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Bi SG, Sokouri DP, Tiékoura K, N׳Nan OA, Lolo M, Gnangbé F, N׳Guetta ASP. Pattern of the evolution of HIV-1 enν gene in Côte d׳Ivoire. Bioinformation 2014; 10:671-8. [PMID: 25512682 PMCID: PMC4261110 DOI: 10.6026/97320630010671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 11/23/2022] Open
Abstract
Cête d׳Ivoire continues to have the highest HIV-1 prevalence rate in West Africa, although the infection number is in constant decline. The external envelope protein of the viruses is a likely site of selection, and responsible for receptor binding and entry into host cells, and therefore constitutes an ideal region with which to investigate the evolutionary processes acting on HIV-1. In this study, we analyse 189 envelope glycoprotein V3 loop region sequences of viruse isolates from 1995 to 2009, from HIV-1 untreated patients living in Cête d׳Ivoire, to decipher the temporal relationship between disease diversity, divergence and selection. Our analyses show that the nonsynonymous and synonymous ratio (dN/dS) was lower than 1 for viral populations analysed within 15 years, which showed the sequences did not undergo adequate immune pressure. The phylogenetic tree of the sequences analysed demonstrated distinctly long internal branches and short external branches, suggesting that only a small number of viruses infected the new host cell at each transmission. In addition to identifying sites under purifying selection, we also identified neutral sites that can cause false positive inference of selection. These sites presented form a resource for future studies of selection pressures acting on HIV-1 enν gene in Cête d׳Ivoire and other West African countries.
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Affiliation(s)
- Sery Gonedelé Bi
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët Boigny, Abidjan, Cête d׳Ivoire, 22 BP 582 Abidjan 22
- Centre Suisse de Recherches Scientifiques en Cête d׳Ivoire, 01 BP 1303 Abidjan 01
| | - Didier P Sokouri
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët Boigny, Abidjan, Cête d׳Ivoire, 22 BP 582 Abidjan 22
| | - Kouakou Tiékoura
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët Boigny, Abidjan, Cête d׳Ivoire, 22 BP 582 Abidjan 22
| | - Oulo Alla N׳Nan
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët Boigny, Abidjan, Cête d׳Ivoire, 22 BP 582 Abidjan 22
| | - Marcel Lolo
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët Boigny, Abidjan, Cête d׳Ivoire, 22 BP 582 Abidjan 22
| | - Félix Gnangbé
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët Boigny, Abidjan, Cête d׳Ivoire, 22 BP 582 Abidjan 22
| | - Assanvo SP N׳Guetta
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët Boigny, Abidjan, Cête d׳Ivoire, 22 BP 582 Abidjan 22
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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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Frange P, Galimand J, Vidal N, Goujard C, Deveau C, Souala F, Peeters M, Meyer L, Rouzioux C, Chaix ML. New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study. Retrovirology 2008; 5:69. [PMID: 18673538 PMCID: PMC2553414 DOI: 10.1186/1742-4690-5-69] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 08/01/2008] [Indexed: 12/02/2022] Open
Abstract
Background Prevalence of HIV-1 non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France. Our objective was to characterize in detail non-B strains which could not be genetically classified into the known subtypes/Circulating Recombinant Forms (CRFs). Methods Among 744 patients enrolled in the ANRS PRIMO Cohort since 1996, 176 (23.7%) were infected with HIV-1 non-B strains. The subtype/CRF could not be identified in RT for 15 (2%). The V3-V5 env region was sequenced and 3 strains (04FR-KZS, 06FR-CRN, 04FR-AUK) were full-length sequenced. Phylogenetic and bootscan analyses were used to characterize the mosaic structures. Results Among V3-V5 sequences, 6 were divergent A, 2 distantly related to E or D, 2 C, 1 B and 2 remained unclassified. 04FR-KZS, isolated in a Congolese woman infected in France, clustered with 2 previously described viruses from the Democratic Republic of Congo. They represent CRF27_cpx involving A/E/G/H/J/K/U subtypes. 06FR-CRN, isolated in a homosexual Caucasian patient, was a B/C/U recombinant involving a Brazilian C strain. 04FR-AUK, isolated in a Congolese patient infected in France, was a A/K/CRF09/U recombinant clustering from gag to vif with HIV-1 MAL. Others PHI were further observed in 2006–2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France. Conclusion This study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France. Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.
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Affiliation(s)
- Pierre Frange
- EA 3620, Université Paris - Descartes, Laboratoire de Virologie, Hôpital Necker - Enfants Malades, AP-HP, Paris, France.
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Derache A, Maiga AI, Traore O, Akonde A, Cisse M, Jarrousse B, Koita V, Diarra B, Carcelain G, Barin F, Pizzocolo C, Pizarro L, Katlama C, Calvez V, Marcelin AG. Evolution of genetic diversity and drug resistance mutations in HIV-1 among untreated patients from Mali between 2005 and 2006. J Antimicrob Chemother 2008; 62:456-63. [PMID: 18556706 DOI: 10.1093/jac/dkn234] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To describe HIV-1 variants circulating in Mali and to estimate the rate of transmission of HIV-1 drug resistance in 2006. PATIENTS AND METHODS Viral reverse transcriptase (RT) and protease (PR) genes from 198 antiretroviral (ARV)-naive patients diagnosed HIV-1 positive in May 2006 in Bamako and Segou were sequenced. RESULTS Although CRF02_AG was always the predominant HIV-1 subtype observed (72%), a higher genetic diversity than that in 2005 was observed. The overall prevalence of primary resistance is 11.5% in Mali in 2006, according to the 2007 IAS-USA list of mutations [nucleoside RT inhibitor (NRTI): 1.5%, non-NRTI (NNRTI): 9% and PI: 1%], and 2.5% (NRTI: 1%, NNRTI: 1.5% and PI: 0%), according to the Stanford list of mutations. There was no significant difference between 2005 and 2006 in the overall primary resistance prevalence or in the prevalence of mutations in the different ARV classes. Resistance mutations found in RT and PR genes are in agreement with the highly active antiretroviral therapy regimen available in Mali, except for V90I, V106I and A98G mutations which are associated with etravirine resistance, but polymorphic in non-B subtypes. CONCLUSIONS HIV-1 genetic diversity seems increased in Mali, but the overall HIV-1 primary resistance prevalence remains low. This is consistent with the findings from other West African countries where prevalence rates are lower than 5%. However, considering the large scaling up of ARV use in this country, it is necessary to regularly monitor the development of primary resistance in Mali.
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Affiliation(s)
- Anne Derache
- UPMC Univ Paris 06, EA2387, 4 Place Jussieu, F-75005 Paris, France
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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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Toni TD, Masquelier B, Minga A, Anglaret X, Danel C, Coulibaly A, Chenal H, Dabis F, Salamon R, Fleury HJ. HIV-1 antiretroviral drug resistance in recently infected patients in Abidjan, Côte d'Ivoire: A 4-year survey, 2002-2006. AIDS Res Hum Retroviruses 2007; 23:1155-60. [PMID: 17919113 DOI: 10.1089/aid.2007.0072] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We performed HIV-1 drug resistance genotypic analysis of viral isolates from 100 antiretroviral (ARV)-naive, recently HIV-1-infected (between 2002 and 2006) individuals from Abidjan (Côte d'Ivoire). The overall prevalence of HIV-1 variants with resistance mutations to reverse transcriptase, protease, or fusion inhibitors was 6%. The majority of isolates were CRF02_AG. Compared with a previous study carried out by our group in 2001-2002 in a similar population in Abidjan, our findings confirm the circulation and transmission of HIV-1 carrying key ARV drug resistance mutation.
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Affiliation(s)
- Thomas d'Aquin Toni
- Programme PAC-CI/Primo-CI ANRS 1220, Abidjan, Côte d'Ivoire
- Centre Intégré de Recherches Biocliniques d'Abidjan (CIRBA), Abidjan, Côte d'Ivoire
| | - Bernard Masquelier
- Laboratoire de Virologie EA 2968, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | - Albert Minga
- Programme PAC-CI/Primo-CI ANRS 1220, Abidjan, Côte d'Ivoire
| | - Xavier Anglaret
- Programme PAC-CI/Primo-CI ANRS 1220, Abidjan, Côte d'Ivoire
- ISPED, INSERM U593, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | | | - Ali Coulibaly
- Programme PAC-CI/Primo-CI ANRS 1220, Abidjan, Côte d'Ivoire
| | - Henri Chenal
- Centre Intégré de Recherches Biocliniques d'Abidjan (CIRBA), Abidjan, Côte d'Ivoire
| | - François Dabis
- ISPED, INSERM U593, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | - Roger Salamon
- ISPED, INSERM U593, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | - Hervé J. Fleury
- Laboratoire de Virologie EA 2968, Université Victor Segalen Bordeaux 2, Bordeaux, France
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Tramuto F, Bonura F, Perna AM, Mancuso S, Firenze A, Romano N, Vitale F. Genetic diversity of HIV-1 non-B strains in Sicily: evidence of intersubtype recombinants by sequence analysis of gag, pol, and env genes. AIDS Res Hum Retroviruses 2007; 23:1131-8. [PMID: 17919109 DOI: 10.1089/aid.2007.0031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The molecular epidemiology of HIV-1 strains in Sicily (Italy) was phylogenetically investigated by the analysis of HIV-1 gag, pol, and env gene sequences from 11 HIV-1 non-B strains from 408 HIV-1-seropositive patients observed from September 2001 to August 2006. Sequences suggestive of recombination were further investigated by bootscanning analysis of various fragments. Overall, we identified several second-generation recombinant (SGRs) strains, which contained genetic material of CRF02_AG in at least one gene. Notably, three individuals were found to be infected with subsubtype A3, and one of them showed genetic recombination with subsubtype A4. The current study emphasizes the genetic analysis of gag, pol, and env genes as a powerful tool to trace the spread of complex HIV-1 recombinant forms, and highlight the genetic diversity of HIV-1 non-B strains in Italy.
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Affiliation(s)
- Fabio Tramuto
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Igiene e Microbiologia, Università degli Studi di Palermo, Palermo, Italy
| | - Filippa Bonura
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Igiene e Microbiologia, Università degli Studi di Palermo, Palermo, Italy
| | - Anna Maria Perna
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Igiene e Microbiologia, Università degli Studi di Palermo, Palermo, Italy
| | - Salvatrice Mancuso
- Servizio di Riferimento Regionale per la Diagnosi di AIDS e Sindromi Correlate, Università degli Studi di Palermo, Palermo, Italy
| | - Alberto Firenze
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Igiene e Microbiologia, Università degli Studi di Palermo, Palermo, Italy
| | - Nino Romano
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Igiene e Microbiologia, Università degli Studi di Palermo, Palermo, Italy
| | - Francesco Vitale
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Igiene e Microbiologia, Università degli Studi di Palermo, Palermo, Italy
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Sankalé JL, Langevin S, Odaibo G, Meloni ST, Ojesina AI, Olaleye D, Kanki P. The complexity of circulating HIV type 1 strains in Oyo state, Nigeria. AIDS Res Hum Retroviruses 2007; 23:1020-5. [PMID: 17725419 DOI: 10.1089/aid.2006.0304] [Citation(s) in RCA: 25] [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
Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to circulate in West Africa. We undertook a survey of HIVs in Oyo state, in southwestern Nigeria. We analyzed 71 samples from Ibadan, the capital city, and 33 samples from Saki, 100 miles west of Ibadan. We sequenced part of the gag gene and the envelope C2V3 region from 102 and 89 samples, respectively. In the 87 samples for which both genes were sequenced, subtype G and CRF02_AG were found in equal proportions (32.2% each). Other samples included CRF06_cpx (8.0%), subtype A (2.3%), C (1.1%), unclassified (1.1%), or discordant sequences suggesting the presence of a large number of recombinants involving CRF02_AG and/or subtype G (20.7%) or other subtypes (2.3%). The subtype/CRF designation was concordant in two gene fragments in the majority of samples evaluated. However, we observed differences in subtype distribution between the two locations with a predominance of subtype G in Ibadan and CRF02 in Saki. This is the first in-depth analysis of HIV variability at a state level in Nigeria. Our analysis revealed a significant level of viral heterogeneity and a geographical difference in subtype distribution, and demonstrated that CRF02_AG does not account for the majority of circulating strains.
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Affiliation(s)
- Jean-Louis Sankalé
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Boston, Massachusetts 02115, USA
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Chin MPS, Chen J, Nikolaitchik OA, Hu WS. Molecular determinants of HIV-1 intersubtype recombination potential. Virology 2007; 363:437-46. [PMID: 17336363 DOI: 10.1016/j.virol.2007.01.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 01/16/2007] [Accepted: 01/29/2007] [Indexed: 11/19/2022]
Abstract
Sequence differences in the dimerization initiation signal (DIS) affect the rate of recombination between subtype B and subtype C HIV-1. To test the hypothesis that DIS sequences can be used to predict intersubtype recombination potentials, we measured the recombination rate between CRF01_A/E (AE) and B, which contain mismatches in the DIS, and between AE and C, which have an identical DIS. Compared with the intrasubtype recombination rate, the recombination rate between AE and subtype B virus was 9-fold lower, and the rate between AE and subtype C virus was 2-fold lower. Thus, DIS sequences can be used to predict the recombination potential between HIV-1 subtypes. Further analyses revealed that the 2-fold lower recombination rate between AE and C viruses can be restored to the intrasubtype recombination rate by matching a part of the LTR and a portion of the viral genome. Therefore, the lower intersubtype recombination rate between AE and C is not caused by a given region but is a cumulative effect by more than one region.
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Affiliation(s)
- Mario P S Chin
- HIV Drug Resistance Program, National Cancer Institute, P.O. Box B, Building 535, Room 336, Frederick, MD 21702, USA
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Marechal V, Jauvin V, Selekon B, Leal J, Pelembi P, Fikouma V, Gabrie P, Heredeibona LS, Goumba C, Serdouma E, Ayouba A, Fleury H. Increasing HIV type 1 polymorphic diversity but no resistance to antiretroviral drugs in untreated patients from Central African Republic: a 2005 study. AIDS Res Hum Retroviruses 2006; 22:1036-44. [PMID: 17067275 DOI: 10.1089/aid.2006.22.1036] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
As the HIV-1 pandemic becomes increasingly complex and as new countries acceed to antiretroviral drugs, the molecular characterization of HIV-1 strains circulating has important implications for vaccine research and for the efficacy of treatments. To follow the evolution of HIV-1 diversity in African countries, we have carried out a molecular analysis of HIV-1 strains collected from 150 HIV-1-positive pregnant women recruited in Bangui, Central African Republic (CAR). We have sequenced reverse transcriptase (RT) and protease (PROT) genes to (1) characterize the subtypes and CRFs, (2) describe the polymorphism of RT and PROT, particularly at the positions of drug resistance mutations in subtype B, and (3) observe potential drug resistance mutations and evaluate the prevalence of isolates bearing such mutations in this untreated population. The results showed that there is a very high and increasing diversity of HIV-1 strains circulating in CAR; out of 117 samples sequenced, we have observed 45 CRF11_cpx, 22 subtypes A1, 13 subtypes G, 7 subtypes CRF01_AE, 3 subtypes B, 3 subtypes CRF02_AG, 2 of each subtype F2 and CRF09_cpx, and one of each subtype D, J, C, H, CRF06_cpx, CRF13_cpx, and CRF19_cpx; the remaining 13 strains showed discordant genomic results suggesting multiple recombinations leading to mosaic viruses. The polymorphism of RT and PROT was high compared to subtype B, particularly at some positions that have been involved in antiretroviral resistance in subtype B, but we could not observe any major resistance mutation in this sample of untreated patients. The prevalence of drug resistance mutations in this population was therefore clearly under the WHO 5% threshold.
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