1
|
Tchiakpe E, Keke RK, Vidal N, Ahoussinou C, Sekpe O, Dagba HG, Gbaguidi E, Tonoukouen C, Afangnihoun A, Bachabi M, Gangbo FA, Diop-Ndiaye H, Toure-Kane C. Moderate rate of transmitted resistance mutations to antiretrovirals and genetic diversity in newly HIV-1 patients diagnosed in Benin. BMC Res Notes 2020; 13:314. [PMID: 32616057 PMCID: PMC7330984 DOI: 10.1186/s13104-020-05151-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/24/2020] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Seventeen years after the start of the IBAARV (Beninese initiative for access to antiretrovirals), transmitted drug resistance mutations in ARV-naïve patients and HIV-1 genetic diversity were investigated in Benin. RESULTS Drug resistance mutations were detected in (27/248; 10.9%) according to the WHO SDRM 2009 list, with a predominance of mutations directed against NNRTIs drugs (24/248; 10%). Phylogenetic and recombination analyses showed a predominance of CRF02_AG strains (165/248; 66.5%) and a high genetic diversity with five other variants and 39 URFs (15.7%) which contained portions of strains that co-circulate in Benin. Eight recent transmission chains revealed active ongoing transmission of HIV-1 strains among ARV-naïve patients. Our study showed a moderate primary drug resistance mutations rate and also provided recent data on the HIV-1 variants that circulate in Benin. Regular monitoring of primary drug resistance is required to adapt HIV-1 treatment strategies and adoption of new WHO recommendations in Benin.
Collapse
Affiliation(s)
- Edmond Tchiakpe
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
- Laboratory of Cell Biology and Physiology, Department of Biochemistry and Cellular Biology, Faculty of Sciences and Technology (FAST) and Institute of Applied Biomedical Sciences (ISBA), University of Abomey-Calavi, 01, BP 918 Cotonou, Benin
| | - Rene K. Keke
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
| | - Nicole Vidal
- UMI233-TransVIHMI, IRD (Institut de Recherche pour le développement), U1175 (INSERM) et Université de Montpellier, Montpellier, France
| | | | - Olga Sekpe
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
| | - Hermione G. Dagba
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
| | - Eric Gbaguidi
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Conrad Tonoukouen
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Aldric Afangnihoun
- Centre de Traitement Ambulatoire de l’Hôpital de zone de Suru Léré, Cotonou, Benin
| | - Moussa Bachabi
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Flore A. Gangbo
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Halimatou Diop-Ndiaye
- Institute for Health Research, Epidemiological Surveillance and Training of Senegal, Dakar, Senegal
| | - Coumba Toure-Kane
- Institute for Health Research, Epidemiological Surveillance and Training of Senegal, Dakar, Senegal
| |
Collapse
|
2
|
Nascimento FF, Baral S, Geidelberg L, Mukandavire C, Schwartz SR, Turpin G, Turpin N, Diouf D, Diouf NL, Coly K, Kane CT, Ndour C, Vickerman P, Boily MC, Volz EM. Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal. Epidemics 2019; 30:100376. [PMID: 31767497 PMCID: PMC10066795 DOI: 10.1016/j.epidem.2019.100376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 01/12/2023] Open
Abstract
Surveillance of HIV epidemics in key populations and in developing countries is often challenging due to sparse, incomplete, or low-quality data. Analysis of HIV sequence data can provide an alternative source of information about epidemic history, population structure, and transmission patterns. To understand HIV-1 dynamics and transmission patterns in Senegal, we carried out model-based phylodynamic analyses using the structured-coalescent approach using HIV-1 sequence data from three different subgroups: reproductive aged males and females from the adult Senegalese population and men who have sex with other men (MSM). We fitted these phylodynamic analyses to time-scaled phylogenetic trees individually for subtypes C and CRF 02_AG, and for the combined data for subtypes B, C and CRF 02_AG. In general, the combined analysis showed a decreasing proportion of effective number of infections among all reproductive aged adults relative to MSM. However, we observed a nearly time-invariant distribution for subtype CRF 02_AG and an increasing trend for subtype C on the proportion of effective number of infections. The population attributable fraction also differed between analyses: subtype CRF 02_AG showed little contribution from MSM, while for subtype C and combined analyses this contribution was much higher. Despite observed differences, results suggested that the combination of high assortativity among MSM and the unmet HIV prevention and treatment needs represent a significant component of the HIV epidemic in Senegal.
Collapse
Affiliation(s)
- Fabrícia F Nascimento
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Stefan Baral
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Lily Geidelberg
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Christinah Mukandavire
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Sheree R Schwartz
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Gnilane Turpin
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | | | | | - Nafissatou Leye Diouf
- Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formations, Dakar, Senegal
| | - Karleen Coly
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Coumba Toure Kane
- Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formations, Dakar, Senegal
| | - Cheikh Ndour
- Division de La Lutte Contre Le Sida et Les IST, Ministry of Health, Dakar, Senegal
| | - Peter Vickerman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Marie-Claude Boily
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Erik M Volz
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK; MRC Centre for Global Infectious Disease Analysis, Imperial College London, UK.
| |
Collapse
|
3
|
Mbange AE, Kaba D, Diouara AAM, Diop-Ndiaye H, Ngom-Ngueye NF, Dieng A, Lo S, Toure KN, Fall M, Mbacham WF, Diallo MS, Cisse M, Mboup S, Kane CT. Surveillance of transmitted HIV-1 antiretroviral drug resistance in the context of decentralized HIV care in Senegal and the Ebola outbreak in Guinea. BMC Res Notes 2018; 11:723. [PMID: 30309385 PMCID: PMC6182815 DOI: 10.1186/s13104-018-3804-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/27/2018] [Indexed: 02/08/2023] Open
Abstract
Objectives Disruption in HIV care provision may enhance the development and spread of drug resistance due to inadequate antiretroviral therapy. This study thus determined the prevalence of HIV-1 transmitted drug resistance (TDR) in settings of decentralized therapy and care in Senegal and, the Ebola outbreak in Guinea. Antiretroviral-naïve patients were enrolled following a modified WHO TDR Threshold Survey method, implemented in Senegal (January–March 2015) and Guinea (August–September 2015). Plasma and dried blood spots specimens, respectively from Senegalese (n = 69) and Guinean (n = 50) patients, were collected for direct sequencing of HIV-1 pol genes. The Stanford Calibrated Population Resistance program v6.0 was used for Surveillance Drug Resistance Mutations (SDRMs). Results Genotyping was successful from 54/69 (78.2%) and 31/50 (62.0%) isolates. In Senegal, TDR prevalence was 0% (mean duration since HIV diagnosis 4.08 ± 3.53 years). In Guinea, two patients exhibited SDRMs M184V (NRTI), T215F (TAM) and, G190A (NNRTI), respectively. TDR prevalence at this second site, however, could not be ascertained because of low sample size. Phylogenetic inference confirmed CRF02_AG predominance in Senegal (62.96%) and Guinea (77.42%). TDR prevalence in Senegal remains extremely low suggesting improved control measures. Continuous surveillance in both settings is mandatory and, should be done closest to diagnosis/transmission time and with larger sample size.
Collapse
Affiliation(s)
- Aristid Ekollo Mbange
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal.,The Biotechnology center, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon.,Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Djiba Kaba
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal.,Laboratoire de Biologie Moléculaire Nestor Bangoura/Hélène Labrousse, Hôpital National Donka, Conakry, Guinée.,Service de Dermatologie-Vénéréologie Hôpital National Donka/UGAN, Conakry, Guinée
| | - Abou Abdallah Malick Diouara
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal.,Département de Génie chimique et de Biologie Appliquée, Ecole Supérieure Polytechnique/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal.,Laboratoire de Bio-informatique, Université du Québec à Montréal, Montréal, Canada
| | - Halimatou Diop-Ndiaye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal.,Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | | | - Ahmed Dieng
- Hôpital régional de Saint-Louis, Saint-Louis, Sénégal
| | - Seynabou Lo
- Hôpital régional de Saint-Louis, Saint-Louis, Sénégal
| | - Kine Ndiaye Toure
- Centre de Traitement Ambulatoire, Fann, Centre Hospitalier Universitaire, Dakar, Sénégal
| | - Mamadou Fall
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Wilfred Fon Mbacham
- The Biotechnology center, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Mariama Sadjo Diallo
- Laboratoire de Biologie Moléculaire Nestor Bangoura/Hélène Labrousse, Hôpital National Donka, Conakry, Guinée
| | - Mohamed Cisse
- Laboratoire de Biologie Moléculaire Nestor Bangoura/Hélène Labrousse, Hôpital National Donka, Conakry, Guinée
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal
| | - Coumba Toure Kane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal. .,Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal. .,Laboratoire de Bactériologie-Virologie CHNU Dalal Jam, Dakar, Sénégal.
| |
Collapse
|
4
|
Jobson G, Struthers H, McIntyre J. "In the fell clutch of circumstance": HIV and men who have sex with men in sub-Saharan Africa. Curr HIV/AIDS Rep 2016; 12:164-72. [PMID: 25637162 DOI: 10.1007/s11904-014-0249-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Men who have sex with men (MSM) in sub-Saharan Africa (SSA) have been repeatedly found to have high risk of HIV infection, and in spite of the differing nature of the HIV epidemic in the general population between East and Southern Africa, and West and Central Africa, MSM are disproportionately affected by HIV across the entire region. Recent research has examined the drivers of HIV risk, and the dynamics of the MSM HIV epidemic in greater detail. However, this growing knowledge has generally not been translated into effective HIV prevention interventions. In part, this is due to the highly stigmatised and frequently criminalised nature of same-sex sexualities in much of the region. Without human-rights-based advocacy targeting governments and interventions aiming to decrease stigma and homophobia, translating research into effective HIV interventions for MSM in SSA at the scale needed to reduce HIV transmission in this population remains highly unlikely.
Collapse
|
5
|
Tamalet C, Ravaux I, Moreau J, Brégigeon S, Tourres C, Richet H, Abat C, Colson P. Emergence of clusters of CRF02_AG and B human immunodeficiency viral strains among men having sex with men exhibiting HIV primary infection in southeastern France. J Med Virol 2015; 87:1327-33. [PMID: 25873310 DOI: 10.1002/jmv.24184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2015] [Indexed: 11/05/2022]
Abstract
The number of new HIV diagnoses is increasing in the western world and transmission clusters have been recently identified among men having sex with men despite Highly Active Antiretroviral Therapy efficacy. The objective of this study was to assess temporal trends, epidemiological, clinical and virological characteristics of primary HIV infections. A retrospective analysis of 79 patients presenting primary HIV infections from 2005 to 2012 was performed in Marseille University Hospitals, southeastern France. Clinical, epidemiological and immunovirological data including phylogeny based on the polymerase gene were collected. 65 males and 14 females were enrolled. The main transmission route was homosexual contact (60.8%). Patients were mostly infected with subtype B (73.4%) and CRF02_AG (21.5%) HIV-1 strains. An increase in the annual number of HIV seroconversions among new HIV diagnoses from 5% in 2005 to 11.2% in 2012 (P = 0.06) and of the proportion of CRF02_AG HIV strains among primary HIV infections in 2011-2012 as compared to 2005-2010 (P = 0.055) was observed. Phylogenetic analysis revealed four transmission clusters including three transmission clusters among men having sex with men: two large clusters of nine CRF02_AG, six B HIV strains; and one small cluster of three B HIV strains. Clusters involved more frequently men (P = 0.01) belonging to caucasian ethicity (P = 0.05), with a higher HIV RNA load at inclusion (P = 0.03). These data highlight the importance of improving epidemiological surveillance and of implementing suitable prevention strategies to control the spread of HIV transmission among men having sex with men.
Collapse
Affiliation(s)
- Catherine Tamalet
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Isabelle Ravaux
- Mediterranean Institute for Infectious Diseases, Conception Hospital, Infectious Diseases Department, Marseille, France
| | - Jacques Moreau
- Mediterranean Institute for Infectious Diseases, Nord Hospital, Tropical and Infectious Diseases Department, Marseille, France
| | - Sylvie Brégigeon
- Immunohematology Unit, Sainte-Marguerite Hospital, INSERM U912 (SESSTIM), Marseille, France
| | - Christian Tourres
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Hervé Richet
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Cedric Abat
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Philippe Colson
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| |
Collapse
|
6
|
Jespersen S, Tolstrup M, Hønge BL, Medina C, Té DDS, Ellermann-Eriksen S, Østergaard L, Wejse C, Laursen AL. High level of HIV-1 drug resistance among patients with HIV-1 and HIV-1/2 dual infections in Guinea-Bissau. Virol J 2015; 12:41. [PMID: 25889017 PMCID: PMC4357169 DOI: 10.1186/s12985-015-0273-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 02/26/2015] [Indexed: 11/10/2022] Open
Abstract
Background With the widespread use of antiretroviral treatment (ART) in Africa, the risk of drug resistance has increased. The aim of this study was to evaluate levels of HIV-1 resistance among patients with HIV-1 and HIV-1/2 dual infections, treated with ART, at a large HIV clinic in Guinea-Bissau. Findings Patients were selected from the Bissau HIV cohort. All patients had HIV-1 or HIV-1/2 dual infection, a CD4 cell count performed before and 3–12 months after starting ART, and a corresponding available plasma sample. We measured viral load in patients with HIV-1 (n = 63) and HIV-1/2 dual (n = 16) infections a median of 184 days after starting ART (IQR: 126–235 days). In patients with virological failure (defined as viral load >1000 copies/ml) and with sufficient plasma available, we performed an HIV-1 genotypic resistance test. Thirty-six patients (46%) had virological failure. The CD4 cell count did not predict treatment failure. Of the 36 patients with virological failure, we performed a resistance test in 15 patients (42%), and nine patients (9/15; 60%) had resistance mutations. The most common mutation was K103N, which confers high-level resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI). No major mutations against protease inhibitors (PI) were found. Conclusions Our results showed that patients with HIV-1 and HIV-1/2 dual infections in Guinea-Bissau had a high rate of virological failure and rapid development of NNRTI resistance. It remains to be determined whether a more robust, PI-based treatment regimen might benefit this population more than NNRTIs.
Collapse
Affiliation(s)
- Sanne Jespersen
- Bandim Health Project, Indepth Network, Apartado 861, Bissau, Guinea-Bissau. .,Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Bo Langhoff Hønge
- Bandim Health Project, Indepth Network, Apartado 861, Bissau, Guinea-Bissau. .,Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark. .,Department of Clinical Immunology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Candida Medina
- National HIV Programme, Ministry of Health, Bissau, CP 1013, Bissau, Guinea-Bissau.
| | - David da Silva Té
- National HIV Programme, Ministry of Health, Bissau, CP 1013, Bissau, Guinea-Bissau.
| | - Svend Ellermann-Eriksen
- Department of Clinical Microbiology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Christian Wejse
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark. .,GloHAU, Center for Global Health, School of Public Health, Aarhus University, Bartholins Allé 2, 8000, Aarhus C, Denmark.
| | - Alex Lund Laursen
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | | |
Collapse
|
7
|
Delatorre E, Mir D, Bello G. Spatiotemporal dynamics of the HIV-1 subtype G epidemic in West and Central Africa. PLoS One 2014; 9:e98908. [PMID: 24918930 PMCID: PMC4053352 DOI: 10.1371/journal.pone.0098908] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/03/2014] [Indexed: 01/25/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the second most prevalent HIV-1 clade in West Africa, accounting for nearly 30% of infections in the region. There is no information about the spatiotemporal dynamics of dissemination of this HIV-1 clade in Africa. To this end, we analyzed a total of 305 HIV-1 subtype G pol sequences isolated from 11 different countries from West and Central Africa over a period of 20 years (1992 to 2011). Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method. Our analyses indicate that subtype G most probably emerged in Central Africa in 1968 (1956–1976). From Central Africa, the virus was disseminated to West and West Central Africa at multiple times from the middle 1970s onwards. Two subtype G strains probably introduced into Nigeria and Togo between the middle and the late 1970s were disseminated locally and to neighboring countries, leading to the origin of two major western African clades (GWA-I and GWA-II). Subtype G clades circulating in western and central African regions displayed an initial phase of exponential growth followed by a decline in growth rate since the early/middle 1990s; but the mean epidemic growth rate of GWA-I (0.75 year−1) and GWA-II (0.95 year−1) clades was about two times higher than that estimated for central African lineages (0.47 year−1). Notably, the overall evolutionary and demographic history of GWA-I and GWA-II clades was very similar to that estimated for the CRF06_cpx clade circulating in the same region. These results support the notion that the spatiotemporal dissemination dynamics of major HIV-1 clades circulating in western Africa have probably been shaped by the same ecological factors.
Collapse
Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
| |
Collapse
|
8
|
High frequency of HIV-1 infections with multiple HIV-1 strains in men having sex with men (MSM) in Senegal. INFECTION GENETICS AND EVOLUTION 2013; 20:206-14. [DOI: 10.1016/j.meegid.2013.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 02/01/2023]
|
9
|
Diouara AAM, Diop-Ndiaye H, Kebe-Fall K, Tchiakpè E, Ndiaye O, Ayouba A, Peeters M, Mboup S, Kane CT. Dried blood spots for HIV-1 drug resistance genotyping in decentralized settings in Senegal. J Med Virol 2013; 86:45-51. [PMID: 24122937 DOI: 10.1002/jmv.23778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2013] [Indexed: 11/11/2022]
Abstract
The aim of this study was to evaluate the use for HIV-1 drug resistance testing dried blood spots collected in remote areas and sent under field conditions to a reference laboratory and also to document virological failure in patients with suspected treatment failure. Samples were collected from patients receiving first line ART at 11 hospital sites around country, kept at room temperature (<37°C) and sent within 15 days maximum to the reference laboratory. Viral nucleic acids were obtained by magnetic extraction with NucliSENS (bioMérieux, Marcy l'Etoile, France). Genotyping of HIV-1 pol gene was performed using the ANRS protocol. Drug resistance mutations were analyzed according to the Stanford University HIV database version 6.0.8. Two hundred thirty one HIV-infected adults' on HAART first line regimen composed study population. The median time on ART was 18 months (range 6-68). Regardless of the treatment duration, the overall rate of virological failure (VL ≥ 3 log10 cp/ml) was 23.8% (n = 55/231). HIV genotypes were obtained successfully in 94.5% (n = 52/55). Drug resistance mutation was found in 41/52 patients in virological failure, for 17.7% (n = 41/231) an overall rate of drug resistance mutations. M184V/I was the most frequent mutation occurring, followed by K103N. Phylogenetic analysis of the 52 genotyped viral isolates showed the predominance of CRF02_AG with 62% (n = 32/52). Use of a DBS specimen is suitable to assist national programs for monitoring in remote areas HIV drug resistance in resources limited-settings.
Collapse
|
10
|
Ndiaye HD, Tchiakpe E, Vidal N, Ndiaye O, Diop AK, Peeters M, Mboup S, Toure-Kane C. HIV type 1 subtype C remains the predominant subtype in men having sex with men in Senegal. AIDS Res Hum Retroviruses 2013; 29:1265-72. [PMID: 23742654 DOI: 10.1089/aid.2013.0140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 epidemics are expanding among men who have sex with men in low- and middle-income countries. To confirm and further explore preliminary data in Senegal, we aimed to determine 3 years after a first study the HIV-1 genetic diversity in three different viral regions. From 109 samples available in 2007, 93 were sequenced in gag, 77 in env, and 60 in pol. Phylogenetic analysis showed that subtype C predominated (38-52%), followed by CRF02_AG (30-40%), subtype B (13-17%), and CRF09_cpx (2.6-5%). Subsubtype A3 and strains tightly linked to CRF43_02G were identified in env and gag, respectively, and 12% of the samples were unique recombinants. Six transmission chains involving two to seven individuals were identified. Some strains carried resistance mutations inside transmission chains. This study confirmed the existence of a dual epidemic in Senegal and emphasized the need to strengthen prevention programs to avoid strains intermixing between low-risk women and high-risk men.
Collapse
Affiliation(s)
- Halimatou Diop Ndiaye
- Laboratoire of Bacteriology-Virology, Hôpital Aristide Le Dantec, Dakar, Senegal and Université Cheikh Anta DIOP, Dakar, Senegal
| | - Edmond Tchiakpe
- Laboratoire of Bacteriology-Virology, Hôpital Aristide Le Dantec, Dakar, Senegal and Université Cheikh Anta DIOP, Dakar, Senegal
| | - Nicole Vidal
- UMI 233, Institut de Recherche pour le Développement (IRD) and Université de Montpellier I, Montpellier, France
| | - Ousseynou Ndiaye
- Laboratoire of Bacteriology-Virology, Hôpital Aristide Le Dantec, Dakar, Senegal and Université Cheikh Anta DIOP, Dakar, Senegal
| | | | - Martine Peeters
- UMI 233, Institut de Recherche pour le Développement (IRD) and Université de Montpellier I, Montpellier, France
| | - Souleymane Mboup
- Laboratoire of Bacteriology-Virology, Hôpital Aristide Le Dantec, Dakar, Senegal and Université Cheikh Anta DIOP, Dakar, Senegal
| | - Coumba Toure-Kane
- Laboratoire of Bacteriology-Virology, Hôpital Aristide Le Dantec, Dakar, Senegal and Université Cheikh Anta DIOP, Dakar, Senegal
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Thiam M, Diop-Ndiaye H, Kebe K, Vidal N, Diakhate-Lô R, Diouara AAM, Leye N, Ndiaye O, Sow A, Ngom-Gueye NF, Mboup S, Toure-Kane C. Performance of the ViroSeq HIV-1 genotyping system v2.0 on HIV-1 strains circulating in Senegal. J Virol Methods 2012; 188:97-103. [PMID: 23266258 DOI: 10.1016/j.jviromet.2012.11.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 11/22/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
The objective of this study was to investigate the performance of the ViroSeq HIV-1 Genotyping System v2.0 on HIV-1 non-B strains identified in Senegalese patients. The study involved 150 patients, and genotyping was performed using the ViroSeq HIV-1 Genotyping System v2.0 or an in-house method developed by the French National Agency on AIDS Research AC11 when the ViroSeq HIV-1 Genotyping System v2.0 failed. The sequences were edited to assess the performance of sequencing primers at their presumed binding regions. The Polymorphism was studied in the regions between the sequences of Senegalese patients and the subtype B strains used as references. The phylogenetic analysis showed a predominance of CRF02_AG (88/150; 58.7%) and the circulation of 11 subtypes/CRFs, 16 unique recombinant forms (URFs) and one unclassified sample. The amplification and sequencing rates were 98% (147/150) and 96.6% (142/147), respectively. This study showed that only primer B exhibited 100% success, while the failure rate ranged from 1.4% to 71.4% for the other primers (D: 71.4%, A and H: 12.2%, F: 7.5%, G: 5.5% and C: 1.4%). These findings suggest the need for an alternative method or alternative primers for non-B strains that were not sequenced successfully using the ViroSeq HIV-1 Genotyping System v2.0.
Collapse
Affiliation(s)
- Moussa Thiam
- Laboratory of Bacteriology and Virology, Le Dantec Hospital, Dakar, Senegal
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
HIV-1 genetic diversity and drug resistance among Senegalese patients in the public health system. J Clin Microbiol 2012; 51:578-84. [PMID: 23241378 DOI: 10.1128/jcm.02452-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we investigated the prevalence of human immunodeficiency virus type 1 (HIV-1) drug resistance mutations and genetic variability among Senegalese patients undergoing highly active antiretroviral therapy (ART) in the public health system. We conducted a cross-sectional study of 72 patients with suspected therapeutic failure. HIV-1 genotyping was performed with Viroseq HIV-1 Genotyping System v2.0 or the procedure developed by the ANRS AC11 resistance study group, and a phylogenetic analysis was performed. The median follow-up visit was at 40 (range, 12 to 123) months, and the median viral load was 4.67 (range, 3.13 to 6.94) log(10) copies/ml. The first-line therapeutic regimen was nucleoside reverse transcriptase inhibitors (NRTIs) plus efavirenz (EFV) or NRTIs plus nevirapine (NVP) (54/72 patients; 75%), and the second-line therapy was NRTIs plus a protease inhibitor (PI/r) (18/72; 25%). Fifty-five patients (55/72; 76.39%) had at least one drug resistance mutation. The drug resistance rates were 72.22 and 88.89% for the first-line and second-line ARTs, respectively. In NRTI mutations, thymidine analog mutations (TAMs) were found in 50.79% and the M184V mutation was found in 34.92% of the samples. For non-NRTI resistance, we noted a predominance of the K103N mutation (46.27%). For PI/r, several cases of mutations were found with a predominance of M46I and L76V/F at 24% each. The phylogenetic analysis revealed CRF02_AG as the predominant circulating recombinant form (43/72; 59.72%). We found a high prevalence of resistance mutations and a high rate of TAMs among Senegalese patients in the public health system. These findings emphasize the need to improve virological monitoring in resource-limited settings.
Collapse
|
14
|
The origin and evolutionary history of HIV-1 subtype C in Senegal. PLoS One 2012; 7:e33579. [PMID: 22470456 PMCID: PMC3314668 DOI: 10.1371/journal.pone.0033579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/15/2012] [Indexed: 12/03/2022] Open
Abstract
Background The classification of HIV-1 strains in subtypes and Circulating Recombinant Forms (CRFs) has helped in tracking the course of the HIV pandemic. In Senegal, which is located at the tip of West Africa, CRF02_AG predominates in the general population and Female Sex Workers (FSWs). In contrast, 40% of Men having Sex with Men (MSM) in Senegal are infected with subtype C. In this study we analyzed the geographical origins and introduction dates of HIV-1 C in Senegal in order to better understand the evolutionary history of this subtype, which predominates today in the MSM population Methodology/Principal Findings We used a combination of phylogenetic analyses and a Bayesian coalescent-based approach, to study the phylogenetic relationships in pol of 56 subtype C isolates from Senegal with 3,025 subtype C strains that were sampled worldwide. Our analysis shows a significantly well supported cluster which contains all subtype C strains that circulate among MSM in Senegal. The MSM cluster and other strains from Senegal are widely dispersed among the different subclusters of African HIV-1 C strains, suggesting multiple introductions of subtype C in Senegal from many different southern and east African countries. More detailed analyses show that HIV-1 C strains from MSM are more closely related to those from southern Africa. The estimated date of the MRCA of subtype C in the MSM population in Senegal is estimated to be in the early 80's. Conclusions/Significance Our evolutionary reconstructions suggest that multiple subtype C viruses with a common ancestor originating in the early 1970s entered Senegal. There was only one efficient spread in the MSM population, which most likely resulted from a single introduction, underlining the importance of high-risk behavior in spread of viruses.
Collapse
|