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Nanfack AJ, Ambada Ndzengue GE, Fokam J, Ka'e AC, Sonela N, Kenou L, Tsoptio M, Sagnia B, Elong E, Beloumou G, Perno CF, Colizzi V, Ndjolo A. Characterization of the Viral Reservoirs Among HIV-1 Non-B Vertically Infected Adolescents Receiving Antiretroviral Therapy: Protocol for an Observational and Comparative Study in Cameroon. JMIR Res Protoc 2022; 11:e41473. [PMID: 36449339 PMCID: PMC9752448 DOI: 10.2196/41473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Antiretroviral therapy (ART) can bring HIV-1 levels in blood plasma to the undetectable level and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, ART is not curative and must be taken for life, because within a few weeks of treatment cessation, HIV viremia rebounds in most patients except for rare elite or posttreatment controllers of viremia. The primary source of this rebound is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of the resting memory cluster of differentiation 4 (CD4+) T cells. To achieve a cure for HIV, understanding the cell reservoir environment is of paramount importance. The size and nature of the viral reservoir might vary according to the timing of therapy, therapeutic response, ART duration, and immune response. The mechanisms of reservoir maintenance generally depend on the levels/type of immune recognition; in addition, the dynamics of viral persistence are different between pediatric and adult populations. This difference could become more evident as children grow toward adolescence. OBJECTIVE We aim to characterize the HIV reservoirs and their variability as per the virological and immunological profiles of HIV-1 non-B vertically infected adolescents receiving ART in Cameroon during the Adolescents' Viral Reservoirs study to provide accurate and reliable data for HIV cure research. METHODS This study will involve HIV-1 non-B vertically infected adolescents selected from an existing cohort in our institution. Blood samples will be collected for analyzing immunological/virological profiles, including CD4/CD8 count, plasma viral load, immune activation/inflammatory markers, genotyping, and quantification of HIV-1 viral reservoirs. We will equally recruit an age-matched group of HIV-negative adolescents as control for immunological profiling. RESULTS This study received funding in November 2021 and was approved by the national institutional review board in December 2021. Sample collection will start in November 2022, and the study will last for 18 months. The HIV-1 sequences generated will provide information on the circulating HIV-1 subtypes to guide the selection of the most appropriate ART for the participants. The levels of immune biomarkers will help determine the immune profile and help identify factors driving persistent immune activation/inflammation in HIV-infected adolescents compared to those in HIV-uninfected adolescents. Analysis of the virological and immunological parameters in addition to the HIV-1 reservoir size will shed light on the characteristics of the viral reservoir in adolescents with HIV-1 non-B infection. CONCLUSIONS Our findings will help in advancing the knowledge on HIV reservoirs, in terms of size and genetic variability in adolescents living with HIV. Such evidence will also help in understanding the effects of ART timing and duration on the size of the reservoirs among adolescents living with HIV-a unique population from whom the findings generated will largely contribute to designing functional cure strategies. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) PRR1-10.2196/41473.
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Affiliation(s)
| | - Georgia Elna Ambada Ndzengue
- International Reference Center Chantal Biya, Yaounde, Cameroon
- Department of Animal Biology and Physiology, University of Yaounde, Yaounde, Cameroon
| | - Joseph Fokam
- International Reference Center Chantal Biya, Yaounde, Cameroon
- Faculty of Health Science, University of Buea, Buea, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde, Cameroon
| | - Aude Christelle Ka'e
- International Reference Center Chantal Biya, Yaounde, Cameroon
- Department of Immunology, University of Rome Tor Vergata, Rome, Italy
| | - Nelson Sonela
- International Reference Center Chantal Biya, Yaounde, Cameroon
- Medical School, University of KwaZulu-Natal, Durban, South Africa
| | - Leslie Kenou
- International Reference Center Chantal Biya, Yaounde, Cameroon
- Department of Microbiology and Parasitology, Protestant University of Central Africa, Yaounde, Cameroon
| | - Michelle Tsoptio
- International Reference Center Chantal Biya, Yaounde, Cameroon
- Faculty of Medicine and Biomedical Science, University of Dschang, Dschang, Cameroon
| | - Bertrand Sagnia
- International Reference Center Chantal Biya, Yaounde, Cameroon
| | - Elise Elong
- International Reference Center Chantal Biya, Yaounde, Cameroon
| | - Grace Beloumou
- International Reference Center Chantal Biya, Yaounde, Cameroon
| | | | - Vittorio Colizzi
- International Reference Center Chantal Biya, Yaounde, Cameroon
- Department of Immunology, University of Rome Tor Vergata, Rome, Italy
| | - Alexis Ndjolo
- International Reference Center Chantal Biya, Yaounde, Cameroon
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Wang X, Zhang Y, Liu Y, Li H, Jia L, Han J, Li T, Wang X, Li J, Wen H, Li L. Phylogenetic Analysis of Sequences in the HIV Database Revealed Multiple Potential Circulating Recombinant Forms in China. AIDS Res Hum Retroviruses 2021; 37:694-705. [PMID: 33390081 DOI: 10.1089/aid.2020.0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
HIV recombination contributes greatly to its diversity and produces many circulating recombinant forms (CRFs) and unique recombinant forms (URFs). In China, 24 CRFs have been reported to date, and CRFs cause more than 80% of HIV infections. However, the prevalence of CRFs might still be underestimated, as a high level of onward transmission of URFs has been reported. In this study, we analyzed all Chinese pol region (2,253-3,252) sequences in the HIV Database to evaluate potential new CRFs in China. HIV-1 genotypes were verified by the Context-based Modeling for Expeditious Typing (COMET) tool. Maximum-likelihood (ML) trees were constructed based on sequences with unassigned genotypes. Cluster Picker 1.2.1 was used to identify transmission clusters. Meanwhile, a jumping-profile hidden Markov model (jpHMM) was used to perform recombination breakpoint analysis. Beast 1.7.5 was used to estimate the time of the most recent common ancestor of new CRFs. In the HIV databases, CRF01_AE was the most prevalent genetic form in China, accounting for 39.69% of all national infections, followed by CRF07_BC (20.47%), subtype B (17.50%), CRF08_BC (6.60%), subtype C (6.28%), CRF55_01B (2.06%), and other CRFs (1.77%). The URFs were responsible for 5.31% of all infections nationwide. Among URFs, genomes comprising BC, 01BC, 01B, and 01C were dominant. Finally, 17 potential CRFs and 1 novel CRF were identified. BEAST analysis indicates that novel CRF originated around in 2009. The data highlight that more CRFs have been spreading in China. HIV-1 pol sequences that are commonly used to explore drug resistance are helpful for the surveillance of epidemics of different HIV-1 genotypes.
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Affiliation(s)
- Xiaorui Wang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory of Infectious Disease Control and Prevention in Universities of Shandong, Jinan, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory of Infectious Disease Control and Prevention in Universities of Shandong, Jinan, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Genetic characteristics of HIV-1 CRF06_cpx and CRF56_cpx strains isolated in Guangzhou, China. Arch Virol 2021; 166:2853-2857. [PMID: 34373969 DOI: 10.1007/s00705-021-05198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 10/20/2022]
Abstract
Strains of the HIV-1 circulating recombinant forms (CRFs) 06_cpx and 56_cpx were identified for the first time in Guangzhou, China. The nearly full-length genome (NFLG) sequence was amplified, and the PCR products were sequenced by the Sanger method. The CRF06_cpx and CRF56_cpx strains were identified using the Basic Local Alignment Search Tool (BLAST) and confirmed by neighbour-joining (NJ) phylogenetic analysis. Additionally, these strains were found to contain transmitted drug resistance mutations that have little effect on first-line efavirenz (EFV)-based treatment. Genetic analysis of the detailed sequence data will provide more information on the HIV-1 epidemic in China.
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Early HIV infection among persons referred for malaria parasite testing in Nigeria. Arch Virol 2017; 163:439-445. [PMID: 29119359 DOI: 10.1007/s00705-017-3599-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
Persons in the early stages of HIV infection are the major drivers of new infections. These individuals may also develop renal dysfunctions at this time. Nigeria, as other African countries, has one of the highest prevalence of newly diagnosed HIV infections. Despite this, limited information exists on early HIV detection in the continent. This may be related to difficulties in providing early HIV diagnosis and treatment. Patients referred for malaria testing may provide a unique opportunity for early HIV detection. In this study, a method for identifying early HIV-infected individuals was assessed. HIV-1 subtype and renal function biomarkers were also analyzed in these persons. To identify early HIV infection, over a period of 18 months blood samples were collected from persons referred by clinicians for malaria parasite tests in Nigeria. A total of 671 samples were collected and analyzed for HIV antigen/antibody and subtypes. 101 of these samples were categorized into one of four groups: early HIV, chronic HIV, malaria infection and control groups for renal function analysis. 29% of HIV infected individuals were at the early stages of infection. The predominant subtype detected was CRF02_AG (57.14%). The early HIV group had the highest mean serum creatinine (95 µmol/L) and urea (5.7 mmol/L) values across all groups with the difference significant at P < 0.05. There was no significant difference between the circulating subtype and the stage of HIV infection. Our results show the feasibility of screening persons referred for malaria tests for early HIV. This can be used to control new HIV infections in sub-Saharan Africa.
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Foley BT, Leitner T, Paraskevis D, Peeters M. Primate immunodeficiency virus classification and nomenclature: Review. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 46:150-158. [PMID: 27789390 PMCID: PMC5136504 DOI: 10.1016/j.meegid.2016.10.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 12/25/2022]
Abstract
The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. This review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.
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Affiliation(s)
- Brian T Foley
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Dimitrios Paraskevis
- National and Kapodistrian University of Athens, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, Athens, Greece
| | - Martine Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France; IBC, Computational Biology Institute, 34095 Montpellier, France
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Delatorre E, Bello G. Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa. BMC Evol Biol 2016; 16:249. [PMID: 27852214 PMCID: PMC5112642 DOI: 10.1186/s12862-016-0824-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/08/2016] [Indexed: 11/29/2022] Open
Abstract
Background Several HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Here we reconstruct the evolutionary history of some of these complex CRFs (09_cpx, 11_cpx, 13_cpx and 45_cpx) and further investigate the dissemination dynamic of the CRF11_cpx clade by using a Bayesian coalescent-based method. Results The analysis of two HIV-1 datasets comprising 181 pol (36 CRF09_cpx, 116 CRF11_cpx, 20 CRF13_cpx and 9 CRF45_cpx) and 125 env (12 CRF09_cpx, 67 CRF11_cpx, 17 CRF13_cpx and 29 CRF45_cpx) sequences pointed to quite consistent onset dates for CRF09_cpx (~1966: 1958–1979), CRF11_cpx (~1957: 1950–1966) and CRF13_cpx (~1965: 1958–1973) clades; while some divergence was found for the estimated date of origin of CRF45_cpx clade [pol = 1970 (1964–1976); env = 1960 (1952–1969)]. Phylogeographic reconstructions indicate that the HIV-1 CRF11_cpx clade most probably emerged in Cameroon and from there it was first disseminated to the Central Africa Republic and Chad in the early 1970s and to other central and western African countries from the early 1980s onwards. Demographic reconstructions suggest that the CRF11_cpx epidemic grew between 1960 and 1990 with a median exponential growth rate of 0.27 year−1, and stabilized after. Conclusions These results reveal that HIV-1 CRFs_cpx clades have been circulating in Central Africa for a period comparable to other much more prevalent HIV-1 group M lineages. Cameroon was probably the epicenter of dissemination of the CRF11_cpx clade that seems to have experienced a long epidemic growth phase before stabilization. The epidemic growth of the CRF11_cpx clade was roughly comparable to other HIV-1 group M lineages circulating in Central Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0824-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz - FIOCRUZ, Av. Brasil 4365, 21040-360, Rio de Janeiro, RJ, Brazil.
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz - FIOCRUZ, Av. Brasil 4365, 21040-360, Rio de Janeiro, RJ, Brazil
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Heipertz RA, Ayemoba O, Sanders-Buell E, Poltavee K, Pham P, Kijak GH, Lei E, Bose M, Howell S, O'Sullivan AM, Bates A, Cervenka T, Kuroiwa J, Akintunde A, Ibezim O, Alabi A, Okoye O, Manak M, Malia J, Peel S, Maisaka M, Singer D, O’Connell RJ, Robb ML, Kim JH, Michael NL, Njoku O, Tovanabutra S. Significant contribution of subtype G to HIV-1 genetic complexity in Nigeria identified by a newly developed subtyping assay specific for subtype G and CRF02_AG. Medicine (Baltimore) 2016; 95:e4346. [PMID: 27512845 PMCID: PMC4985300 DOI: 10.1097/md.0000000000004346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
While abundant sequence information is available from human immunodeficiency virus type 1 (HIV-1) subtypes A, B, C and CRF01_AE for HIV-1 vaccine design, sequences from West Africa are less represented. We sought to augment our understanding of HIV-1 variants circulating in 6 Nigerian cities as a step to subsequent HIV-1 vaccine development.The G/CRF02_AG multi-region hybridization assay (MHA) was developed to differentiate subtype G, CRF02_AG and their recombinants from other subtypes based on 7 HIV-1 segments. Plasma from 224 HIV-1 infected volunteers enrolled in a cohort examining HIV-1 prevalence, risk factor, and subtype from Makurdi (30), Abuja (18), Enugu (11), Kaduna (12), Tafa (95), and Ojo/Lagos (58) was analyzed using MHA. HIV-1 genomes from 42 samples were sequenced to validate the MHA and fully explore the recombinant structure of G and CRF02_AG variants.The sensitivity and specificity of MHA varied between 73-100% and 90-100%, respectively. The subtype distribution as identified by MHA among 224 samples revealed 38% CRF02_AG, 28% G, and 26% G/CRF02_AG recombinants while 8% remained nontypeable strains. In envelope (env) gp120, 38.84% of the samples reacted to a G probe while 31.25% reacted to a CRF02 (subtype A) probe. Full genome characterization of 42 sequences revealed the complexity of Nigerian HIV-1 variants.CRF02_AG, subtype G, and their recombinants were the major circulating HIV-1 variants in 6 Nigerian cities. High proportions of samples reacted to a G probe in env gp120 confirms that subtype G infections are abundant and should be considered in strategies for global HIV-1 vaccine development.
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Affiliation(s)
- Richard A. Heipertz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Ojor Ayemoba
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Eric Sanders-Buell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Kultida Poltavee
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Phuc Pham
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Gustavo H. Kijak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Esther Lei
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Meera Bose
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Shana Howell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Anne Marie O'Sullivan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Adam Bates
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Taylor Cervenka
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Janelle Kuroiwa
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | | | - Onyekachukwu Ibezim
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Abraham Alabi
- US Military HIV Research Program (HJF-MRI), Abuja, Nigeria
- Centre de Recherches Medicales de Lambarene (CERMEL) Fondation Internationale de l’Hôpital Albert Schweitzer Lambarene, Gabon
| | - Obumneke Okoye
- Emergency Plan Implementation Committee, Nigerian Ministry of Defense, Abuja, Nigeria
| | - Mark Manak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Jennifer Malia
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- United States Public Health Service, Rockville, Maryland
| | - Sheila Peel
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Darrell Singer
- United States Public Health Service, Rockville, Maryland
- Department of Defense HIV Program, Abuja, Nigeria
| | - Robert J. O’Connell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | - Jerome H. Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Nelson L. Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Jia L, Li L, Li H, Liu S, Wang X, Bao Z, Li T, Zhuang D, Liu Y, Li J. Correction: Recombination Pattern Reanalysis of Some HIV-1 Circulating Recombination Forms Suggest the Necessity and Difficulty of Revision. PLoS One 2016; 11:e0155750. [PMID: 27168068 PMCID: PMC4864214 DOI: 10.1371/journal.pone.0155750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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Compaore TR, Soubeiga ST, Ouattara AK, Obiri-Yeboah D, Tchelougou D, Maiga M, Assih M, Bisseye C, Bakouan D, Compaore IP, Dembele A, Martinson J, Simpore J. APOBEC3G Variants and Protection against HIV-1 Infection in Burkina Faso. PLoS One 2016; 11:e0146386. [PMID: 26741797 PMCID: PMC4704832 DOI: 10.1371/journal.pone.0146386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/16/2015] [Indexed: 01/27/2023] Open
Abstract
Studies on host factors, particularly the APOBEC3G gene, have previously found an association with AIDS progression in some populations and against some HIV-1 strains but not others. Our study had two main objectives: firstly, to screen a population from Burkina Faso for three variants of APOBEC3G previously described, and secondly to analyze the effect of these three variants and their haplotypes on HIV-1 infection with Circulating Recombinant Forms (CRFs) present in Burkina Faso. This case control study involved 708 seropositive and seronegative individuals. Genotyping was done by the TaqMan allelic discrimination method. Minor allele frequencies of rs6001417 (p<0.05), rs8177832 (P<0.05), and rs35228531 (P<0.001) were higher in seronegative subjects. The rs6001417 and rs8177832 SNPs were associated with HIV-1 infection in an additive model (P<0.01). Furthermore the SNP rs35228531 was also associated with HIV-1 infection in a dominant model (P<0.001). Odds ratio analysis of genotypes and alleles of the different APOBEC3G variants showed that there is a strong association between the minor genetic variants, genotype of the three SNPs, and HIV-1 status. Haplotype analysis demonstrated that rs6001417, rs8177832, and rs35228531 are in linkage disequilibrium. The haplotype GGT from the rs6001417, rs8177832 and rs35228531 respectively has a protective effect OR = 0.54 [0.43-0.68] with P<0.001. There was also associations between the haplotypes GGC OR = 1.6 [1.1;-2.3] P<0.05, and CGC OR = 5.21 [2.4-11.3] P<0.001, which increase the risk of infection by HIV-1 from almost two (2) to five (5) fold. This study demonstrates an association of rs6001417, rs8177832, and rs35228531 of APOBEC3G with HIV-1 infection in a population from Burkina Faso.
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Affiliation(s)
- Tegwinde Rebeca Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Serge Theophile Soubeiga
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Dorcas Obiri-Yeboah
- University of Cape Coast, School of Medical Sciences, Microbiology Department, Cape Coast, Ghana
| | - Damehan Tchelougou
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Mamoudou Maiga
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Maleki Assih
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Cyrille Bisseye
- Laboratory of Molecular and Cellular Biology, University of Sciences and Techniques of Masuku (USTM), Franceville, Gabon
| | - Didier Bakouan
- Permanent Secretary against AIDS and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Issaka Pierre Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Augustine Dembele
- Permanent Secretary against AIDS and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacques Simpore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
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11
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Jia L, Li L, Li H, Liu S, Wang X, Bao Z, Li T, Zhuang D, Liu Y, Li J. Recombination pattern reanalysis of some HIV-1 circulating recombination forms suggest the necessity and difficulty of revision. PLoS One 2014; 9:e107349. [PMID: 25203725 PMCID: PMC4159329 DOI: 10.1371/journal.pone.0107349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 08/09/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Recombination is one of the major mechanisms underlying the generation of HIV-1 variability. Currently 61 circulating recombinant forms of HIV-1 have been identified. With the development of recombination detection techniques and accumulation of HIV-1 reference stains, more accurate mosaic structures of circulating recombinant forms (CRFs), like CRF04 and CRF06, have undergone repeated analysis and upgrades. Such revisions may also be necessary for other CRFs. Unlike previous studies, whose results are based primarily on a single recombination detection program, the current study was based on multiple recombination analysis, which may have produced more impartial results. METHODS Representative references of 3 categories of intersubtype recombinants were selected, including BC recombinants (CRF07 and CRF08), BG recombinants (CRF23 and CRF24), and BF recombinants (CRF38 and CRF44). They were reanalyzed in detail using both the jumping profile hidden Markov model and RDP3. RESULTS The results indicate that revisions and upgrades are very necessary and the entire re-analysis suggested 2 types of revision: (i) length of inserted fragments; and (ii) number of inserted fragments. The reanalysis also indicated that determination of small regions of about 200 bases or fewer should be performed with more caution. CONCLUSION Results indicated that the involvement of multiple recombination detection programs is very necessary. Additionally, results suggested two major challenges, one involving the difficulty of accurately determining the locations of breakpoints and the second involving identification of small regions of about 200 bases or fewer with greater caution. Both indicate the complexity of HIV-1 recombination. The resolution would depend critically on development of a recombination analysis algorithm, accumulation of HIV-1 stains, and a higher sequencing quality. With the changes in recombination pattern, phylogenetic relationships of some CRFs may also change. All these results may be critical to understand the role of recombination in a complex and dynamic HIV evolution.
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Affiliation(s)
- Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
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Abstract
OBJECTIVE To investigate the origin and spatiotemporal dynamics of dissemination of the HIV-1 CRF06_cpx clade in western Africa. DESIGN A total of 180 HIV-1 CRF06_cpx-like pol sequences isolated from 12 different countries from west and west-central Africa over a period of 16 years (1995-2010) were analyzed. METHODS Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method and combined with molecular epidemiology and spatial accessibility data. RESULTS The CRF06_cpx most probably emerged in Burkina Faso in 1979 (1970-1985). From Burkina Faso, the virus was first disseminated to Mali and Nigeria during the 1980s and later to other countries from west and west-central Africa. Demographic reconstruction indicates that the CRF06_cpx epidemic grew exponentially during the 1980s, with a median growth rate of 0.82 year (0.60-1.09 year), and after stabilize. We found a negative correlation between CRF06_cpx prevalence and the geographical distance to Burkina Faso's capital. Regional accessibility information agrees with the overall geographical range of the CRF06_cpx, but not fully explains the highly heterogeneous distribution pattern of this CRF at regional level. CONCLUSION The CRF06_cpx epidemic in western Africa probably emerged at the late 1970s and grew during the 1980s at a rate comparable to the HIV-1 epidemics in the United States and Europe. Burkina Faso seems to be the most important epicenter of dissemination of the HIV-1 CRF06_cpx strain at regional level. The explanation for the current geographical distribution of CRF06_cpx is probably multifactorial.
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13
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Laisaar KT, Avi R, DeHovitz J, Uusküla A. Estonia at the threshold of the fourth decade of the AIDS era in Europe. AIDS Res Hum Retroviruses 2011; 27:841-51. [PMID: 21142588 DOI: 10.1089/aid.2010.0223] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This article describes the trends of HIV/AIDS and related conditions in Estonia during the past decade (2000-2009), with special focus on the potential for epidemic transition. Key transmission determinants and major risk groups are examined and problems and barriers to fighting HIV/AIDS with possible applications in prevention and control are described. Estonian routine data sources and published literature were reviewed, supplemented with information from personal communication with physicians and public health specialists. For comparative European data, international HIV/AIDS and drug addiction surveillance documents, administrative data, and published literature were reviewed. In Eastern Europe (including Estonia) the predominant HIV transmission mode is injection drug use (IDU), closely followed by heterosexual transmission, an increasing risk factor for new cases. Although the contribution of cases acquired by sexual contact with high-risk partners such as IDUs is not known, characteristics of the sexual networks of IDUs may be important in determining the evolution of the HIV/AIDS epidemics in the region. In Estonia, despite major gaps in available data, the HIV/AIDS epidemic is still presumably confined to IDUs (and probably, to their sexual partners). In Eastern Europe, young women in IDU-non-IDU partnerships engaging in unprotected sex potentially serve as a bridge to the general population, yet knowledge of and research into the population characteristics and potential magnitude of bridging are limited. In Estonia, as in other Eastern European countries, HIV prevention and harm reduction initiatives should be tailored not only to the predominantly male HIV-positive IDU population, but also to their noninfected non-IDU female sexual partners.
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Affiliation(s)
| | - Radko Avi
- Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Jack DeHovitz
- Downstate Medical Center, State University of New York, New York, New York
| | - Anneli Uusküla
- Department of Public Health, University of Tartu, Tartu, Estonia
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Tebit DM, Arts EJ. Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease. THE LANCET. INFECTIOUS DISEASES 2011; 11:45-56. [PMID: 21126914 DOI: 10.1016/s1473-3099(10)70186-9] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Kanmogne GD, Kuate CT, Cysique LA, Fonsah JY, Eta S, Doh R, Njamnshi DM, Nchindap E, Franklin DR, Ellis RJ, McCutchan JA, Binam F, Mbanya D, Heaton RK, Njamnshi AK. HIV-associated neurocognitive disorders in sub-Saharan Africa: a pilot study in Cameroon. BMC Neurol 2010; 10:60. [PMID: 20626870 PMCID: PMC2912842 DOI: 10.1186/1471-2377-10-60] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Accepted: 07/13/2010] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The disease burden of human immunodeficiency virus (HIV)--acquired immunodeficiency syndrome (AIDS) is highest in sub-Saharan Africa but there are few studies on the associated neurocognitive disorders in this region. The objectives of this study were to determine whether Western neuropsychological (NP) methods are appropriate for use in Cameroon, and to evaluate cognitive function in a sample of HIV-infected adults. METHODS We used a battery of 19 NP measures in a cross-sectional study with 44 HIV+ adults and 44 demographically matched HIV- controls, to explore the validity of these NP measures in Cameroon, and evaluate the effect of viral infection on seven cognitive ability domains. RESULTS In this pilot study, the global mean z-score on the NP battery showed worse overall cognition in the HIV+ individuals. Significantly lower performance was seen in the HIV+ sample on tests of executive function, speed of information processing, working memory, and psychomotor speed. HIV+ participants with AIDS performed worse than those with less advanced HIV disease. CONCLUSIONS Similar to findings in Western cohorts, our results in Cameroon suggest that HIV infection, particularly in advanced stages, is associated with worse performance on standardized, Western neurocognitive tests. The tests used here appear to be promising for studying NeuroAIDS in sub-Saharan Africa.
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Affiliation(s)
- Georgette D Kanmogne
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Callixte T Kuate
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Department of Neurology, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Lucette A Cysique
- HIV Neurobehavioral Research Center, University of California, San Diego, USA
- Brain Sciences, University of New South Wales, Sydney, Australia
| | - Julius Y Fonsah
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Department of Neurology, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Sabine Eta
- Department of Neurology, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Roland Doh
- Department of Neurology, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Dora M Njamnshi
- HIV Day-Care Hospital, Yaoundé Central Hospital, Yaoundé, Cameroon
| | | | - Donald R Franklin
- HIV Neurobehavioral Research Center, University of California, San Diego, USA
| | - Ronald J Ellis
- HIV Neurobehavioral Research Center, University of California, San Diego, USA
| | - John A McCutchan
- HIV Neurobehavioral Research Center, University of California, San Diego, USA
| | - Fidele Binam
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- University Hospital Center, Yaoundé, Cameroon
| | - Robert K Heaton
- HIV Neurobehavioral Research Center, University of California, San Diego, USA
| | - Alfred K Njamnshi
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Department of Neurology, Yaoundé Central Hospital, Yaoundé, Cameroon
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16
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Powell R, Barengolts D, Mayr L, Nyambi P. The Evolution of HIV-1 Diversity in Rural Cameroon and its Implications in Vaccine Design and Trials. Viruses 2010; 2:639-654. [PMID: 21072143 PMCID: PMC2975583 DOI: 10.3390/v2020639] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
West-Central Africa is an epicenter of the HIV pandemic; endemic to Cameroon are HIV-1 viruses belonging to all (sub)subtypes and numerous Circulating Recombinant Forms (CRFs). The rural villages of Cameroon harbor many strains of HIV-1, though these areas are not as well monitored as the urban centers. In the present study, 82 specimens obtained in 2000 and 2001 from subjects living in the rural villages of the South and West Regions of Cameroon were subtyped in gag, pol, and env and compared to 90 specimens obtained in 2006–2008 in the same regions, in order to analyze HIV-1 evolution in these rural areas. It was found that in the South Region, the proportion of unique recombinant forms (URFs) remained constant (∼40%), while the amount of URFs containing fragments of a CRF increased by 25%. (Sub)subtypes A1, F2, H, and K, and CRF09_cpx, identified in 2000 and 2001, were replaced by CRFs 01_AE, 13_cpx, 14_BG, and 18_cpx in 2006–2008. In the West Region, (sub)subtypes A2, C, G, and H, and CRFs 01_AE and 09_cpx, identified in 2000–2001, were replaced by sub-subtype A1 and CRFs 25_cpx and 37_cpx in 2006–2008. The proportion of URFs in the West Region dropped significantly over the time period by 43%. In both Regions, the proportion of CRF02_AG increased at all loci. These findings demonstrate that the evolution of HIV-1 is distinct for each endemic region, and suggests that the proportion of URFs containing CRF fragments is increasing as the genetic identity of the virus continues to shift dramatically. This highlights the concern that subtype-specific vaccines may not be relevant in Cameroon, and that the distribution of viral diversity in these regions of Cameroon must be carefully monitored.
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Affiliation(s)
- Rebecca Powell
- Department of Microbiology, New York University School of Medicine, New York, NY, USA; E-Mail:
| | - Denis Barengolts
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Luzia Mayr
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Phillipe Nyambi
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Veterans Affairs New York Harbor Healthcare Systems, New York, NY, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1 (212) 263-4159; Fax: +1 (212) 951-6321
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Huang DD, Foley BT, Tolzmann CA, Ouma A, Bremer JW. Complex mosaic composition of near full-length genomes of two NED (NIH-ENVA-DOD) subtype panel HIV type 1 strains, BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC). AIDS Res Hum Retroviruses 2009; 25:1039-43. [PMID: 19795987 DOI: 10.1089/aid.2009.0078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sequence characterization of the near full-length genomes of HIV-1 isolates BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC), was continued. These NED panel isolates, contributed by F. Brun-Vezinet (ENVA-France), were first identified as subtypes G and H, respectively. Our earlier analyses of portions of their pol genes showed that both were likely to be intersubtype recombinants of different composition. This study analyzed the remainder of each genome, confirming them to be complex recombinants. The BCF-Dioum genome resembles CRF06_cpx strains found in West Africa, composed of subtypes A/G/J/K. The BCF-Kita genome is a unique complex recombinant A-F-G-H-K-U strain. These data support previous observations of the complexity of strains originating from the DRC. BCF-Dioum may be a suitable strain for standards and reagents since it matches a defined circulating recombinant form. Studies and reagents made from BCF-Kita should take into account its complex genome.
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Affiliation(s)
- Diana D. Huang
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - Brian T. Foley
- HIV Sequence Database, Theoretical Biology and Biophysics Group (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Catlin A. Tolzmann
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - Annastasia Ouma
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - James W. Bremer
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
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18
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Avi R, Huik K, Sadam M, Karki T, Krispin T, Ainsalu K, Paap P, Schmidt J, Nikitina N, Lutsar I. Absence of genotypic drug resistance and presence of several naturally occurring polymorphisms of human immunodeficiency virus-1 CRF06_cpx in treatment-naive patients in Estonia. J Med Virol 2009; 81:953-8. [PMID: 19382254 DOI: 10.1002/jmv.21482] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
All non-B HIV-1 subtypes and circulating recombinant forms (CRFs) are characterized by several polymorphisms in protease (PR) region. In addition, in recent years the increasing use of antiretroviral treatment (ART) has rapidly raised the spread of transmitted drug resistance. We aimed to determine the presence of naturally occurring polymorphisms and transmitted drug resistance mutations (DRMs) in ART naïve HIV-1-positive subjects in Estonia. A total of 115 drug-naive HIV-1-infected subjects (mean age 27 years; 70% male; 65% infected via intravenous drug use and 34% by heterosexual contact) were enrolled. Viral genomic RNA from plasma was directly sequenced in PR, revertase (RT), and envelope (env) regions. Phylogenetic analysis of RT and env regions revealed that 89% and 3% of sequenced viruses belonged to CRF06_cpx and subtype A1, respectively, and 6% were described as unique recombinants (signed A1-06) between CRF06_cpx and subtype A1 viruses. No primary DRMs were found in PR or RT regions indicating the absence of transmitted drug resistance. The most common polymorphisms in the PR region were K14R, M36I, H69K, and L89M seen in 96%, 100%, 99%, and 100%, respectively. The clinical relevance of these polymorphisms in terms of success of ART has to be monitored in future clinical studies.
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Affiliation(s)
- Radko Avi
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia.
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19
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High frequency of HIV-1 dual infections among HIV-positive individuals in Cameroon, West Central Africa. J Acquir Immune Defic Syndr 2009; 50:84-92. [PMID: 19295338 DOI: 10.1097/qai.0b013e31818d5a40] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To determine the frequency of dual inter- and intra-subtype HIV-1 infection among a cohort of 64 longitudinally-studied, HIV-1-positive individuals in Yaoundé, Cameroon. METHODS Blood was collected every 3-6 months for up to 36 months and RNA was extracted from plasma. Gag fragment (HxB2 location 1577-2040) was amplified by nested RT-PCR, and mixed-time-point Heteroduplex Assays (HDAs) were performed. As heteroduplexes in this assay indicate >or=5% genetic discordance in the gag fragment, their presence reveals dual infection. Results were confirmed by phylogenetic analysis. RESULTS Heteroduplexes were generated by specimens of 10 subjects (15.6%). Kaplan-Meier nonparametric estimate of maintenance of single infection was calculated; the rate/year of a 2 infection was found to be approximately 11%. Dual infection was identified in the final specimens of five subjects, after as much as 18 months follow-up, while for the remaining five subjects, dual infection was identified in interim specimens within an average of 10 months follow-up. Analysis of samples obtained after dual infection from each of these latter five subjects revealed two patterns: reversion to initial strain, or replacement of initial strain. Four subjects were dually-infected with HIV-1 strains of the same subtype, while 6 were infected with different subtypes. CONCLUSIONS The high prevalence of recombinant HIV-1 strains in Cameroon may in part be explained by the high frequency of dual infection. In this genetically-diverse HIV-1 milieu, dual infections and the recombinant viruses they generate are strongly driving viral evolution, complicating vaccine strategies.
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20
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Imamichi H, Koita O, Dabitao D, Dao S, Ibrah M, Sogoba D, Dewar RL, Berg SC, Jiang MK, Parta M, Washington JA, Polis MA, Lane HC, Tounkara A. Identification and characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx recombinant subtypes in Mali, West Africa. AIDS Res Hum Retroviruses 2009; 25:45-55. [PMID: 19182920 DOI: 10.1089/aid.2008.0111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.
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Affiliation(s)
- Hiromi Imamichi
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Ousmane Koita
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Djeneba Dabitao
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Sounkalo Dao
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Mahamadou Ibrah
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Dramane Sogoba
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
| | - Robin L. Dewar
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Steve C. Berg
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Min-Kang Jiang
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Mark Parta
- Clinical Services Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Janice A. Washington
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael A. Polis
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - H. Clifford Lane
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Anatole Tounkara
- Center for Research and Training on HIV and Tuberculosis, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Bamako, Mali
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Stürmer M, Carlebach A, Staszewski S, Linde R, Königs C, Doerr HW, Däumer M, Berger A. Short communication: Different mutation patterns in subtype CRF06_cpx after mother-to-child transmission. AIDS Res Hum Retroviruses 2008; 24:1429-33. [PMID: 19032066 DOI: 10.1089/aid.2007.0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract Development of drug resistance mutation patterns (DRMP) in HIV after treatment failure depends on the drugs used in the failing regimen. However, selected patterns may not be unique; there is evidence that selection of DRMP for nelfinavir is dependent on subtype and/or background polymorphisms. Here we describe the selection of DRMP in a mother and son infected with subtype CRF06_cpx by mother-to-child transmission. Four years after delivery the mother received stavudine/lamivudine/nelfinavir as first-line therapy. Genotypic resistance tests (GRT) during follow-up showed selection of M184V/L283I in reverse transcriptase (RT) and H63Q/A71V/L90M in protease (PR). The child started treatment 8 months after birth with stavudine/didanosine/nelfinavir followed by an intensification period with efavirenz. Due to toxicity, efavirenz was removed from the regimen again. GRT during follow-up showed selection of L74V/K103N/M184V/M230L in RT and M46I/H63Q/N88S in PR. The viral load (VL) of the mother was initially undetectable followed by intermediate replication (1000-21,000 copies/ml), whereas the child had both periods of undetectable VL and low-level replication. Although both patients were infected with the same virus and treated with the same protease inhibitor, different DRMPs were selected. Whether the nucleoside backbone, course of antiretroviral therapy, or different host environment is responsible for this variability must be determined in larger studies.
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Affiliation(s)
- Martin Stürmer
- J.W. Goethe University Hospital, Institute for Medical Virology, 60596 Frankfurt, Germany
| | - Amina Carlebach
- J.W. Goethe University Hospital, Medical HIV Treatment and Research Unit, Department of Internal Medicine II, 60590 Frankfurt, Germany
- HIV Speciality Practice, 60311 Frankfurt, Germany
| | - Schlomo Staszewski
- J.W. Goethe University Hospital, Medical HIV Treatment and Research Unit, Department of Internal Medicine II, 60590 Frankfurt, Germany
| | - Richard Linde
- J.W. Goethe University Hospital, Immunodeficiency Unit, Department of Pediatrics III, 60590 Frankfurt, Germany
| | - Christoph Königs
- J.W. Goethe University Hospital, Immunodeficiency Unit, Department of Pediatrics III, 60590 Frankfurt, Germany
| | - Hans W. Doerr
- J.W. Goethe University Hospital, Institute for Medical Virology, 60596 Frankfurt, Germany
| | - Martin Däumer
- Institute for Immunology and Genetic, Medical Laboratory Dr. med. B. Thiele, 67653 Kaiserslautern, Germany
| | - Annemarie Berger
- J.W. Goethe University Hospital, Institute for Medical Virology, 60596 Frankfurt, Germany
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22
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Ntemgwa M, Toni TD, Brenner BG, Routy JP, Moisi D, Oliveira M, Wainberg MA. Near full-length genomic analysis of a novel subtype A1/C recombinant HIV type 1 isolate from Canada. AIDS Res Hum Retroviruses 2008; 24:655-9. [PMID: 18366312 DOI: 10.1089/aid.2007.0282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The rapid introduction of non-B HIV-1 subtypes into Quebec, mostly from persons from regions where HIV prevalence is high and where different variants circulate, means that recombination must now be an important consideration in the epidemiologic surveillance of HIV infection. No circulating recombinant form (CRF), currently involving exclusively subtypes A1 and C, exists in the Los Alamos HIV database. This study presents a near full-length genomic analysis of a novel HIV-1 recombinant involving subtypes A1 and C. Bootscanning revealed that the recombinant structure involves three breakpoints that separate the genome into four regions, alternating between subtypes A1 and C. The intersubtype recombinant breakpoint in the pol gene was at midpoint between the protease and reverse transcriptase open reading frames. This is the first report of a recombinant involving subtypes A1 and C in Canada, the epidemiologic significance of which is not yet known.
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Affiliation(s)
- Michel Ntemgwa
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H3A 2T5, Canada
| | - Thomas D'Aquin Toni
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, Quebec H3A 2T5, Canada
| | - Bluma G. Brenner
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Jean-Pierre Routy
- Immunodeficiency Service and Division of Hematology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Daniela Moisi
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Mark A. Wainberg
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H3A 2T5, Canada
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Lakhashe S, Tripathy S, Paranjape R, Bhattacharya J. Characterization of B/C recombinants of near full-length HIV type 1 from northeastern India with mosaics identical to ARE195FL but with a different ancestral origin. AIDS Res Hum Retroviruses 2008; 24:92-9. [PMID: 18275353 DOI: 10.1089/aid.2007.0214] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have characterized near full-length genomes of three B/C recombinants of HIV-1 from the northeastern state of India. The recombinant viruses showed a backbone of subtype C virus with a single insertion of the subtype B genome in the envelope region. While all of them were distinct from B/C recombinants CRF_07 and CRF_08 circulating in China and CRF_04BR137 circulating in Brazil, two of them presented with break-points identical to the Argentinean B/C recombinant ARE195FL. However, neighbor-joining analysis followed by phylogenetic clustering showed that gp120 belonging to subtype B of all the recombinants clustered with Thai B sequences, while subtype C gag clustered with an Indian subtype C sequence, suggesting a unique ancestral origin of these recombinants.
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Affiliation(s)
- Samir Lakhashe
- Division of Molecular Virology, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune-411026, India
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24
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Holguín A, Lospitao E, López M, de Arellano ER, Pena MJ, del Romero J, Martín C, Soriano V. Genetic characterization of complex inter-recombinant HIV-1 strains circulating in Spain and reliability of distinct rapid subtyping tools. J Med Virol 2008; 80:383-91. [DOI: 10.1002/jmv.21105] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Buonaguro L, Tornesello ML, Buonaguro FM. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol 2007; 81:10209-19. [PMID: 17634242 PMCID: PMC2045484 DOI: 10.1128/jvi.00872-07] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- L Buonaguro
- Laboratory of Viral Oncogenesis and Immunotherapy & AIDS Reference Center, Ist. Naz. Tumori Fond. G. Pascale, Via Mariano Semmola, 1, 80131 Naples, Italy.
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26
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Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM. Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol 2007; 81:8543-51. [PMID: 17553886 PMCID: PMC1951349 DOI: 10.1128/jvi.00463-07] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is classified in nine subtypes (A to D, F, G, H, J, and K), a number of subsubtypes, and several circulating recombinant forms (CRFs). Due to the high level of genetic diversity within HIV-1 and to its worldwide distribution, this classification system is widely used in fields as diverse as vaccine development, evolution, epidemiology, viral fitness, and drug resistance. Here, we demonstrate how the high recombination rates of HIV-1 may confound the study of its evolutionary history and classification. Our data show that subtype G, currently classified as a pure subtype, has in fact a recombinant history, having evolved following recombination between subtypes A and J and a putative subtype G parent. In addition, we find no evidence for recombination within one of the lineages currently classified as a CRF, CRF02_AG. Our analysis indicates that CRF02_AG was the parent of the recombinant subtype G, rather than the two having the opposite evolutionary relationship, as is currently proposed. Our results imply that the current classification of HIV-1 subtypes and CRFs is an artifact of sampling history, rather than reflecting the evolutionary history of the virus. We suggest a reanalysis of all pure subtypes and CRFs in order to better understand how high rates of recombination have influenced HIV-1 evolutionary history.
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Affiliation(s)
- Ana B Abecasis
- Katholieke Universiteit Leuven, Laboratory for Clinical and Epidemiological Virology, AIDS Reference Laboratory, Rega Institute and University Hospitals, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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27
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Derache A, Traore O, Koita V, Sylla A, Tubiana R, Simon A, Canestri A, Carcelain G, Katlama C, Calvez V, Cisse M, Marcelin AG. Genetic Diversity and Drug Resistance Mutations in HIV type 1 from Untreated Patients in Bamako, Mali. Antivir Ther 2007. [DOI: 10.1177/135965350701200117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Objective To determine the genetic diversity of HIV-1 reverse transcriptase (RT) and protease sequences and the presence of mutations linked to antiretroviral (ARV) resistance in treatment-naive, HIV-1-infected individuals living in Mali. Methods Ninety-eight samples from ARV drug-naive, HIV-1-infected patients were collected in one clinical centre in Bamako, Mali in 2005. RT and protease genes were sequenced in order to perform phylogenetic and resistance analyses. Results The most prevalent subtype was CRF02-AG (75% of cases), followed by the CRF06-cpx subtype (20%). Intersubtype recombinants between CRF02-AG, CRF01-AE and CRF06-cpx were also described in 5% of cases. After 4 years of ARV use in Mali, two previously untreated individuals (2%; 95% CI: 0.00–4.77%) were found to have resistant viruses, one with a single nucleoside mutation and one with K103N non-nucleoside reverse transcriptase inhibitor resistance mutation. No evidence of transmitted protease inhibitor resistance mutations was found. Conclusion These data provide direct evidence for the circulation of HIV-1 isolates containing resistance mutations in treatment-naive patients in Mali. Since ARV use in Mali began, more than 5,000 patients have started treatment, mostly with Triomune (stavudine/lamivu-dine/nevirapine). The resistance-associated mutations detected in the present study are consistent with this treatment regimen. Continued surveillance will be required to monitor the emergence of ARV resistance in this country.
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Affiliation(s)
- Anne Derache
- Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, EA 2387, Université Pierre et Marie Curie, Paris, France
| | - Ousmane Traore
- Centre d'Ecoute, de Soins, d'Animations et de Conseils, Bamako, Mal
| | - Victoria Koita
- Centre d'Ecoute, de Soins, d'Animations et de Conseils, Bamako, Mal
| | - Aliou Sylla
- Centre d'Ecoute, de Soins, d'Animations et de Conseils, Bamako, Mal
- Cellule Multisectorielle de Lutte contre le Sida, Bamako, Mal
| | - Roland Tubiana
- Department of Infectious Diseases, Pitié-Salpêtrière Hospital, AP-HP, Université Pierre et Marie Curie, Paris, France
| | - Anne Simon
- Department of Internal Medicine Pitié-Salpêtrière Hospital, AP-HP, Université Pierre et Marie Curie, Paris, France
| | - Ana Canestri
- Department of Infectious Diseases, Pitié-Salpêtrière Hospital, AP-HP, Université Pierre et Marie Curie, Paris, France
| | - Guislaine Carcelain
- Department of Immunology, Pitié-Salpêtrière Hospital, AP-HP, Université Pierre et Marie Curie, Paris, France
| | - Christine Katlama
- Department of Infectious Diseases, Pitié-Salpêtrière Hospital, AP-HP, Université Pierre et Marie Curie, Paris, France
| | - Vincent Calvez
- Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, EA 2387, Université Pierre et Marie Curie, Paris, France
| | - Mamadou Cisse
- Centre d'Ecoute, de Soins, d'Animations et de Conseils, Bamako, Mal
| | - Anne-Geneviève Marcelin
- Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, EA 2387, Université Pierre et Marie Curie, Paris, France
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28
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Tehe A, Maurice C, Hanson DL, Borget MY, Abiola N, Maran M, Yavo D, Tomasik Z, Böni J, Schüpbach J, Nkengasong JN. Quantification of HIV-1 p24 by a highly improved ELISA: An alternative to HIV-1 RNA based treatment monitoring in patients from Abidjan, Côte d’Ivoire. J Clin Virol 2006; 37:199-205. [PMID: 16973409 DOI: 10.1016/j.jcv.2006.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2006] [Revised: 07/18/2006] [Accepted: 08/02/2006] [Indexed: 11/23/2022]
Abstract
BACKGROUND Quantification of HIV-1 RNA remains difficult to implement in Africa. Simple and inexpensive tests for antiretroviral treatment (ART) monitoring are needed. OBJECTIVE To evaluate an HIV-1 p24 ELISA, which combines efficient virus disruption, heat-denaturation and signal amplification, in a West African setting. STUDY DESIGN Eighty-six HIV-1 infected patients from Abidjan, Côte d'Ivoire, were tested for p24, HIV-1 RNA, and CD4+ count at baseline, and twice within 8 months after ART initiation. RESULTS All patients responded to ART with a minimal HIV-1 RNA drop of 0.5 log(10) at first follow-up. Forty-one (47.7%) then rebounded >0.5 log(10) or persisted above 1000 copies/mL by week 24. The predicted baseline concentration of p24 corresponding to 100,000 copies/mL of HIV-1 RNA, above which ART is recommended, was 4546 fg/mL (95% confidence interval 3148-6566). A prediction model of virologic failure, occurring after an initial response to ART, correctly classified 84% of patients using baseline p24, p24 change on therapy, and achievement of undetectable p24 as explanatory variables. The model and further bootstrap evaluation suggested a good ability to discriminate between sustained or failing virologic response to ART. CONCLUSION HIV-1 p24 and RNA based-ART monitoring in a low-resource country dominated by HIV-1 CRF02 AG appeared comparable.
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Affiliation(s)
- Andre Tehe
- Projet RETRO-CI, Abidjan, Côte d'Ivoire.
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29
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Tagliamonte M, Vidal N, Tornesello ML, Peeters M, Buonaguro FM, Buonaguro L. Genetic and phylogenetic characterization of structural genes from non-B HIV-1 subtypes in Italy. AIDS Res Hum Retroviruses 2006; 22:1045-51. [PMID: 17067276 DOI: 10.1089/aid.2006.22.1045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A molecular and phylogenetic characterization on env and gag subgenomic regions has been performed in our laboratory on HIV-1 variants identified in seropositive individuals residing in Italy, infected in the 1999-2001 period, and five non-B-subtype HIV-1 isolates have been described. To confirm the phylogenetic characterization and to determine the genomic organization of three non-B HIV-1 isolates (A, G, and CRF02- AG), the complete gag, pol, and gp120 ORFs (approx. 6900 bp) have been sequenced for each of them. The phylogenetic tree analyses performed on the whole sequence or on individual genes suggested, for the A and G isolates, the identification of divergent strains that do not cluster into any of the known subsubtypes. This has been further validated by pairwise distance analysis. On the contrary, the phylogenetic classification of the CRF02-AG isolate has been confirmed and an overall typical pattern of intragenomic breakpoints has been observed by a Simplot analysis. These results confirm the constant HIV-1 molecular evolution and indicate the relevance of a continuous molecular monitoring of HIV-1 isolates for the development of appropriate vaccine candidates.
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Affiliation(s)
- M Tagliamonte
- Laboratory of Viral Oncogenesis and Immunotherapy and AIDS Reference Center, Istituto Nazionale Tumori Fond. G. Pascale, 80131 Naples, Italy
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Abstract
Human immunodeficiency virus (HIV) is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS). HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.
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Affiliation(s)
- Henry I Z Requejo
- Seção de Imunologia, Instituto Adolfo Lutz, Av. Dr. Arnaldo 351, 01246-902 São Paulo, SP, Brazil.
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31
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Vidal N, Mulanga C, Bazepeo SE, Mwamba JK, Tshimpaka JW, Kashi M, Mama N, Laurent C, Lepira F, Delaporte E, Peeters M. Distribution of HIV-1 variants in the Democratic Republic of Congo suggests increase of subtype C in Kinshasa between 1997 and 2002. J Acquir Immune Defic Syndr 2006; 40:456-62. [PMID: 16280702 DOI: 10.1097/01.qai.0000159670.18326.94] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Democratic Republic of Congo (DRC) is characterized by low and stable HIV prevalences and high HIV-1 genetic diversity and is most probably the epicenter of HIV-1 group M. Our major goal was to study the distribution of HIV-1 variants over a 5-year period against a background of political instability and civil war. A total of 288 HIV-1-positive samples collected in 2002 from sentinel population groups in an HIV serosurveillance study performed in 4 cities (Kinshasa [capital city], Mbuji-Mayi [south], Lubumbashi [southeast], and Kisangani [northeast]) were genetically characterized by sequencing and phylogenetic analysis of the V3-V5 env region. The results were compared with those obtained in 1997. Similarly, as in 1997, an extremely high genetic diversity of HIV-1 strains overall and a heterogeneous geographic distribution were seen in 2002. All subtypes and several circulating recombinant forms were present, high intrasubtype diversity was observed, and 5.6% of the samples could not be classified. In each geographic region of the DRC, the genetic diversity was significantly higher than in neighboring countries. Comparison of subtype distribution in similar population groups in Kinshasa in 1997 and 2002 revealed an overall increase of subtype C in Kinshasa from 2.1% to 9.7% and, more precisely, from 0% to 18.9% in female sex workers (P = 0.013). Genetic characterization of HIV-positive samples from sentinel surveys adds significant additional information on new trends in the HIV epidemic. These changes could have implications regarding the spread of HIV infection in the DRC as well on vaccine and/or treatment strategies.
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Affiliation(s)
- Nicole Vidal
- UR36, Institut de Recherche pour e Developement (IRD), Montpellier, France
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32
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Toni T, Adjé-Touré C, Vidal N, Minga A, Huet C, Borger MY, Recordon-Pinson P, Masquelier B, Nolan M, Nkengasong J, Fleury HJ, Delaporte E, Peeters M. Presence of CRF09_cpx and complex CRF02_AG/CRF09_cpx recombinant HIV type 1 strains in Côte d'Ivoire, West Africa. AIDS Res Hum Retroviruses 2005; 21:667-72. [PMID: 16060839 DOI: 10.1089/aid.2005.21.667] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Based on partial env and pol (protease and RT) subtyping, we recently documented that the majority (>80%) of the HIV-1 strains that circulate in Côte d'Ivoire were CRF02_AG and about 11% were recombinants or could not be clearly assigned to a known subtype or CRF. In order to determine in more detail the precise structure of these viruses we sequenced the full-length genomes for six such strains. Bootscan and phylogenetic tree analysis showed that four strains were complex and unique CRF02_AG/CRF09_cpx recombinants, one was a CRF02_AG/CRF06_cpx recombinant, and one was a pure CRF09_cpx. Reanalysis of the remaining recombinants asserted the predominance of CRF09_cpx within intersubtype recombinants and circulation of CRF09_cpx in Côte d'Ivoire. More detailed analysis of the CRF09_cpx strains revealed also that part of the pol gene belonged to subtype K. This is the first time that such recombinants are described.
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Monno L, Brindicci G, Lo Caputo S, Punzi G, Scarabaggio T, Riva C, Di Bari C, Pierotti P, Saracino A, Lagioia A, Mazzotta F, Balotta C, Angarano G. HIV-1 subtypes and circulating recombinant forms (CRFs) from HIV-infected patients residing in two regions of central and southern Italy. J Med Virol 2005; 75:483-90. [PMID: 15714483 DOI: 10.1002/jmv.20300] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A total of 347 pol gene sequences from 88 Tuscan and 259 Apulian subjects (including 52 non-Italians and 9 children) were analyzed phylogenetically. Forty-four (12.6%) non-B subtypes were found, including 3.4% C, 1.4% F1, 0.8% G, and 0.3% each for J and A pure subtypes, and 3.7% CRF02_AG, 1.4% CRF01_AE, 0.6% BF, and 0.3% CRF06-cpx recombinant forms. An additional sample close-matched the pol gene of an unique recombinant form (URF AGK 99GR303). The non-B subtypes were from 40 adults and 4 children; 12 of these 44 patients were epidemiologically linked. Thirty-three of the 44 non-B viruses pertained to non-Italian immigrants and 11 to Italians, signifying that 63.4% immigrants and 3.7% Italians harbored non-B subtypes. The overall frequency of non-B subtypes was higher in Tuscany than in Apulia (18.1% vs. 10.8%). Moreover, 6.1% and 3.0% non-B subtypes were found among Italians from Florence and Apulia, respectively, while 52.1% and 72.4% of immigrants living in Tuscany and Apulia harbored non-B subtypes. Women infected by means of sexual contact prevailed among non-Italian adults; the majority of Italians were males and admitted high-risk sexual behavior. Four Italians had a history of extensive travel in countries of high endemicity. Social and epidemiological changes are responsible for an increasing circulation of non-B subtypes in Italy. Although non-B subtypes principally infect non-Italian patients, in Italy they can no longer be considered exclusively restricted to subjects from endemic areas.
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Affiliation(s)
- Laura Monno
- Clinic of Infectious Diseases, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy.
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Zetterberg V, Ustina V, Liitsola K, Zilmer K, Kalikova N, Sevastianova K, Brummer-Korvenkontio H, Leinikki P, Salminen MO. Two viral strains and a possible novel recombinant are responsible for the explosive injecting drug use-associated HIV type 1 epidemic in Estonia. AIDS Res Hum Retroviruses 2004; 20:1148-56. [PMID: 15588336 DOI: 10.1089/aid.2004.20.1148] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 infection has been rare in Estonia. In 2000, an explosive epidemic among injecting drug users was detected in the Eastern border region, resulting in 3603 newly reported cases by the end of 2003. The molecular epidemiology of the outbreak was studied to establish whether the Estonian epidemic is linked to the epidemics in Eastern Europe. Over 200 newly infected individuals were prospectively sampled from June 2000 to March 2002 in a geographically representative way, with known dates of diagnosis and information of probable route of transmission. Viral regions coding for two viral gene regions were directly sequenced from plasma viral RNA and phylogenetically analyzed. In addition, a larger region coding for the entire env gene was sequenced from one sample and studied for indications of possible recombinant structure. The Estonian HIV outbreak was found to be caused by simultaneous introduction of two strains: a minor subtype A strain very similar to the Eastern European subtype A strain (approximately 8% of cases), and a second major strain (77%) found to be most closely related to the CRF06-cpx strain, previously described only from African countries. The variability in the two clusters was very low, suggesting point source introductions. Ten percent of cases seemed to be newly generated recombinants of the A and CRF06-cpx strains. Analysis of viral diversification over time revealed a rate of change within the V3 region of 0.83%/year for the CRF06-cpx strain, consistent with findings from other subtypes. Due to the relatively frequently found novel recombinant forms, the Estonian HIV-1 epidemic may allow studies of coinfection and intersubtype recombination in detail.
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Affiliation(s)
- Veera Zetterberg
- HIV-Laboratory, Department of Infectious Disease Epidemiology, National Public Health Institute, Helsinki, Finland
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35
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Fischetti L, Opare-Sem O, Candotti D, Sarkodie F, Lee H, Allain JP. Molecular epidemiology of HIV in Ghana: Dominance of CRF02_AG. J Med Virol 2004; 73:158-66. [PMID: 15122787 DOI: 10.1002/jmv.20070] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent studies showed the importance of CRF02_AG in West Africa, although the clinical relevance of these recombinant forms of HIV remains unknown. The present study aimed at determining the molecular diversity of HIV in Ghana and investigating the possible epidemiologic advantage of recombinant HIV-1. Plasma samples collected in 1999-2002 from two populations of HIV infected individuals (144 asymptomatic candidate blood donors and 169 AIDS patients) were studied and 249 of them were molecularly characterised in gag, pol, and env regions. Five molecular groups were identified: strains clustering with CRF02_AG in all regions (147/249 or 59%), recombinant strains clustering with CRF02_AG in one or two regions (50/249 or 20%), other subtypes, pure or recombinant, but not involving CRF02_AG (37/249 or 15%), HIV-2 (11/249 or 4.5%), and double infections (4/249 or 1.5%). There was no significant difference in the distribution of HIV-1 recombinant strains according to clinical presentation. No evidence of a significant increase in CRF02_AG prevalence between 1999 and 2002 was found. Irrespective of clinical condition, CRF02_AG is the predominant molecular form of HIV-1 in Kumasi, Ghana.
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Affiliation(s)
- Lucia Fischetti
- Department of Haematology, Division of Transfusion Medicine, University of Cambridge, Cambridge, England
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36
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37
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Papathanasopoulos MA, Hunt GM, Tiemessen CT. Evolution and diversity of HIV-1 in Africa--a review. Virus Genes 2003; 26:151-63. [PMID: 12803467 DOI: 10.1023/a:1023435429841] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The HIV/AIDS pandemic represents a major development crisis for the African continent, which is the worst affected region in the world. Currently, almost 30 of the 42 million people infected with HIV worldwide live in Africa. AIDS in humans is caused by two lentiviruses, HIV-1 and HIV-2, which entered the human population by zoonotic transmissions from at least two different African primate species. Extensive phylogenetic analyses of partial and full-length genome sequences have helped to gain insights into the evolutionary biology and population dynamics of HIV. One of the major characteristics of HIV is its rapid evolution, which has resulted in substantial genetic diversity amongst different isolates, the majority of which are represented in Africa. Genetic variability of HIV and any consequent phenotypic variation poses a significant challenge to disease control and surveillance in different geographic regions of Africa. This review focuses on the origins and evolution of HIV, current classification and diversity of HIV isolates in Africa and provides an extensive account of the geographic distribution of HIV types, groups, and subtypes in each of the 49 African countries. Numerous epidemiological studies have provided a picture of HIV distribution patterns in most countries in Africa, and these show increasing evidence of the importance of HIV-1 recombinants. In particular, this review highlights that our current understanding of HIV distribution in Africa is incomplete and inadequately represents the diversity of the virus, and underscores the need for ongoing surveillance.
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Affiliation(s)
- Maria A Papathanasopoulos
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Department of Virology, University of the Witwatersrand, Johannesburg, South Africa.
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38
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Toni TD, Recordon-Pinson P, Minga A, Ekouevi D, Bonard D, Bequet L, Huet C, Chenal H, Rouet F, Dabis F, Lafon ME, Salamon R, Masquelier B, Fleury HJ. Presence of key drug resistance mutations in isolates from untreated patients of Abidjan, Côte d'Ivoire: ANRS 1257 study. AIDS Res Hum Retroviruses 2003; 19:713-7. [PMID: 14506786 DOI: 10.1089/088922203322280946] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A total of 107 HIV-1 isolates from untreated adult patients recruited in Abidjan, CMte d'Ivoire, in 2001 and 2002 were sequenced in the env, reverse transcriptase (RT), and protease genes. The results show that CRF02_AG is still predominant in this west African population; key mutations of resistance to antiretroviral drugs (NRTI, NNRTI, and PIs) were detected in 5.6% of the patients. We hypothesize that these resistant mutants have been acquired through horizontal transmission. Compared to a previous study carried out by our group in 1997-2000 in a similar population of Abidjan, it seems that there is a dynamic process of resistance and that a survey will be necessary.
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Nájera R, Delgado E, Pérez-Alvarez L, Thomson MM. Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS 2003; 16 Suppl 4:S3-16. [PMID: 12698994 DOI: 10.1097/00002030-200216004-00002] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rafael Nájera
- Department of Viral Patogénesis, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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Ouédraogo-Traoré R, Montavon C, Sanou T, Vidal N, Sangaré L, Sanou I, Soudré R, Mboup S, Delaporte E, Peeters M. CRF06-cpx is the predominant HIV-1 variant in AIDS patients from Ouagadougou, the capital city of Burkina Faso. AIDS 2003; 17:441-2. [PMID: 12556699 DOI: 10.1097/00002030-200302140-00019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mamadou S, Vidal N, Montavon C, Ben A, Djibo A, Rabiou S, Soga G, Delaporte E, Mboup S, Peeters M. Emergence of complex and diverse CRF02-AG/CRF06-cpx recombinant HIV type 1 strains in Niger, West Africa. AIDS Res Hum Retroviruses 2003; 19:77-82. [PMID: 12596728 DOI: 10.1089/08892220360474005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
On the basis of partial env and gag subtyping, we documented that the majority of HIV-1 strains circulating in Niger were CRF02-AG (54.3%) or CRF06-cpx (18.1%) and that 9% of the samples were possible recombinants between CRF02 and CRF06. To determine in more detail the precise structure of these viruses we sequenced the full-length genomes for three such strains (97NE-003, 00NE-036, and 00NE-095). From the bootscan and phylogenetic tree analysis it is evident that the new viruses are the result of recombination events between CRF02-AG and CRF06-cpx strains. Importantly, each virus had a different complex recombinant structure with multiple breakpoints, leading to viruses with complex mosaic patterns.
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Lawrence JG, Hatfull GF, Hendrix RW. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 2002; 184:4891-905. [PMID: 12169615 PMCID: PMC135278 DOI: 10.1128/jb.184.17.4891-4905.2002] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2002] [Accepted: 04/23/2002] [Indexed: 11/20/2022] Open
Abstract
The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.
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Affiliation(s)
- Jeffrey G Lawrence
- Department of Biological Sciences, Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Mamadou S, Montavon C, Ben A, Djibo A, Rabiou S, Mboup S, Delaporte E, Peeters M. Predominance of CRF02-AG and CRF06-cpx in Niger, West Africa. AIDS Res Hum Retroviruses 2002; 18:723-6. [PMID: 12167280 DOI: 10.1089/088922202760072357] [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: 11/13/2022] Open
Abstract
A total of 110 HIV-1-positive samples obtained in 1997 (n = 44) and 2000 (n = 66) were genetically characterized in the V3-V5 envelope region and the p24 gag region. The majority of the strains were CRF02-AG (54.3%) or CRF06-cpx (18.1%) in env and gag. More than 9% of the samples were recombinants between CRF02 and CRF06; 9 were CRF06 in env but CRF02 in gag, and for one sample the opposite was seen. Overall for 23 (20.9%) samples, the subtype designation was different between env and gag, and in 20 of these 23 samples a CRF was involved in the recombination event. No significant differences were seen between subtype distributions in 1997 and 2000, except that the proportion of recombinants increased from 13.6% in 1997 to 27.2% in 2000.
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