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Hunter JR, dos Santos DEM, Munerato P, Janini LM, Castelo A, Sucupira MC, Truong HHM, Diaz RS. Fitness Cost of Antiretroviral Drug Resistance Mutations on the pol Gene during Analytical Antiretroviral Treatment Interruption among Individuals Experiencing Virological Failure. Pathogens 2021; 10:pathogens10111425. [PMID: 34832581 PMCID: PMC8622617 DOI: 10.3390/pathogens10111425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
HIV cure studies require patients to enter an analytical treatment interruption (ATI). Here, we describe previously unanalyzed data that sheds light on ATI dynamics in PLHIV (People Living with HIV). We present drug resistance mutation dynamics on the pol gene among individuals with antiretroviral virological failure who underwent ATI. The study involved a 12-week interruption in antiretroviral therapy (ART), monitoring of viral load, CD4+/CD8+ T cell counts, and sequencing of the pol gene from 38 individuals experiencing virological failure and harboring 3-class resistant HIV strains: nucleoside reverse transcriptase inhibitors (NRTI) non-nucleoside inhibitors (NNRTI), and protease inhibitors (PI). Protease and reverse transcriptase regions of the pol gene were sequenced at baseline before ATI and every four weeks thereafter from PBMCs and at baseline and after 12 weeks from plasma HIV RNA using population-based Sanger sequencing. Average viral load increased 0.559 log10 copies per milliliter. CD4+ T cell count decreased as soon as ART was withdrawn, an average loss of 99.0 cells/mL. Forty-three percent of the mutations associated with antiretroviral resistance in PBMCs disappeared and fifty-seven percent of the mutations in plasma reverted to wild type, which was less than the 100% reversion expected. In PBMC, the PI mutations reverted more slowly than reverse transcriptase mutations. The patients were projected to need an average of 33.7 weeks for PI to revert compared with 20.9 weeks for NRTI and 19.8 weeks for NNRTI. Mutations in the pol gene can cause virological failure and difficulty in re-establishing effective virological suppression.
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Affiliation(s)
- James R. Hunter
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Domingos E. Matos dos Santos
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Patricia Munerato
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Luiz Mario Janini
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Adauto Castelo
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Maria Cecilia Sucupira
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Hong-Ha M. Truong
- Department of Medicine, University of California, San Francisco, CA 94158, USA;
| | - Ricardo Sobhie Diaz
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
- Correspondence:
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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.
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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
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Vidal N, Diop H, Montavon C, Butel C, Bosch S, Ngole EM, Touré-Kane C, Mboup S, Delaporte E, Peeters M. A novel multiregion hybridization assay reveals high frequency of dual inter-subtype infections among HIV-positive individuals in Cameroon, West Central Africa. INFECTION GENETICS AND EVOLUTION 2012; 14:73-82. [PMID: 23232100 DOI: 10.1016/j.meegid.2012.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/21/2012] [Indexed: 11/15/2022]
Abstract
In West and West Central Africa, multiple subtypes, circulating recombinant forms (CRF), and high proportions of unique recombinant forms (URF) are documented. The predominance of recombinants strongly suggests that dual infections occur frequently. In the present study, we adapted the multi-region hybridization assay (MHA), previously developed to identify dual infections in geographic regions where few HIV-1 variants circulate, to identify HIV-1 variants and dual infections. We designed clade-specific probes in three genomic regions (gag p17, vpu, nef) to detect eight different variants that are common in this part of Africa (A, B/D, C, F, G, CRF02_AG, CRF06_cpx, CRF22_01A1). The assay was validated with 163 samples representing the corresponding HIV-1 variants. Depending on the genomic regions, the global sensitivity of the assay ranged from 86% to 94%, and the global specificity was between 85% and 96%. The assay was then applied on 156 antiretroviral treatment-naive patients from Cameroon. The MHA assay identified 79%, 85% and 90% of the strains in nef, gag and vpu regions, respectively. The subtype/CRF distribution and the proportion of inter-region recombinants obtained by the new MHA assay were in accordance with known subtype/CRF distribution in Cameroon. Moreover, the MHA assay identified 35 (22.4%) patients as dually infected, from which 20 were reactive in more than one region and/or with concordant multigenomic recombination pattern. Despite the high genetic diversity, we successfully developed an hybridization assay allowing identification of eight common HIV-1 variants circulating in West and West Central Africa. We documented high rates of dual infection in a low-risk population group, illustrating that the global evolution of HIV diversity is driven by dual infections. This assay could become a useful screening tool for the global surveillance and monitoring of inter-subtype/CRF dual infections in West and West Central Africa.
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Affiliation(s)
- Nicole Vidal
- UMI 233, Institut de Recherches pour le Développement (IRD) et Université de Montpellier I, Montpellier, France.
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Melo FL, Jamal LF, Zanotto PMDA. Characterization of primary isolates of HIV type 1 CRF28_BF, CRF29_BF, and unique BF recombinants circulating in São Paulo, Brazil. AIDS Res Hum Retroviruses 2012; 28:1082-8. [PMID: 22176121 PMCID: PMC3423645 DOI: 10.1089/aid.2011.0123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report for the first time the genetic and biological characterization of 10 HIV-1 primary isolates representing CRF28_BF and CRF29_BF together with additional unique BF recombinant forms (URFs) obtained by PBMC cocultivation. Recombination is an important factor promoting the increase in the genetic diversity of HIV-1. Notably, more than 20% of HIV-1 sequences worldwide were recombinants. Several recombinant viruses were reported in Brazil, and six circulating recombinant forms (CRFs) have been identified (CRF28_BF, CRF29_BF, CRF31_BC, CRF39_BF, CRF40_BF, and CRF46_BF). CRF28_BF and CRF29_BF were found to infect almost 30% of the patients in São Paulo State. The near full-length genomes of these 10 primary isolates were amplified by nested PCR in three overlapping segments, purified, and sequenced. Three samples were related to CRF28_BF, three to CRF29_BF, and four were unique recombinant forms (URFs), as determined by their breakpoint profile determined with the jpHMM program. Additionally, the coreceptor usage of these isolates was investigated in vitro using GHOST assays, which revealed three dual-tropic (X4/R5) viruses, four lymphotropic (X4) viruses, and three macrophage-tropic (R5) viruses with different V3-loop motifs, which challenges the notion that GWGR-carrying viruses are macrophage-tropic only. In sum, we report a much-anticipated well-characterized panel of viruses representing CRF28_BF, CRF29_BF, and URFs from São Paulo State, Brazil.
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Affiliation(s)
- Fernando Lucas Melo
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute-ICBII, University of São Paulo, Brazil
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Cavalcanti AMS, Brito AMD, Salustiano DM, Lima KOD, Silva SPD, Diaz RS, Lacerda HR. Primary resistance of HIV to antiretrovirals among individuals recently diagnosed at voluntary counselling and testing centres in the metropolitan region of Recife, Pernambuco. Mem Inst Oswaldo Cruz 2012; 107:450-7. [DOI: 10.1590/s0074-02762012000400002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 02/27/2012] [Indexed: 11/21/2022] Open
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