infected individual, a population of highly related but nonidentical strains exists. At the population level, multiple subtypes often cocirculate, leading to the generation of intersubtype recombinant forms. As a result, the geographic distribution of subtypes and recombinant forms is complex and uneven. Genetic subtyping of HIV-1 isolates has been shown to be helpful for understanding the genetic evolution, the worldwide spread of the virus, and the evaluation of drug resistance. Materials and methods We determined the genetic heterogeneity of HIV-1 group M in southwestern Greece. Protease and partial reverse-transcriptase sequences were generated from 150 HIV-1-infected individuals attending the Division of Infectious Diseases of Patras University Hospital, Greece, from 2006 to 2012, and analyzed using online subtyping tools and phylogenetic methods. Results The majority of the infected individuals were male (77%). HIV-1 subtype A1 was responsible for 51.3% of infections, followed by subtypes B (34%), G (4%), F1 (2%), and the circulating recombinant forms 02_AG (2.7%), 14_BG (1.3%), 35_AD (1.3%), and 01_AE (0.7%). Additionally, we identified three cases with a recombinant B/CRF02_AG strain (2%) and one with a recombinant G/GRF_AG strain. Sexual transmission was responsible for 96.3% of cases. Heterosexual transmission was responsible for 70.2% of subtype-A1 infections, whereas subtype B was transmitted by men who have sex with men in 75.5% of cases. Protease substitutions I13V, E35D, M36I, R57K, H69K, and L89M, which serve as drug-resistance support mutations in subtype B, were present in the majority of subtype-A1 sequences of the population. Conclusion HIV-1 infection in southwestern Greece is sexually transmitted and highly heterogeneous. Subtype A1 has surpassed subtype B, and is the most prevalent strain. In the population studied, subtype A1 exhibited certain polymorphisms in the protease region, which may serve as drug-resistance support mutations in subtype B.
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Affiliation(s)
- Nikolaos Davanos
- Division of Hematology, Department of Internal Medicine, Faculty of Medicine, University of Patras, Patras, Greece
| | - George Panos
- Division of Infectious Diseases, Department of Internal Medicine, University Hospital, University of Patras, Patras, Greece
| | - Charalambos A Gogos
- Division of Infectious Diseases, Department of Internal Medicine, University Hospital, University of Patras, Patras, Greece
| | - Athanasia Mouzaki
- Division of Hematology, Department of Internal Medicine, Faculty of Medicine, University of Patras, Patras, Greece
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Abstract
Objective: HIV-1 is typically categorized by genetically distinct viral subtypes. Viral subtypes are usually compartmentalized by ethnicity and transmission group and, thus, convey important epidemiological information, as well as possibly influencing the rate of disease progression. We aim to describe the prevalence and time trends of subtypes observed among key populations living with HIV-1 in the UK. Design: Analyses of reverse transcriptase and protease sequences generated from HIV-1-positive antiretroviral-naive patients as part of routine resistance testing between 2002 and 2010 in all public health and NHS laboratories in the UK. Methods: Subtype was assigned centrally using the SCUEAL algorithm. Subtyping results were combined with data from the UK Collaborative HIV Cohort Study and the UK HIV and AIDS Reporting System. Analyses adjusted for the number of national HIV-1 diagnoses made each year within demographic subgroups. Viral subtypes were described overall, over time and by demographic subgroup. Results: Subtype B diagnoses (39.9%) have remained stable since 2005, whereas subtype C diagnoses (34.3%) were found to decline in prevalence from 2004. Across most demographic subgroups, the prevalence of non-B non-C subtypes has increased over time, in particular novel recombinant forms (9.9%), subtype G (2.7%), and CRF01 AE (2.0%). Conclusion: HIV-1 subtypes are increasingly represented across all demographic subgroups and this could be evidence of sexual mixing. Between 2002 and 2010, the prevalence of novel recombinant forms has increased in all demographic subgroups. This increasing genetic diversity and the effect of subtype on disease progression may impact future HIV-1 treatment and prevention.
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Tramuto F, Maida CM, Bonura F, Perna AM, Vitale F. Dynamics and molecular evolution of HIV-1 strains in Sicily among antiretroviral naïve patients. INFECTION GENETICS AND EVOLUTION 2013; 16:290-7. [PMID: 23470353 DOI: 10.1016/j.meegid.2013.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 11/25/2022]
Abstract
HIV-1 subtype B is the most frequent strain in Sicily. To date, there is no available data about the genetic diversity of HIV-1 viral strains circulating in Sicily among antiretroviral (ARV) naïve subjects and the role of immigration as potential determinant of evolutionary dynamics of HIV-1 molecular epidemiology. For this purpose, HIV-1 polymerase (pol) sequences obtained from 155 ARV naïve individuals from 2004 to 2009 were phylogenetically analysed. The overall rate of HIV-1 non-B infections was 31.0% (n=48/155), increasing from 7.8% in 2004-2006 to 40.9% in 2009, and about one-third were identified as unique recombinant forms. CRF02_AG was the prevalent non-B clade (n=28/48, 58.3%), while subtype C-related strains were responsible for about 30% HIV-1 infections. Non-B viruses strictly associated with heterosexual transmission (85.4%) and were mostly found among immigrants (77.1%). Phylogenetic analysis of non-B sequences found in foreign-born subjects was geographically correlated to the respective country of origin. Moreover, the detection of non-B viral variants in the autochthonous population may support an increasing genetic diversity in Sicily as well as a local circulation of HIV strains also uncommon in our country. In Sicily, HIV-1 epidemic is still mostly attributable to the B subtype. Nevertheless, migration and population movements are progressively introducing novel HIV-1 subtypes causing a continuous increase of HIV-1 molecular dynamic at local level. Molecular surveillance is needed to monitor the genetic evolution of HIV-1 epidemic.
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Affiliation(s)
- F Tramuto
- Department of Sciences for Health Promotion G. D'Alessandro - Hygiene Section, University of Palermo, Palermo, Italy.
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7
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Rank C, Njihia JG, Remis RS, Shah L, Swantee C, Brooks JI, Jayaraman GC, Archibald CP. Characterizing viral subtypes to assess patterns of HIV transmission. Int J STD AIDS 2012; 23:e6-9. [PMID: 23104760 DOI: 10.1258/ijsa.2009.009303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We characterized HIV-1 subtypes among 204 persons newly diagnosed with HIV in Ontario from 2003 to 2005 using samples from the Canadian HIV Strain and Drug Resistance Surveillance Program. We examined HIV-1 subtype by demographic characteristics and exposure category, and determined independent predictors of infection with a non-B HIV subtype using multivariate logistic regression. The distribution of HIV subtypes was: B 77.0%, C 10.3%, AG 4.9%, A 2.5%, AE 2.5% and others 3.0%. Overall, 23.0% were non-B, greater in women than in men (62.8% versus 12.4%, P < 0.0001) and persons under 35 years (31.1% versus 18.5% in those ≥35, P = 0.04). Non-B subtype was predominant (78.9%) among persons from HIV-endemic regions and considerable (28.6%) among other persons infected heterosexually. In multivariate modelling adjusted for gender, non-B subtype was significantly associated with birth in an HIV-endemic region (adjusted odds ratio [aOR] 59.2, P < 0.0001) and heterosexual exposure (aOR 6.3, P = 0.02). Additionally, compared with men who had sex with men, non-B subtype was greater among heterosexual women (aOR 17.8, P < 0.001) and women who injected drugs (injection drug use, aOR 13.4, P = 0.01). We found a non-negligible proportion of non-B subtypes among women infected heterosexually not from HIV-endemic countries, providing interesting insights into HIV transmission patterns.
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Affiliation(s)
- C Rank
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Canada
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Gräf T, Pinto AR. The increasing prevalence of HIV-1 subtype C in Southern Brazil and its dispersion through the continent. Virology 2012; 435:170-8. [PMID: 22999094 DOI: 10.1016/j.virol.2012.08.048] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 01/15/2023]
Abstract
The HIV-1 has evolved swiftly and the scenario of HIV-1 genetic diversity is constantly changing. In South America, recombinant forms of subtypes B, F1, and BF1 have historically driven the HIV-1 epidemic. In recent years, however, infection with subtype C has gained prominence as its prevalence increased in Southern Brazil as well as neighboring countries. Current studies point to a single introduction of closely related strains as the beginning of the Brazilian subtype C epidemic. However, the place of origin of these strains, date, and route of introduction are under continuous debate as well as the clinical outcomes of the emergence of subtype C. Therefore, this paper reviews the history of the HIV-1 subtype C in Brazil, particularly in the Southern region, covering its demographic and evolutionary history and the possible implications to the Brazilian AIDS epidemic as well as to neighboring countries.
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Affiliation(s)
- Tiago Gräf
- Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
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Ten years of external quality assessment of human immunodeficiency virus type 1 RNA quantification. J Clin Microbiol 2012; 50:3614-9. [PMID: 22952265 DOI: 10.1128/jcm.01221-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral load testing is an essential parameter in guiding antiretroviral therapy for individuals infected with human immunodeficiency virus type 1 (HIV-1). An external quality assessment scheme for the molecular quantification of HIV-1 RNA was introduced by the United Kingdom National External Quality Assessment Service for Microbiology in 2000. Specimen pairs of freeze-dried plasma were distributed to a median of 141 participants three times a year. The aim of this study was to analyze the quantification of HIV-1 RNA results between 2000 and 2010. Overall variability, measured by the standard deviations of all viral load results for each specimen, was below 0.5 log copy/ml (n = 48). When we compared assay results, the medians of the viral load by assay were within a range of 0.25 to 1.08 log copies/ml, with the lowest median values being consistently reported with the Siemens branched-chain DNA assay. The spread of participant results and, hence, differences between assay medians were greater when quantifying non-B subtypes. Laboratories were scored on the proximity of their reported log difference for the specimen pair to the median log difference reported by all laboratories. The overall level of performance with the HIV-1 RNA specimens over the past 10 years has been consistently good, with more than 90% of the participants reporting in the accepted range (median difference, ±0.5 log unit). Future distributions may result in tightening the acceptance levels of quantification and the use of more challenging specimens, including a variety of subtypes, with developments focusing on maintaining the clinical relevance and educational value of the scheme.
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Javaugue FC, Recordon-Pinson P, Decoin M, Masquelier B, Cazanave C, Neau D, Dupon M, Ragnaud JM, Fleury HJ. Molecular characterization of non-B HIV type 1 isolates from patients of a department of infectious diseases, University Hospital of Bordeaux, France, 1989-2009. AIDS Res Hum Retroviruses 2012; 28:1124-30. [PMID: 22129096 DOI: 10.1089/aid.2011.0321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular characterization of non-B HIV type 1 subtypes and the sociodemographic baseline characteristics have been studied for 114 non-B HIV-1-infected patients followed at the University Hospital of Bordeaux, France, and diagnosed as HIV infected between 1989 and 2009. Individuals enrolled in this study were mainly women with heterosexual transmission in West and Central Africa and who have been discovered to be HIV positive during pregnancy. Nevertheless, HIV acquisition among individuals born in France was significantly increasing. Recombinant form CRF02_AG was the most frequent subtype (38%) among a highly diverse viral background since 19 subtypes and CRFs have been characterized with a maximal diversity observed in the past decade.
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Affiliation(s)
- François-Charles Javaugue
- Laboratoire de Virologie (WHO accredited for HIV resistance), Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux et CNRS UMR 5234, Bordeaux, France
| | - Patricia Recordon-Pinson
- Laboratoire de Virologie (WHO accredited for HIV resistance), Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux et CNRS UMR 5234, Bordeaux, France
| | - Madeleine Decoin
- Fédération des Maladies Infectieuses, Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Institut de Santé Publique, d'Epidémiologie et de Développement (ISPED), Université Victor Segalen Bordeaux 2, Bordeaux, France
| | - Bernard Masquelier
- Laboratoire de Virologie (WHO accredited for HIV resistance), Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux et CNRS UMR 5234, Bordeaux, France
| | - Charles Cazanave
- Fédération des Maladies Infectieuses, Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Didier Neau
- Fédération des Maladies Infectieuses, Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Michel Dupon
- Fédération des Maladies Infectieuses, Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Jean-Marie Ragnaud
- Fédération des Maladies Infectieuses, Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Hervé J. Fleury
- Laboratoire de Virologie (WHO accredited for HIV resistance), Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux et CNRS UMR 5234, Bordeaux, France
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Silveira J, Santos AF, Martínez AMB, Góes LR, Mendoza-Sassi R, Muniz CP, Tupinambás U, Soares MA, Greco DB. Heterosexual transmission of human immunodeficiency virus type 1 subtype C in southern Brazil. J Clin Virol 2012; 54:36-41. [PMID: 22326760 DOI: 10.1016/j.jcv.2012.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 01/06/2012] [Accepted: 01/23/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype B predominates in Brazil, but in the southern region subtype C is the most frequent, followed by subtypes B, F1 and recombinant forms. In southern Brazil, these subtypes co-circulate in subjects with homogeneous demographic and clinical features, enabling a better understanding of the role of HIV-1 subtypes on the characteristics of infection. OBJECTIVES To evaluate the prevalence of different HIV-1 subtypes in subjects with recent diagnosis for HIV infection in the extreme south of Brazil, and to study their association with demographic, behavioral, clinical and laboratorial characteristics. STUDY DESIGN We have determined the genetic sequence of viral protease and reverse transcriptase (polymerase, connection and RNase H domains) isolated from studied subjects. Viral subtype was inferred by comparison with reference HIV sequences, and recombination was determined with Simplot analysis. The association of HIV-1 subtypes with studied characteristics was evaluated by chi-square, Fisher's exact, Student's t and Kruskal-Wallis tests. RESULTS Two hundred and forty-five HIV isolates were molecularly characterized, and the association with variables was studied for 233 (95.1%) patients. Of those, 46.8% followed AIDS defining criteria. HIV-1C was responsible for 56.3% of infections, and was associated with heterosexual transmission (p=0.001) and with higher CD4(+) T-cell counts (p=0.02). CONCLUSIONS The molecular epidemiology of HIV-1 in the southernmost Brazil is currently steady with predominance of HIV-1C. This is the first study showing a robust association of the infection by this subtype and heterosexual transmission in the state of Rio Grande do Sul, Brazil.
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Affiliation(s)
- Jussara Silveira
- Faculdade de Medicina, Universidade Federal de Rio Grande, Rio Grande, Brazil
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Khawcharoenporn T, Apisarnthanarak A, Gesprasert G, Jaiyen Y, Mundy LM, Thitithanyanont A. Predictors for recombinant HIV infection in a Thai cohort. Sex Transm Dis 2012; 38:1046-9. [PMID: 21992982 DOI: 10.1097/olq.0b013e31822c8d90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Recombinant human immunodeficiency virus (HIV) infection was associated with exchange of sex for money, ≥1 sex partner within the prior 6 months, and decline in CD4 cell count in this Thai cohort study. These findings suggest that recombinant HIV infection may have implications for HIV disease progression, safer sex practices, and vaccine development.
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Affiliation(s)
- Thana Khawcharoenporn
- Division of Infectious Diseases, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
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Luft LM, Gill MJ, Church DL. HIV-1 viral diversity and its implications for viral load testing: review of current platforms. Int J Infect Dis 2011; 15:e661-70. [PMID: 21767972 DOI: 10.1016/j.ijid.2011.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 05/10/2011] [Accepted: 05/16/2011] [Indexed: 01/04/2023] Open
Affiliation(s)
- LeeAnne M Luft
- Department of Medicine, University of Calgary, 2500 University Dr. N.W. Calgary, AB, Canada T2N 1N4
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Abstract
The molecular epidemiology of HIV-1 is constantly changing, mainly as a result of human migratory flows and the high adaptive ability of the virus. In recent years, Spain has become one of Europe's main destinations for immigrants and one of the western European countries with the highest rates of HIV-positive patients. Using a phylogeographic approach, we have analyzed the relationship between HIV-1 variants detected in immigrant and native populations of the urban area of Madrid. Our project was based on two coincidental facts. First, resistance tests were extended to naïve and newly diagnosed patients, and second, the Spanish government legislated the provision of legal status to many immigrants. This allowed us to obtain a large data set (n = 2,792) from 11 Madrid hospitals of viral pol sequences from the two populations, and with this unique material, we explored the impact of immigration in the epidemiological trends of HIV-1 variants circulating in the largest Spanish city. The prevalence of infections by non-B HIV-1 variants in the studied cohort was 9%, rising to 25% among native Spanish patients. Multiple transmission events involving different lineages and subsubtypes were observed in all the subtypes and recombinant forms studied. Our results also revealed strong social clustering among the most recent immigrant groups, such as Russians and Romanians, but not in those groups who have lived in Madrid for many years. Additionally, we document for the first time the presence of CRF47_BF and CRF38_BF in Europe, and a new BG recombinant form found in Spaniards and Africans is tentatively proposed. These results suggest that the HIV-1 epidemic will evolve toward a more complex epidemiological landscape.
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Peeters M, Aghokeng AF, Delaporte E. Genetic diversity among human immunodeficiency virus-1 non-B subtypes in viral load and drug resistance assays. Clin Microbiol Infect 2011; 16:1525-31. [PMID: 20649800 DOI: 10.1111/j.1469-0691.2010.03300.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tremendous diversity of human immunodeficiency virus (HIV)-1 strains circulating worldwide has an important impact on almost all aspects of the management of this infection, from the identification of infected persons, through treatment efficacy and monitoring, and prevention strategies such as vaccine design. The areas where HIV-1 genetic diversity is highest are those where the majority of patients in need of treatment and biological monitoring live. With increased access to treatment in these areas, it is expected that the demand for monitoring tools such as viral load assays and resistance tests will also increase, and their reliability will be critical. Regular updates of these assays during the last two decades have aimed at improving their performances in different ways that include their reliability with different HIV-1 strains. We here review to what extent HIV-1 genetic diversity still limits or not the use of currently available viral load and resistance tests.
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Affiliation(s)
- M Peeters
- UMR 145 VIH et Maladies Associées Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France.
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Treviño A, Soriano V, Rodríguez C, Arredondo M, Rivas P, Herrero-Mendoza D, Parra P, del Romero J, Anta L, Puente S, de Mendoza C. Changing rate of non-B subtypes and coinfection with hepatitis B/C viruses in newly diagnosed HIV type 1 individuals in Spain. AIDS Res Hum Retroviruses 2011; 27:633-8. [PMID: 21039316 DOI: 10.1089/aid.2010.0247] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Immigration from developing regions to Western countries has resulted in an increased rate of non-B subtypes in the HIV population. However, it is unclear whether these HIV variants remain confined to foreigners or are already spreading among natives. Since many immigrants come from regions in which hepatitis B virus (HBV) and hepatitis C virus (HCV) are endemic, HIV-hepatitis coinfection might be more frequent in newly diagnosed HIV persons. Herein, we report changes in the prevalence and distribution of HIV-1 subtypes in Madrid, Spain over the past 10 years as well as the rate of chronic HBV and HCV coinfection in 1854 newly diagnosed HIV-1 individuals. Overall 18.2% carried HIV-1 non-B subtypes, although the prevalence increased over time reaching a peak of 19.4% in the last period (2007-2010). The most common non-B variants were CRF02_AG (37%), G (12%), A (9.9%), and C (7.8%). In native Spaniards the rate of non-B subtypes increased from 1.5% in 2000-2002 to 7.2% in 2003-2006 and to 11.4% in 2007-2010 (p = 0.04). Chronic hepatitis B and C were found, respectively, in 4.2% and 8.3% of the study population. While the prevalence of chronic hepatitis B has remained fairly stable over time across distinct populations, the rate of chronic HCV infection has experienced a significant decline, mainly in native Spaniards as a result of a reduction in intravenous drug use. In summary, the prevalence of HIV-1 non-B subtypes is rising in newly diagnosed HIV-1 individuals in Spain, including the native population. In contrast, the rate of HBV coinfection remains unchanged and the rate of HCV coinfection has declined.
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Affiliation(s)
- Ana Treviño
- Infectious Diseases Department, Hospital Carlos III, Madrid, Spain
| | - Vincent Soriano
- Infectious Diseases Department, Hospital Carlos III, Madrid, Spain
| | | | - Miguel Arredondo
- Infectious Diseases Department, Hospital Carlos III, Madrid, Spain
| | - Pablo Rivas
- Infectious Diseases Department, Hospital Carlos III, Madrid, Spain
| | | | - Patricia Parra
- Infectious Diseases Department, Hospital Carlos III, Madrid, Spain
| | | | - Lourdes Anta
- Infectious Diseases Department, Hospital Carlos III, Madrid, Spain
| | - Sabino Puente
- Infectious Diseases Department, Hospital Carlos III, Madrid, Spain
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Abstract
OBJECTIVES To describe the frequency and risk factors of non-B HIV-1 subtypes in men who have sex with men (MSM) in the UK. DESIGN Observational study. METHODS MSM diagnosed with HIV-1 infection from 1980-2007, with HIV genotype held in the UK HIV Drug Resistance Database were identified. Protease and reverse transcriptase sequences were collected and viral clade determined using the REGA algorithm. Associations between demographic variables and subtype were analysed using logistic regression. RESULTS The prevalence of non-B HIV-1 infection amongst MSM in the UK was 5.4% (437/8058). In the UK this increased with year of diagnosis from pre1996 to 2002, and has subsequently remained relatively stable at around 7-9% after 2002, with a recent increase in 2007 to 13%. Multivariate analysis showed that acquisition of non-B HIV-1 infection was independently associated with later year of HIV diagnosis (P < 0.001), black ethnicity (P < 0.001) and non-European country of birth (P = 0.01). Age was also associated with subtype with individuals aged 25-39 years being less likely to have non-B virus than those aged less than 25 years (P = 0.01). Restricting the analysis to white men born in the UK, the association between subtype and year of diagnosis remained statistically significant (P < 0.001), as did the association with age (P < 0.001). DISCUSSION The number of MSM in the UK infected with non-B clade HIV-1 is increasing, suggesting that the sociodemographic boundaries between HIV-1 viral subtypes globally are diminishing. Should viral subtypes be relevant to clinical disease progression or vaccine design, the changing pattern of distribution will need to be taken into account.
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Evolution of HIV-1 in India. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2010; 21:3-7. [PMID: 23637473 DOI: 10.1007/s13337-010-0001-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 05/23/2010] [Indexed: 10/19/2022]
Abstract
Nearly 25 years after the discovery of the human immunodeficiency virus type 1 (HIV-1) effective control of the AIDS pandemic remains elusive. At the root of this challenge is the evolution of this virus to elude immune control. Error-prone nature of replication and retro-transcription is the hallmark of this virus. This fidelity of replication in HIV-1 is due to the absence of proof-reading/repair and post-replicative error correction mechanisms that normally operate during replication of DNA viruses. Advances in sequencing technology and expanded disease surveillance have allowed researchers to characterize the variation in HIV-1 around the world and within individual patient overtime. Although HIV-1 has been classified into distinct subtypes, the classification does not reflect dynamic genetic evolution of HIV-1 through which new strains are constantly emerging. The resultant viral diversity has implications for differential rates of disease progression in different geographical areas, differential responses to antiretroviral therapy (including the development of resistance), and vaccine development. In this review evolution of HIV-1 in India is discussed.
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High genetic diversity of HIV-1 viruses in Macao, China. J Infect 2010; 61:164-72. [DOI: 10.1016/j.jinf.2010.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Revised: 02/06/2010] [Accepted: 04/30/2010] [Indexed: 11/21/2022]
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Lam TTY, Hon CC, Tang JW. Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Crit Rev Clin Lab Sci 2010; 47:5-49. [PMID: 20367503 DOI: 10.3109/10408361003633318] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
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21
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de Oliveira T, Pillay D, Gifford RJ. The HIV-1 subtype C epidemic in South America is linked to the United Kingdom. PLoS One 2010; 5:e9311. [PMID: 20174561 PMCID: PMC2824804 DOI: 10.1371/journal.pone.0009311] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 01/29/2010] [Indexed: 12/28/2022] Open
Abstract
Background The global spread of HIV-1 has been accompanied by the emergence of genetically distinct viral strains. Over the past two decades subtype C viruses, which predominate in Southern and Eastern Africa, have spread rapidly throughout parts of South America. Phylogenetic studies indicate that subtype C viruses were introduced to South America through a single founder event that occurred in Southern Brazil. However, the external route via which subtype C viruses spread to the South American continent has remained unclear. Methodology/Principal Findings We used automated genotyping to screen 8,309 HIV-1 subtype C pol gene sequences sampled within the UK for isolates genetically linked to the subtype C epidemic in South America. Maximum likelihood and Bayesian approaches were used to explore the phylogenetic relationships between 54 sequences identified in this screen, and a set of globally sampled subtype C reference sequences. Phylogenetic trees disclosed a robustly supported relationship between sequences from Brazil, the UK and East Africa. A monophyletic cluster comprised exclusively of sequences from the UK and Brazil was identified and dated to approximately the early 1980s using a Bayesian coalescent-based method. A sub-cluster of 27 sequences isolated from homosexual men of UK origin was also identified and dated to the early 1990s. Conclusions Phylogenetic, demographic and temporal data support the conclusion that the UK was a crucial staging post in the spread of subtype C from East Africa to South America. This unexpected finding demonstrates the role of diffuse international networks in the global spread of HIV-1 infection, and the utility of globally sampled viral sequence data in revealing these networks. Additionally, we show that subtype C viruses are spreading within the UK amongst men who have sex with men.
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Affiliation(s)
- Tulio de Oliveira
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Deenan Pillay
- Department of Infection, University College London, London, United Kingdom
- Centres for Infection, Health Protection Agency, Colindale, United Kingdom
| | - Robert J. Gifford
- Zoology Department, University of Oxford, Oxford, United Kingdom
- * E-mail:
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22
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HIV Genetic Diversity and Drug Resistance. Viruses 2010; 2:503-531. [PMID: 21994646 PMCID: PMC3185604 DOI: 10.3390/v2020503] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 12/11/2009] [Accepted: 02/01/2010] [Indexed: 02/07/2023] Open
Abstract
Most of the current knowledge on antiretroviral (ARV) drug development and resistance is based on the study of subtype B of HIV-1, which only accounts for 10% of the worldwide HIV infections. Cumulative evidence has emerged that different HIV types, groups and subtypes harbor distinct biological properties, including the response and susceptibility to ARV. Recent laboratory and clinical data highlighting such disparities are summarized in this review. Variations in drug susceptibility, in the emergence and selection of specific drug resistance mutations, in viral replicative capacity and in the dynamics of resistance acquisition under ARV selective pressure are discussed. Clinical responses to ARV therapy and associated confounding factors are also analyzed in the context of infections by distinct HIV genetic variants.
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Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A, Leigh Brown AJ. Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog 2009; 5:e1000590. [PMID: 19779560 PMCID: PMC2742734 DOI: 10.1371/journal.ppat.1000590] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 08/25/2009] [Indexed: 11/25/2022] Open
Abstract
The heterosexual risk group has become the largest HIV infected group in the United Kingdom during the last 10 years, but little is known of the network structure and dynamics of viral transmission in this group. The overwhelming majority of UK heterosexual infections are of non-B HIV subtypes, indicating viruses originating among immigrants from sub-Saharan Africa. The high rate of HIV evolution, combined with the availability of a very high density sample of viral sequences from routine clinical care has allowed the phylodynamics of the epidemic to be investigated for the first time. Sequences of the viral protease and partial reverse transcriptase coding regions from 11,071 patients infected with HIV of non-B subtypes were studied. Of these, 2774 were closely linked to at least one other sequence by nucleotide distance. Including the closest sequences from the global HIV database identified 296 individuals that were in UK-based groups of 3 or more individuals. There were a total of 8 UK-based clusters of 10 or more, comprising 143/2774 (5%) individuals, much lower than the figure of 25% obtained earlier for men who have sex with men (MSM). Sample dates were incorporated into relaxed clock phylogenetic analyses to estimate the dates of internal nodes. From the resulting time-resolved phylogenies, the internode lengths, used as estimates of maximum transmission intervals, had a median of 27 months overall, over twice as long as obtained for MSM (14 months), with only 2% of transmissions occurring in the first 6 months after infection. This phylodynamic analysis of non-B subtype HIV sequences representing over 40% of the estimated UK HIV-infected heterosexual population has revealed heterosexual HIV transmission in the UK is clustered, but on average in smaller groups and is transmitted with slower dynamics than among MSM. More effective intervention to restrict the epidemic may therefore be feasible, given effective diagnosis programmes. Since 1995, HIV among heterosexuals in the UK increased to the point where the total number of heterosexuals infected with HIV, predominantly of non-B subtypes, exceeds the number of HIV-positive homosexual men. To understand the dynamics of this epidemic, we have applied the novel technique of phylodynamics to the analysis of viral sequences taken in the course of routine clinical care from approximately 40% of the HIV-infected heterosexual population in the UK. Phylodynamics reconstructs the pattern of viral sequence divergence in time, revealing the size of transmission clusters and the dynamics of transmission within them. Of 11,071 patients studied, 296 were linked to at least two others in the UK. There were 8 clusters comprising 10 or more individuals among these, yielding a total of 143 or 5% of all individuals with links, much lower than seen earlier among homosexual men (25%). Viral transmissions within clusters also occurred less rapidly, only 2% being dated to the first 6 months of infection, compared to 25% among homosexual men. Overall, transmission clusters exist in the UK heterosexual HIV epidemic but they are generally smaller than among homosexuals; onward transmission occurs less rapidly and is not associated with acute HIV infection.
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Affiliation(s)
- Gareth J. Hughes
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Esther Fearnhill
- Medical Research Council Clinical Trials Unit, London, United Kingdom
| | - David Dunn
- Medical Research Council Clinical Trials Unit, London, United Kingdom
| | - Samantha J. Lycett
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Andrew J. Leigh Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- * E-mail:
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Piñeiro Pérez R, Mellado Peña MJ, Holguín A, Cilleruelo MJ, García Hortelano M, Villota J, Martín Fontelos P. [HIV-1 genetic variability in non Spaniard infected children]. An Pediatr (Barc) 2009; 70:20-6. [PMID: 19174115 DOI: 10.1016/j.anpedi.2008.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 07/22/2008] [Accepted: 08/01/2008] [Indexed: 10/20/2022] Open
Abstract
INTRODUCTION The prevalence of HIV-1 non-B subtypes (HIV-NBS) is increasing in Europe, because of emigration from countries where genetic variants are endemic. Although HIV-NBS could have a different clinical evolution and could respond differently to antiretrovirals (AR) than B-subtypes, these variant's response remain undocumented. AIMS To identify HIV-1 genetic variants and to determine clinical evolution in a non-Spaniard children infected with HIV-1. PATIENTS AND METHOD Children with HIV-1 infection from endemic countries were tested for HIV-1 subtypes between 1-1-1988 and 31-12-2006. Twelve children less than 18 years old and born abroad were selected. RESULTS HIV-NBS were isolated in 5 children (42%): CRF2_AG recombinant in 3 cases (Equatorial Guinea), Subtype C in one (Equatorial Guinea) and CRF13_cpx in last one (India). DISCUSSION Because of the increasing frequency of patients with HIV-NBS and their unknown long-term evolution, all children from endemic countries should be tested for HIV subtypes. We believe new studies with more patients during longer times could reveal differences in these patient's clinical, immunological and virological evolution.
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Yebra G, Rivas P, Herrero MD, López M, de Mulder M, Puente S, Ramírez-Olivencia G, Soriano V, Holguín A. Clinical differences and viral diversity between newly HIV type 1-diagnosed African and non-African patients in Spain (2005-2007). AIDS Res Hum Retroviruses 2009; 25:37-44. [PMID: 19182919 DOI: 10.1089/aid.2008.0134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract The diagnosis of HIV-1 is increasing in African-born persons residing in Europe. They present a high prevalence of HIV-1 non-B variant infections and of parasitic infections, both of which are infrequent in Western countries. Immigration favors their presence in nonendemic countries. In this study, all newly HIV-diagnosed individuals at an HIV/AIDS and Tropical Medicine reference center in Madrid from 2005 through 2007 were retrospectively studied. HIV-1 subtyping was performed in gag, pol, and gp41 coding regions by phylogenetic analyses. The presence of other pathogens was also evaluated. Furthermore, all HIV-1-infected Africans were screened for parasitic infections. Newly diagnosed HIV-1 subjects included 90 sub-Saharan Africans and 188 non-Africans (116 Spaniards, 13 other Europeans, and 59 Latin Americans). Significantly higher numbers of HIV-1-infected Africans than non-Africans were females, acquired HIV-1 by heterosexual contact, and presented a more advanced clinical CDC stage and criteria for starting antiretroviral therapy in the first clinical visit. They predominantly carried non-B subtype infections, mainly intersubtype recombinants. Half of HIV-1-infected Africans had parasitic infections. CD4(+) T cell counts were lower among Africans than Europeans at the time of HIV-1 diagnosis. At 12 months of follow-up after starting antiretroviral treatment, a significantly lower proportion of Africans than non-Africans achieved undetectable viremia due to their higher loss to follow-up. However, CD4(+) T cell recovery and virological failure rates were similar. Therefore, the profile of African HIV-1-infected immigrants varies widely with respect to Spanish HIV-infected individuals. More advanced immunodeficiency and the coexistence of parasitic diseases and infections with a large diversity of HIV-1 non-B and recombinant variants are expected.
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Affiliation(s)
- Gonzalo Yebra
- HIV-1 Molecular Epidemiology Laboratory, Service of Microbiology, Hospital Ramón y Cajal and CIBER-ESP, Madrid, Spain
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | - Pablo Rivas
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | | | - Marisa López
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | - Miguel de Mulder
- HIV-1 Molecular Epidemiology Laboratory, Service of Microbiology, Hospital Ramón y Cajal and CIBER-ESP, Madrid, Spain
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | - Sabino Puente
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | | | - Vincent Soriano
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | - Africa Holguín
- HIV-1 Molecular Epidemiology Laboratory, Service of Microbiology, Hospital Ramón y Cajal and CIBER-ESP, Madrid, Spain
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
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Fromme BJ, Coetsee M, Van Der Watt P, Chan MC, Sperling KM, Katz AA, Flanagan CA. High-affinity binding of southern African HIV type 1 subtype C envelope protein, gp120, to the CCR5 coreceptor. AIDS Res Hum Retroviruses 2008; 24:1527-36. [PMID: 19018669 DOI: 10.1089/aid.2008.0105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 subtype C is the fastest spreading subtype worldwide and predominantly uses the CCR5 coreceptor, showing minimal transition to the X4 phenotype. This raises the possibility that envelope proteins of HIV-1 subtype C have structural features that favor interaction with CCR5. Preference for CCR5 could arise from enhanced affinity of HIV-1 subtype C for CCR5. To test this, we have characterized the interaction of gp120 envelope proteins from HIV-1 subtype C clones with CD4 and CCR5. Recombinant gp120 proteins from isolates of HIV-1 subtypes B and C were expressed, purified, and assessed in a CD4 binding assay and a CCR5 chemokine competition binding assay. All gp120 proteins bound to CD4-expressing cells, except one, 97ZA347ts, which had Arg substituted for the Cys239 in the conserved C2 loop. Reconstitution of Cys239, using site-directed mutagenesis, restored CD4 binding, while introducing Arg or Ser into position 239 of the functional Du151 gp120 protein abrogated CD4 binding. This shows that the Cys228-Cys239 disulfide bond of gp120 is required for high-affinity binding to CD4. Recombinant gp120 proteins from two HIV-1 subtype B clones bound CCR5 in the presence of CD4, while gp120 from the X4-tropic, HxB2, clone did not bind CCR5. gp120 from two functional HIV-1 subtype C clones, Du151 and MOLE1, bound CCR5 with high affinity in the presence of CD4 and Du151 showed significant CCR5 binding in the absence of CD4. A gp120 from a nonfunctional subtype C clone had lower affinity for CCR5. These results indicate that HIV-1 subtype C proteins have high affinity for CCR5 with variable dependence on CD4.
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Affiliation(s)
- Bernhard J. Fromme
- MRC/UCT Research Group for Receptor Biology, University of Cape Town, Cape Town, South Africa
| | - Marla Coetsee
- MRC/UCT Research Group for Receptor Biology, University of Cape Town, Cape Town, South Africa
| | - Pauline Van Der Watt
- MRC/UCT Research Group for Receptor Biology, University of Cape Town, Cape Town, South Africa
| | - Mei-Chi Chan
- MRC/UCT Research Group for Receptor Biology, University of Cape Town, Cape Town, South Africa
| | - Karin M. Sperling
- MRC/UCT Research Group for Receptor Biology, University of Cape Town, Cape Town, South Africa
| | - Arieh A. Katz
- MRC/UCT Research Group for Receptor Biology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Colleen A. Flanagan
- MRC/UCT Research Group for Receptor Biology, University of Cape Town, Cape Town, South Africa
- School of Physiology, University of the Witwatersrand, Parktown, South Africa
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Holguín A, López M, Molinero M, Soriano V. Performance of three commercial viral load assays, Versant human immunodeficiency virus type 1 (HIV-1) RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2, testing HIV-1 non-B subtypes and recombinant variants. J Clin Microbiol 2008; 46:2918-23. [PMID: 18596140 PMCID: PMC2546710 DOI: 10.1128/jcm.02414-07] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 04/21/2008] [Accepted: 06/14/2008] [Indexed: 02/06/2023] Open
Abstract
Monitoring antiretroviral therapy requires that human immunodeficiency virus type 1 (HIV-1) viremia assays are applicable to all distinct variants. This study evaluates the performance of three commercial viral load assays-Versant HIV-1 RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2-in testing 83 plasma specimens from patients carrying HIV-1 non-B subtypes and recombinants previously defined by phylogenetic analysis of the pol gene. All 28 specimens from patients under treatment presented viremia values below the detection limit with the three methods. In the remaining 55 specimens from naive individuals viremia could not be detected in 32.7, 20, and 14.6% using the NucliSens, Versant, or TaqMan tests, respectively, suggesting potential viral load underestimation of some samples by all techniques. Only 32 (58.2%) samples from naive subjects were quantified by the three methods; the NucliSens test provided the highest HIV RNA values (mean, 4.87 log copies/ml), and the Versant test provided the lowest (mean, 4.16 log copies/ml). Viremia differences of greater than 1 log were seen in 8 (14.5%) of 55 specimens, occurring in 10.9, 7.3, and 5.4%, respectively, of the specimens in comparisons of Versant versus NucliSens, Versant versus TaqMan, and TaqMan versus NucliSens. Differences greater than 0.5 log, considered significant for clinicians, occurred in 45.5, 27.3, and 29% when the same assays were compared. Some HIV-1 strains, such as subtype G and CRF02_AG, showed more discrepancies in distinct quantification methods than others. In summary, an adequate design of primers and probes is needed for optimal quantitation of plasma HIV-RNA in non-B subtypes. Our data emphasize the need to use the same method for monitoring patients on therapy and also the convenience of HIV-1 subtyping.
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Affiliation(s)
- Africa Holguín
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
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Everett DB, Weiss HA, Changalucha J, Anemona A, Chirwa T, Ross DA, Watson-Jones D, Parry JV, Hayes R, Mabey DC. Low specificity of the Murex fourth-generation HIV enzyme immunoassay in Tanzanian adolescents. Trop Med Int Health 2007; 12:1323-6. [DOI: 10.1111/j.1365-3156.2007.01933.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Siddappa NB, Kashi VP, Venkatramanan M, Balasiddaiah A, Jayasuryan N, Mahadevan A, Desai A, Satish KS, Shankar SK, Ravi V, Ranga U. Gene expression analysis from human immunodeficiency virus type 1 subtype C promoter and construction of bicistronic reporter vectors. AIDS Res Hum Retroviruses 2007; 23:1268-78. [PMID: 17961115 DOI: 10.1089/aid.2006.0305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report the cloning and sequence analysis of the long terminal repeat (LTR) of several primary HIV-1 subtype C strains of India. Phylogenetically, all the LTRs and the paired env sequences clustered with subtype C reference strains. The LTRs demonstrated extensive polymorphism in the transcription factor binding sites (TFBS) within the enhancer and the modulator regions. We generated reporter vectors under the control of a select subset of the subtype C LTRs. The reporter vectors are distinguished by the simultaneous expression of two independent reporter genes, secreted alkaline phosphatase (SEAP) and enhanced green fluorescence protein (EGFP), in response to Tat. Expression of EGFP was facilitated by engineering an internal ribosome entry site (IRES) into the expression cassette. Although subtype C strains cause a large majority of the global infections, and important differences in the transcription factor binding sites have been identified in the subtype C promoter, few reporter vectors containing subtype C-LTR have been described. We analyzed gene expression from the C-LTR reporter vectors in different cell lines under diverse experimental conditions and compared it to the B-LTR reporter vector. The reporter vectors were responsive to Tat derived from diverse viral subtypes. Furthermore, a positive correlation was observed between the expression of the reporter genes and the viral structural protein p24 when the cells were infected with viral molecular clones. The LTR reporters we developed could be of significant use in the study of viral transactivation, in the evaluation of biological properties of viral subtypes, and in the screening for antiviral inhibitors.
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Affiliation(s)
- Nagadenahalli Byrareddy Siddappa
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Venkatesh Prasanna Kashi
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Mohanram Venkatramanan
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Center for Infectious Medicine, Karolinska Institutet, Department of Medicine Karolinska Huddinge, Stockholm, Sweden
| | - Anangi Balasiddaiah
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Anita Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | | | - Susarla K. Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Vasanthapuram Ravi
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Udaykumar Ranga
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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Cortina-Borja M, Williams D, Cubitt WD, Tookey PA, Newell ML, Peckham CS. HIV-1 subtypes in pregnant women in the UK. Int J STD AIDS 2007; 18:160-2. [PMID: 17362546 DOI: 10.1258/095646207780132352] [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: 11/18/2022]
Abstract
We analyse the distribution of HIV-1 subtypes in HIV-1-seropositive samples from 333,270 residual neonatal dried blood spot samples tested for routine newborn screening tests in the UK between July 1999 and December 2002. Of the 813 antibody-positive samples shown to contain passively acquired, maternal HIV-1 for which subtyping was attempted, 333 (41%) could not be subtyped due to cross-reactivity or low values of the assay results, and 480 (59%) were classified as B (35, 7.3%) or non-B (445, 92.7%). The proportions of subtyped B samples differed significantly (P=0.004) between those from neonates whose mothers were born in the UK (21.4%) and those from neonates whose mothers were known to be born abroad (7%). Using a serological approach to establish viral serotype, we document the distribution of HIV-1 subtypes in infected pregnant women in the UK.
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Affiliation(s)
- M Cortina-Borja
- Centre for Paediatric Epidemiology and Biostatistics, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK.
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Swanson P, Huang S, Abravaya K, de Mendoza C, Soriano V, Devare SG, Hackett J. Evaluation of performance across the dynamic range of the Abbott RealTime™ HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses. J Virol Methods 2007; 141:49-57. [PMID: 17184853 DOI: 10.1016/j.jviromet.2006.11.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 11/14/2006] [Accepted: 11/20/2006] [Indexed: 12/22/2022]
Abstract
Performance of the Abbott m2000 instrument system and the Abbott RealTime HIV-1 assay was evaluated using a panel of 37 group M (subtypes A-D, F, G, CRF01_AE, CRF02_AG and unique recombinant forms) and 2 group O virus isolates. Testing was performed on 273 sample dilutions and compared to VERSANT HIV-1 RNA 3.0 (bDNA) and AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) test results. RealTime HIV-1, bDNA, and Monitor v1.5 tests quantified 87%, 78%, and 81% of samples, respectively. RealTime HIV-1 detected an additional 31 samples at < 40 copies/mL. For group M, RealTime HIV-1 dilution profiles and viral loads were highly correlated with bDNA and Monitor v1.5 values; 87% and 89% of values were within 0.5 log(10) copies/mL. In contrast, the group O viruses were not detected by Monitor v1.5 and were substantially underquantified by approximately 2 log(10) copies/mL in bDNA relative to the RealTime HIV-1 assay. Sequence analysis revealed that RealTime HIV-1 primer/probe binding sites are highly conserved and exhibit fewer nucleotide mismatches relative to Monitor v1.5. The automated m2000 system and RealTime HIV-1 assay offer the advantages of efficient sample processing and throughput with reduced "hands-on" time while providing improved sensitivity, expanded dynamic range and reliable quantification of genetically diverse HIV-1 strains.
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Affiliation(s)
- Priscilla Swanson
- Abbott Diagnostics, AIDS Research and Retrovirus Discovery, D-09NG, Bldg. AP20, 100 Abbott Park Road, Abbott Park, IL 60064-6015, USA
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Chin MPS, Chen J, Nikolaitchik OA, Hu WS. Molecular determinants of HIV-1 intersubtype recombination potential. Virology 2007; 363:437-46. [PMID: 17336363 DOI: 10.1016/j.virol.2007.01.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 01/16/2007] [Accepted: 01/29/2007] [Indexed: 11/19/2022]
Abstract
Sequence differences in the dimerization initiation signal (DIS) affect the rate of recombination between subtype B and subtype C HIV-1. To test the hypothesis that DIS sequences can be used to predict intersubtype recombination potentials, we measured the recombination rate between CRF01_A/E (AE) and B, which contain mismatches in the DIS, and between AE and C, which have an identical DIS. Compared with the intrasubtype recombination rate, the recombination rate between AE and subtype B virus was 9-fold lower, and the rate between AE and subtype C virus was 2-fold lower. Thus, DIS sequences can be used to predict the recombination potential between HIV-1 subtypes. Further analyses revealed that the 2-fold lower recombination rate between AE and C viruses can be restored to the intrasubtype recombination rate by matching a part of the LTR and a portion of the viral genome. Therefore, the lower intersubtype recombination rate between AE and C is not caused by a given region but is a cumulative effect by more than one region.
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Affiliation(s)
- Mario P S Chin
- HIV Drug Resistance Program, National Cancer Institute, P.O. Box B, Building 535, Room 336, Frederick, MD 21702, USA
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Swanson P, Holzmayer V, Huang S, Hay P, Adebiyi A, Rice P, Abravaya K, Thamm S, Devare SG, Hackett J. Performance of the automated Abbott RealTime™ HIV-1 assay on a genetically diverse panel of specimens from London: Comparison to VERSANT HIV-1 RNA 3.0, AMPLICOR HIV-1 MONITOR v1.5, and LCx® HIV RNA Quantitative assays. J Virol Methods 2006; 137:184-92. [PMID: 16876263 DOI: 10.1016/j.jviromet.2006.06.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 06/06/2006] [Accepted: 06/13/2006] [Indexed: 11/29/2022]
Abstract
Automated RNA extraction and quantitation of HIV-1 by real-time PCR offer potential advantages of efficient sample processing, improved sensitivity, expanded dynamic range and reduced contamination risk. In this study, plasma was collected from 100 HIV-1 infected patients visiting The Courtyard Clinic of St. George's Hospital in London, United Kingdom (UK). Viral loads measured using the automated Abbott RealTime HIV-1 assay (m2000sp sample preparation and m2000rt amplification and detection instruments) were compared to results obtained with Versant HIV-1 RNA 3.0 (bDNA), AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) and LCx HIV RNA Quantitative (LCx HIV) assays. Based on gag p24, pol integrase, and env gp41 sequences, the panel included 26 subtype A, 20 B, 27 C, 10 D, 1 CRF01_AE, 3 CRF02_AG and 13 recombinant viruses. RealTime HIV-1, bDNA, Monitor v1.5 and LCx HIV quantitated 82, 74, 82, and 83% of samples, respectively, with 82, 71, 69 and 80 of the 100 samples measured within the dynamic ranges. Viral loads were highly correlated with 99% of values within 1 log(10) copies/ml between tests. The automated m2000 system and RealTime HIV-1 assay can increase laboratory throughput, enhance overall efficiency and reduce operator-associated errors while providing reliable quantitation of genetically diverse strains of HIV-1.
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Affiliation(s)
- Priscilla Swanson
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, D-09NG, Bldg. AP20, 100 Abbott Park Road, Abbott Park, IL 60064-6015, USA
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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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Cowan FF, Pascoe SJS, Barlow KL, Langhaug LF, Jaffar S, Hargrove JW, Robinson NJ, Latif AS, Bassett MT, Wilson D, Brown DWG, Hayes RJ. Association of genital shedding of herpes simplex virus type 2 and HIV-1 among sex workers in rural Zimbabwe. AIDS 2006; 20:261-7. [PMID: 16511420 DOI: 10.1097/01.aids.0000198086.39831.4a] [Citation(s) in RCA: 31] [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
INTRODUCTION Herpes simplex virus type 2 (HSV-2) facilitates sexual acquisition of HIV-1 but data on transmission are less clear. In this study the interaction between genital shedding of HIV-1 and HSV-2 was explored among Zimbabwean sex workers. METHODS Women (n = 214) were interviewed about genital symptoms. Blood samples were analysed for HIV-1 and HSV-2 antibodies, HIV-1 plasma viral load (PVL) and CD4 lymphocyte count and genital swabs for detection of HIV-1 and HSV-2 genital shedding, Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis, and a cervico-vaginal lavage (CVL) for quantitative measurement of HIV-1 shedding. Shedding analyses were undertaken on women co-infected with HSV-2 and HIV-1. RESULTS A total of 124 women were co-infected with HIV-1 and HSV-2; 58 were infected with HSV-2 alone. Most HIV-1-infected women were co-infected with HSV-2 (95.4%). Genital HIV-1 shedding was detected in 84.3% of co-infected women and was associated with low CD4 cell count and high PVL but not with reported symptoms of genital herpes or genital shedding of HSV-2. There was no difference in HIV-1 shedding among women shedding HSV-2 (79.3%) and women not shedding HSV-2 (83.2%) (P = 0.64). The adjusted odds ratio for HIV-1 shedding between HSV-2 shedders and non-shedders was 0.8 [95% confidence interval (CI), 0.2-3.3]. HIV-1 PVL(log10) and CVL viral load(log10) were correlated (r = 0.38; 95%CI, 0.2-0.5). After adjusting for PVL, genital symptoms and age, HSV-2 shedding had no effect on CVL viral load (P = 0.13). CONCLUSION Rate and quantity of HIV-1 genital shedding do not appear to be altered by presence of HSV-2 genital shedding.
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Affiliation(s)
- Frances F Cowan
- Royal Free and University College Medical School, London, UK.
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Kijak GH, McCutchan FE. HIV diversity, molecular epidemiology, and the role of recombination. Curr Infect Dis Rep 2005; 7:480-8. [PMID: 16225787 DOI: 10.1007/s11908-005-0051-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The magnitude of the HIV pandemic and its extensive genetic variation may earn it a unique place among infectious agents. A high mutation rate and a rampant recombination are driving HIV's evolution. Nine subtypes and a variety of recombinant forms of HIV now exist. The source of recombinant forms is the multiple infection of target cells, which becomes highly significant when individuals become infected with two or more divergent strains. In the current paper, we re-examine the role of dual infection and recombination in the generation of HIV-1 diversity, both in individuals and on a global scale. The current molecular epidemiology of HIV-1 is reviewed, emphasizing the latest reports from regional epidemics.
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Affiliation(s)
- Gustavo H Kijak
- US Military HIV Research Program, Henry M. Jackson Foundation, 1600 East Gude Drive, Rockville, MD 20850, USA.
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Saunders NA, Alexander S, Tatt I. env Gene typing of human immunodeficiency virus type 1 strains on electronic microarrays. J Clin Microbiol 2005; 43:1910-6. [PMID: 15815017 PMCID: PMC1081343 DOI: 10.1128/jcm.43.4.1910-1916.2005] [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: 11/20/2022] Open
Abstract
The NanoChip system was used for subtyping human immunodeficiency virus type 1 (HIV-1) strains using probes complementary to the V1 region of the env gene. Probes for six subtypes (A to D, F, and G) and two circulating recombinant forms (AG and AE) of HIV-1 group M were included. The specificity of these oligonucleotides had been evaluated previously in a DNA enzyme immunoassay. Samples from 112 patient sera were used as templates in a nested reverse transcription-PCR to produce amplicons that were applied to the array. The array was then hybridized successively to pairs of oligonucleotide probes. The strains were assigned a subtype on the basis of their probe hybridization patterns. One strain gave a contradictory pattern and was designated as untypeable by the NanoChip assay. Eighty-eight strains gave hybridization patterns that allowed a correct subtype designation to be made by the NanoChip assay compared to either the sequence or the heteroduplex mobility assay (HMA)-determined subtypes. Thirteen strains that reacted with the subtype A probe (SA2) were incorrectly assigned to subtype A, or to one of the related circulating recombinant types (AE or AG), on the basis of reactions with probe SAE1 or SAG1. The results indicate that these oligonucleotides have relatively low specificities. The probe subtypes of three strains matched the subtypes determined for the gag and pol genes but not the env gene, suggesting that a recombination event may have occurred within the env gene. Overall, the NanoChip assay gave results comparable to those for HMA and sequencing and provides a convenient and cost-effective means by which to subtype HIV-1.
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Affiliation(s)
- N A Saunders
- Genomics Proteomics Bioinformatics Unit, Centre for Infections, HPA (Colindale), 61 Colindale Ave., London NW9 5HT, UK.
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Bocket L, Cheret A, Deuffic-Burban S, Choisy P, Gerard Y, de la Tribonnière X, Viget N, Ajana F, Goffard A, Barin F, Mouton Y, Yazdanpanah Y. Impact of Human Immunodeficiency Virus Type 1 Subtype on First-Line Antiretroviral Therapy Effectiveness. Antivir Ther 2005. [DOI: 10.1177/135965350501000206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Objective The effectiveness of antiretroviral treatment (ART) was compared in 416 naive patients from a French clinical cohort infected with B and non-B HIV-1 subtypes. Methods Time to HIV viral load (VL) undetectability was calculated for each subtype group. Three other parameters were estimated 3, 6 and 12 months after enrolment: clinical progression (that is, AIDS-defining events or death), changes in CD4 cell counts from baseline and proportion of patients achieving an undetectable VL (<400 HIV-RNA copies/ml). Results In this cohort, 317 patients (76%) were infected with a B subtype and 99 (24%) with a non-B subtype. Median time to VL undetectability was similar in the B subtype group [147 days, 95% confidence interval (CI) 119–165] and non-B subtype group (168 days, 95% CI: 105–234; P=0.16). After adjusting for AIDS-defining events at enrolment, baseline CD4 cell counts and VL, and for the treatment on which patients were initiated, no association was found between HIV subtypes and time to VL undetectability (B subtype vs non-B subtype: hazard ratio=0.80, 95% CI: 0.62–1.02, P=0.07). In the 3, 6 and 12 months after enrolment, subtype had no impact on clinical progression, CD4 cell count or VL responses to ART. This suggests that B and non-B subtypes do not affect first-line therapy efficacy, which is encouraging in view of the worldwide spread of non-B HIV-1 subtypes and the increasing availability of ART in developing countries. However, in this study we did not take into account individual non-B subtype species, therefore further studies should be designed to evaluate the efficacy of these regimens in patients with particular non-B subtypes.
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Affiliation(s)
- Laurence Bocket
- Virology Department, Centre Hospitalier Universitaire de Lille, France
| | - Antoine Cheret
- Infectious Diseases Department, Centre Hospitalier de Tourcoing, France
| | | | - Philippe Choisy
- Infectious Diseases Department, Centre Hospitalier de Tourcoing, France
| | - Yann Gerard
- Infectious Diseases Department, Centre Hospitalier de Tourcoing, France
| | | | - Nathalie Viget
- Infectious Diseases Department, Centre Hospitalier de Tourcoing, France
| | - Faïzo Ajana
- Infectious Diseases Department, Centre Hospitalier de Tourcoing, France
| | - Anne Goffard
- Virology Department, Centre Hospitalier Universitaire de Lille, France
| | - Francis Barin
- Virology Department, CNR du VIH, CHU Bretonneau, Tours, France
| | - Yves Mouton
- Infectious Diseases Department, Centre Hospitalier de Tourcoing, France
| | - Yazdan Yazdanpanah
- Infectious Diseases Department, Centre Hospitalier de Tourcoing, France
- CRESGE-LABORES CNRS URA 362, Lille, France
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