1
|
Gonçalves P, Barreto J, Santos M, Leal S, Marcelino J, Abecasis A, Palladino C, Taveira N. HIV-1 drug resistance and genetic diversity in people with HIV-1 in Cape Verde. AIDS 2024; 38:1101-1110. [PMID: 38349224 DOI: 10.1097/qad.0000000000003866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
OBJECTIVES To characterize the genetic diversity and drug resistance profiles of people with HIV-1 failing ART in Cape Verde (CV). DESIGN Cross-sectional study conducted between January 2019 and December 2021 in 24 health centres on the islands of Santiago and São Vicente. METHODS The HIV-1 pol gene was sequenced in individuals with a detectable viral load. HIV-1 genetic diversity was determined by phylogenetic analysis. Drug resistance mutation patterns and resistance phenotypes were estimated using the Stanford algorithm. RESULTS Viral load was detected in 73 of 252 (29%) enrolled participants and sequencing data were produced for 58 (79%) participants. CRF02 AG strains predominated (46.5%), followed by subtype G (22.4%). Most patients (80%) had mutations conferring resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs) (67%), nucleoside reverse transcriptase inhibitors (55%), integrase inhibitors (10%) and/or protease inhibitors (7%) used in Cape Verde, a significant increase compared with a study conducted in 2010-2011. The most common mutations were M184V/I (43%), K103N/S (36%) and G190A/S (19%). NNRTI resistance was associated with younger age and exposure to two or more drug regimens. CONCLUSION The HIV-1 epidemic in Cape Verde is mainly driven by CRF02_AG and subtype G. Resistance to NNRTIs and/or NRTIs is highly prevalent and resistance to LPV/r and DTG is emerging. Our results support the use of DTG-based first-line ART and protease inhibitor-based regimens for patients with virological failure, but emerging resistance to LPV/r and DTG is a concern. Continued monitoring of drug resistance is essential to ensure adequate healthcare for PWH in Cape Verde.
Collapse
Affiliation(s)
- Paloma Gonçalves
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
| | | | - Menilita Santos
- Instituto Nacional de Saúde Pública de Cabo Verde, Praia, Cape Verde
| | - Silvania Leal
- Instituto Nacional de Saúde Pública de Cabo Verde, Praia, Cape Verde
| | - José Marcelino
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Claudia Palladino
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica
| |
Collapse
|
2
|
Nii-Trebi NI, Brandful JAM, Ibe S, Sugiura W, Barnor JS, Bampoh PO, Yamaoka S, Matano T, Yoshimura K, Ishikawa K, Ampofo WK. Dynamic HIV-1 genetic recombination and genotypic drug resistance among treatment-experienced adults in northern Ghana. J Med Microbiol 2017; 66:1663-1672. [PMID: 29068286 DOI: 10.1099/jmm.0.000621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE There have been hardly any reports on the human immunodeficiency virus type 1 (HIV-1) drug-resistance profile from northern Ghana since antiretroviral therapy (ART) was introduced over a decade ago. This study investigated prevailing HIV-1 subtypes and examined the occurrence of drug resistance in ART-experienced patients in Tamale, the capital of the Northern Region of Ghana. METHODOLOGY A cross-sectional study was carried out on HIV-infected adult patients receiving first-line ART. HIV viral load (VL) and CD4+ T-cell counts were measured. The pol gene sequences were analysed for genotypic resistance by an in-house HIV-1 drug-resistance test; the prevailing HIV-1 subtypes were analysed in detail.Results/Key findings. A total of 33 subjects were studied. Participants comprised 11 males (33.3 %) and 22 (66.7 %) females, with a median age of 34.5 years [interquartile range (IQR) 30.0-40.3]. The median duration on ART was 12 months (IQR 8.0-24). Of the 24 subjects successfully genotyped, 10 (41.7 %) viruses possessed at least one mutation conferring resistance to nucleoside or non-nucleoside reverse-transcriptase inhibitors (NRTIs/NNRTIs). Two-class drug resistance to NRTI and NNRTI was mostly detected (25 %, 6/24). The most frequent mutations were lamivudine-resistance M184V and efavirenz/nevirapine-resistance K103N. HIV-1 subtype CRF02_AG was predominant (79.2 %). Other HIV-1 subtypes detected were G (8.3 %), A3 (4.2 %) and importantly two (8.3 %) unique HIV-1 recombinant forms with CRF02_AG/A3 mosaic. CONCLUSION HIV-1 shows high genetic diversity and on-going viral genetic recombination in the study region. Nearly 42 % of the patients studied harboured a drug-resistant virus. The study underscores the need for continued surveillance of HIV-1 subtype diversity; and of drug-resistance patterns to guide selection of second-line regimens in northern Ghana.
Collapse
Affiliation(s)
- Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana.,Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Shiro Ibe
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Nagoya, Japan
| | - Wataru Sugiura
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Nagoya, Japan.,Department of AIDS Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jacob Samson Barnor
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Shoji Yamaoka
- Department of Molecular Virology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Kazuhisa Yoshimura
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - William Kwabena Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| |
Collapse
|
3
|
Yebra G, Kalish ML, Leigh Brown AJ. Reconstructing the HIV-1 CRF02_AG and CRF06_cpx epidemics in Burkina Faso and West Africa using early samples. INFECTION GENETICS AND EVOLUTION 2016; 46:209-218. [PMID: 27063411 DOI: 10.1016/j.meegid.2016.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND HIV-1 circulating recombinant forms (CRFs) represent viral recombinant lineages that play a significant role in the global epidemic. Two of them dominate the epidemic in Burkina Faso: CRF06_cpx (first described in this country) and CRF02_AG. We reconstructed the phylodynamics of both recombinant viruses in Burkina Faso and throughout West Africa. METHODS We analysed CRF06_cpx and CRF02_AG sequences (protease/gp41) from early samples collected in Burkina Faso in 1986 together with other GenBank sequences (1984-2013) in 4 datasets: African CRF06_cpx (210/60); down-sampled CRF06_cpx (146/45); Burkina Faso CRF02_AG (130/39) and West/Central African CRF02_AG (691/298). For each dataset, we analysed both protease and gp41 jointly using the BEAST multilocus analysis and conducted phylogeographic analysis to reconstruct the early migration routes between countries. RESULTS The time to the most recent common ancestor (tMRCA) of CRF06_cpx was 1979 (1973-1983) for protease and 1981 (1978-1983) for gp41. The gp41 analysis inferred the origin of CRF06_cpx (or at least its parental subtype G lineage) in the Democratic Republic of Congo but migrated to Burkina Faso soon after (1982). Both genes showed that CRF06_cpx radiated to the rest of West Africa predominantly after around 1990. These results were robust to the oversampling of Burkina Faso sequences as they were confirmed in the down-sampled dataset. The tMRCA of the Burkina Faso CRF02_AG lineage was 1979 (1977-1983) for protease and 1980 (1978-1981) for gp41. However, we reconstructed its presence in West Africa much earlier (mid-1960s), with an initial origin in Cameroon and/or Nigeria, and its phylogeographic analysis revealed much interconnection within the region with a lack of country-specific phylogenetic patterns, which prevents tracking its exact migration routes. CONCLUSIONS Burkina Faso presents a relatively young HIV epidemic, with the diversification of the current in-country CRF02_AG and CRF06_cpx lineages taking place around 1980. This country represents the main source of CRF06_cpx in West Africa. The CRF02_AG epidemic started at least a decade earlier and showed much interchange between West African countries (especially involving coastal countries) suggesting great population mobility and an extensive viral spread in the region.
Collapse
Affiliation(s)
- Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Marcia L Kalish
- Institute for Global Health, Vanderbilt University, Nashville, TN, USA
| | | |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Tongo M, Essomba RG, Nindo F, Abrahams F, Nanfack AJ, Fokam J, Takou D, Torimiro JN, Mpoudi-Ngole E, Burgers WA, Martin DP, Dorfman JR. Phylogenetics of HIV-1 subtype G env: Greater complexity and older origins than previously reported. INFECTION GENETICS AND EVOLUTION 2015; 35:9-18. [PMID: 26190450 DOI: 10.1016/j.meegid.2015.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
Abstract
HIV-1 subtype G has played an early and central role in the emergent complexity of the HIV-1 group M (HIV-1M) epidemic in central/west Africa. Here, we analysed new subtype G env sequences sampled from 8 individuals in Yaoundé, Cameroon during 2007-2010, together with all publically available subtype G-attributed full-length env sequences with known sampling dates and locations. We inferred that the most recent common ancestor (MRCA) of the analysed subtype G env sequences most likely occurred in ∼1953 (95% Highest Posterior Density interval [HPD] 1939-1963): about 15 years earlier than previous estimates. We found that the subtype G env phylogeny has a complex structure including seven distinct lineages, each likely dating back to the late 1960s or early 1970s. Sequences from Angola, Gabon and the Democratic Republic of Congo failed to group consistently in these lineages, possibly because they are related to more ancient sequences that are poorly sampled. The circulating recombinant form (CRF), CRF06_cpx env sequences but not CRF25_cpx env sequences are phylogenetically nested within the subtype G clade. This confirms that the CRF06_cpx env plausibly was derived through recombination from a subtype G parent, and suggests that the CRF25_cpx env was likely derived from an HIV-1M lineage related to the MRCA of subtype G that has remained undiscovered and may be extinct. Overall, this fills important gaps in our knowledge of the early events in the spread of HIV-1M.
Collapse
Affiliation(s)
- Marcel Tongo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Faculty of Health Sciences, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon
| | - René G Essomba
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Frederick Nindo
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Fatima Abrahams
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa
| | - Aubin Joseph Nanfack
- Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon
| | - Joseph Fokam
- Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon; Faculty of Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Desire Takou
- Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon
| | - Judith N Torimiro
- Centre International de Référence «Chantal Biya» pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Yaoundé, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Eitel Mpoudi-Ngole
- Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon
| | - Wendy A Burgers
- Division of Medical Virology, Faculty of Health Sciences, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jeffrey R Dorfman
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| |
Collapse
|