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Gillespie SW, Reddy AS, Burris DM, Naqvi SH, Byrareddy SN, Lorson CL, Singh K. Islatravir: evaluation of clinical development for HIV and HBV. Expert Opin Investig Drugs 2024; 33:85-93. [PMID: 38235744 DOI: 10.1080/13543784.2024.2305130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
INTRODUCTION Islatravir (ISL) is a nucleoside reverse transcriptase translocation inhibitor (NRTTI) that inhibits HIV RT through multiple mechanisms. Contrary to all approved NtRTIs, islatravir retains a 3'OH group. In vitro and clinical data show that ISL is an ultrapotent investigational drug with high tolerability. AREAS COVERED The historical development of islatravir and its mechanisms of HIV and HBV inhibition and resistance are covered. Additionally, the outcomes of Phase I and Phase II clinical trials are discussed. EXPERT OPINION Current first-line antiretroviral therapy, preexposure, and postexposure prophylactic interventions are highly effective in maintaining low or undetectable viral load. Despite these measures, an unusually high rate of new infections every year warrants developing novel antivirals that can suppress drug-resistant HIV and improve compliance. ISL, an NRTTI once deemed a long-acting drug, was placed on a clinical hold. The outcome of ongoing clinical trials with a reduced ISL dose will decide its future clinical application. Additionally, MK-8527, which inhibits HIV via same mechanism as that of ISL may supersede ISL. Data on ISL inhibition of HBV are scarce, and preclinical data show dramatically lower ISL efficacy against HBV than currently preferred nucleos(t)ide drugs, indicating that ISL may not be a potent anti-HBV drug.
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Affiliation(s)
| | - Athreya S Reddy
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Dana M Burris
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - S Hasan Naqvi
- Department of Medicine, University of Missouri, Columbia, MO, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
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Datta J, Majumder S, Chaudhuri D, Giri K. In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes. J Biomol Struct Dyn 2023; 41:14977-14988. [PMID: 36858595 DOI: 10.1080/07391102.2023.2184634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
HIV-1, the causative agent of AIDS leads to many deaths worldwide though few options are available as therapeutics. To deal with the continuous mutation in the virus genome, requirement of new drugs is always there. Subtype variation plays a crucial role in case of HIV-1 therapeutics development. In this study, we want to investigate some pre examined molecules that can be effective for HIV-1 VPR. Inhibition of several protein-protein interactions with the small molecules will lead to identify some molecules as therapeutics other than the conventional drugs. We retrieved the sequences of different subtypes from the database and representative sequences were identified. Representative structures were modelled and validated using MD simulations. Forty molecules, showing anti Vpr activity in vitro were identified from literature survey and those were docked with each subtype representative structures. Two molecules a stable Hematoxylin Derivative (SHD) and Damnacanthal (D3), these were shown to be bind more effectively for all the subtypes. The stability of the protein and those two small molecule complexes were identified again with MD simulation followed by the binding energy calculation. Thus, these molecules can be thought as any option other than the conventional drug targeting HIV-1 Vpr.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Joyeeta Datta
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | | | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India
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Troyano-Hernáez P, Reinosa R, Holguín A. Genetic Diversity and Low Therapeutic Impact of Variant-Specific Markers in HIV-1 Pol Proteins. Front Microbiol 2022; 13:866705. [PMID: 35910645 PMCID: PMC9330395 DOI: 10.3389/fmicb.2022.866705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of new HIV-1 variants pose a challenge for the effectiveness of antiretrovirals (ARV) targeting Pol proteins. During viral evolution, non-synonymous mutations have fixed along the viral genome, leading to amino acid (aa) changes that can be variant-specific (V-markers). Those V-markers fixed in positions associated with drug resistance mutations (DRM), or R-markers, can impact drug susceptibility and resistance pathways. All available HIV-1 Pol sequences from ARV-naïve subjects were downloaded from the United States Los Alamos HIV Sequence Database, selecting 59,733 protease (PR), 6,437 retrotranscriptase (RT), and 6,059 integrase (IN) complete sequences ascribed to the four HIV-1 groups and group M subtypes and circulating recombinant forms (CRFs). Using a bioinformatics tool developed in our laboratory (EpiMolBio), we inferred the consensus sequences for each Pol protein and HIV-1 variant to analyze the aa conservation in Pol. We analyzed the Wu–Kabat protein variability coefficient (WK) in PR, RT, and IN group M to study the susceptibility of each site to evolutionary replacements. We identified as V-markers the variant-specific aa changes present in >75% of the sequences in variants with >5 available sequences, considering R-markers those V-markers that corresponded to DRM according to the IAS-USA2019 and Stanford-Database 9.0. The mean aa conservation of HIV-1 and group M consensus was 82.60%/93.11% in PR, 88.81%/94.07% in RT, and 90.98%/96.02% in IN. The median group M WK was 10 in PR, 4 in RT, and 5 in IN. The residues involved in binding or catalytic sites showed a variability <0.5%. We identified 106 V-markers: 31 in PR, 28 in RT, and 47 in IN, present in 11, 12, and 13 variants, respectively. Among them, eight (7.5%) were R-markers, present in five variants, being minor DRM with little potential effect on ARV susceptibility. We present a thorough analysis of Pol variability among all HIV-1 variants circulating to date. The relatively high aa conservation observed in Pol proteins across HIV-1 variants highlights their critical role in the viral cycle. However, further studies are needed to understand the V-markers’ impact on the Pol proteins structure, viral cycle, or treatment strategies, and periodic variability surveillance studies are also required to understand PR, RT, and IN evolution.
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Joussef-Piña S, Nankya I, Nalukwago S, Baseke J, Rwambuya S, Winner D, Kyeyune F, Chervenak K, Thiel B, Asaad R, Dobrowolski C, Luttge B, Lawley B, Kityo CM, Boom WH, Karn J, Quiñones-Mateu ME. Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology 2022; 19:1. [PMID: 35033105 PMCID: PMC8760765 DOI: 10.1186/s12977-022-00587-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our understanding of the peripheral human immunodeficiency virus type 1 (HIV-1) reservoir is strongly biased towards subtype B HIV-1 strains, with only limited information available from patients infected with non-B HIV-1 subtypes, which are the predominant viruses seen in low- and middle-income countries (LMIC) in Africa and Asia. RESULTS In this study, blood samples were obtained from well-suppressed ART-experienced HIV-1 patients monitored in Uganda (n = 62) or the U.S. (n = 50), with plasma HIV-1 loads < 50 copies/ml and CD4+ T-cell counts > 300 cells/ml. The peripheral HIV-1 reservoir, i.e., cell-associated HIV-1 RNA and proviral DNA, was characterized using our novel deep sequencing-based EDITS assay. Ugandan patients were slightly younger (median age 43 vs 49 years) and had slightly lower CD4+ counts (508 vs 772 cells/ml) than U.S. individuals. All Ugandan patients were infected with non-B HIV-1 subtypes (31% A1, 64% D, or 5% C), while all U.S. individuals were infected with subtype B viruses. Unexpectedly, we observed a significantly larger peripheral inducible HIV-1 reservoir in U.S. patients compared to Ugandan individuals (48 vs. 11 cell equivalents/million cells, p < 0.0001). This divergence in reservoir size was verified measuring proviral DNA (206 vs. 88 cell equivalents/million cells, p < 0.0001). However, the peripheral HIV-1 reservoir was more diverse in Ugandan than in U.S. individuals (8.6 vs. 4.7 p-distance, p < 0.0001). CONCLUSIONS The smaller, but more diverse, peripheral HIV-1 reservoir in Ugandan patients might be associated with viral (e.g., non-B subtype with higher cytopathicity) and/or host (e.g., higher incidence of co-infections or co-morbidities leading to less clonal expansion) factors. This highlights the need to understand reservoir dynamics in diverse populations as part of ongoing efforts to find a functional cure for HIV-1 infection in LMICs.
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Affiliation(s)
- Samira Joussef-Piña
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sophie Nalukwago
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Joy Baseke
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sandra Rwambuya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Dane Winner
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Keith Chervenak
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bonnie Thiel
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Asaad
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Curtis Dobrowolski
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin Luttge
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand
| | - Cissy M Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - W Henry Boom
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand.
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand.
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Weyland C, Mirani G, Gillespie SL, Paul ME. A Case of in utero Transmission of Drug-resistant HIV in the United States. Pediatr Infect Dis J 2022; 41:57-59. [PMID: 34609103 DOI: 10.1097/inf.0000000000003329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Thanks to the development of antiretroviral drugs and the implementation of routine perinatal prophylaxis, primarily containing zidovudine, modern-day rates of perinatal transmission of HIV are very low in developed countries. We present a case of perinatal transmission of HIV with extensive nucleoside reverse transcriptase inhibitor resistance as a reminder that perinatal transmission of resistance mutations can occur. This case calls for further investigation into the utility of using genotype to determine neonatal prophylaxis in the setting of maternal HIV drug resistance.
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Affiliation(s)
- Cassie Weyland
- From the Internal Medicine-Pediatrics, PGY-1, Baylor College of Medicine, Houston, Texas
| | - Gayatri Mirani
- Section of Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Susan L Gillespie
- Section of Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Mary E Paul
- Section of Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
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Drug resistance mutations in protease gene of HIV-1 subtype C infected patient population. Virusdisease 2021; 32:480-491. [PMID: 34631975 DOI: 10.1007/s13337-021-00725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/29/2021] [Indexed: 10/20/2022] Open
Abstract
Failure of antiretroviral therapy (ART) in HIV-1 infection is a critical issue for the physicians treating HIV patients. The major cause of drug failure is the development of resistance mutations in reverse transcriptase (RT) and/or protease (PR) genes. Mutations associated with drug resistance decrease drug effectiveness. This study was conducted to assess drug resistance profile of the entire PR gene in 90 HIV-1 patients consisting of 23 ART non-responsive, 32 ART responsive and 35 drug naive patients. It was observed that the majority of the sequences (94.4%) belonged to subtype C and (5.5%) to subtype A1. The ART non-responsive and responsive patients were treated with either first line of ART regimen (two NRTI and one NNRTI) or second line of ART regimen that included additional one protease inhibitor (PI). All the patients in each group except one responsive patient had various minor resistance mutations. Thus, drug failures in ART non-responsive patients may not always be due to drug resistance mutations instead other factors may also be responsible for drug failures such as non-compliance, suboptimal dose or drug interaction. The presence of minor drug resistance mutations in drug naive patients is suggestive of transmitted resistance mutations.
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Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Comput Biol 2021; 17:e1008363. [PMID: 34491984 PMCID: PMC8448360 DOI: 10.1371/journal.pcbi.1008363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 09/17/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Although combination antiretroviral therapies seem to be effective at controlling HIV-1 infections regardless of the viral subtype, there is increasing evidence for subtype-specific drug resistance mutations. The order and rates at which resistance mutations accumulate in different subtypes also remain poorly understood. Most of this knowledge is derived from studies of subtype B genotypes, despite not being the most abundant subtype worldwide. Here, we present a methodology for the comparison of mutational networks in different HIV-1 subtypes, based on Hidden Conjunctive Bayesian Networks (H-CBN), a probabilistic model for inferring mutational networks from cross-sectional genotype data. We introduce a Monte Carlo sampling scheme for learning H-CBN models for a larger number of resistance mutations and develop a statistical test to assess differences in the inferred mutational networks between two groups. We apply this method to infer the temporal progression of mutations conferring resistance to the protease inhibitor lopinavir in a large cross-sectional cohort of HIV-1 subtype C genotypes from South Africa, as well as to a data set of subtype B genotypes obtained from the Stanford HIV Drug Resistance Database and the Swiss HIV Cohort Study. We find strong support for different initial mutational events in the protease, namely at residue 46 in subtype B and at residue 82 in subtype C. The inferred mutational networks for subtype B versus C are significantly different sharing only five constraints on the order of accumulating mutations with mutation at residue 54 as the parental event. The results also suggest that mutations can accumulate along various alternative paths within subtypes, as opposed to a unique total temporal ordering. Beyond HIV drug resistance, the statistical methodology is applicable more generally for the comparison of inferred mutational networks between any two groups. There is a disparity in the distribution of infections by HIV-1 subtype in the world. Subtype B is predominant in America, Australia and western and central Europe, and most therapeutic strategies are based on research and clinical studies on this subtype. However, non-B subtypes represent the majority of global HIV-1 infections; e.g., subtype C alone accounts for nearly half of all HIV-1 infections. We present a statistical framework enabling the comparison of patterns of accumulating mutations in different HIV-1 subtypes. Specifically, we compare the temporal ordering of lopinavir resistance mutations in HIV-1 subtypes B versus C. To this end, we combine the Hidden Conjunctive Bayesian Network (H-CBN) model with an approximate inference scheme enabling comparisons of larger networks. We show that the development of resistance to lopinavir differs significantly between subtypes B and C, such that findings based on subtype B sequences can not always be applied to sybtype C. The described methodology is suitable for comparing different subgroups in the context of other evolutionary processes.
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Sun Z, Ouyang J, Zhao B, An M, Wang L, Ding H, Han X. Natural polymorphisms in HIV-1 CRF01_AE strain and profile of acquired drug resistance mutations in a long-term combination treatment cohort in northeastern China. BMC Infect Dis 2020; 20:178. [PMID: 32102660 PMCID: PMC7045473 DOI: 10.1186/s12879-020-4808-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The impacts of genetic polymorphisms on drug resistance mutations (DRMs) among various HIV-1 subtypes have long been debated. In this study, we aimed to analyze the natural polymorphisms and acquired DRM profile in HIV-1 CRF01_AE-infected patients in a large first-line antiretroviral therapy (ART) cohort in northeastern China. METHODS The natural polymorphisms of CRF01_AE were analyzed in 2034 patients from a long-term ART cohort in northeastern China. The polymorphisms in 105 treatment failure (TF) patients were compared with those in 1148 treatment success (TS) patients. The acquired DRM profile of 42 patients who experienced TF with tenofovir/lamivudine/efavirenz (TDF/3TC/EFV) treatment was analyzed by comparing the mutations at TF time point to those at baseline. The Stanford HIVdb algorithm was used to interpret the DRMs. Binomial distribution, McNemar test, Wilcoxon test and CorMut package were used to analyze the mutation rates and co-variation. Deep sequencing was used to analyze the evolutionary dynamics of co-variation. RESULTS Before ART, there were significantly more natural polymorphisms of 31 sites on reverse transcriptase (RT) in CRF01_AE than subtype B HIV-1 (|Z value| ≥ 3), including five known drug resistance-associated sites (238, 118, 179, 103, and 40). However, only the polymorphism at site 75 was associated with TF (|Z value| ≥ 3). The mutation rate at 14 sites increased significantly at TF time point compared to baseline, with the most common DRMs comprising G190S/C, K65R, K101E/N/Q, M184 V/I, and V179D/I/A/T/E, ranging from 66.7 to 45.2%. Moreover, two unknown mutations (V75 L and L228R) increased by 19.0 and 11.9% respectively, and they were under positive selection (Ka/Ks > 1, log odds ratio [LOD] > 2) and were associated with several other DRMs (cKa/Ks > 1, LOD > 2). Deep sequencing of longitudinal plasma samples showed that L228R occurred simultaneously or followed the appearance of Y181C. CONCLUSION The high levels of natural polymorphisms in CRF01_AE had little impact on treatment outcomes. The findings regarding potential new CRF01_AE-specific minor DRMs indicate the need for more studies on the drug resistance phenotype of CRF01_AE.
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Affiliation(s)
- Zesong Sun
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Jinming Ouyang
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Minghui An
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Lin Wang
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Haibo Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China. .,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China.
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Abstract
Human immunodeficiency virus-1 (HIV-1) is characterised by a vast genetic diversity classified into distinct phylogenetic strains and recombinant forms. We describe the HIV-1 molecular epidemiology and evolution of 129 consecutive HIV-1 positive migrants living in Milan (northern Italy). Polymerase gene sequences of 116 HIV-1 subtype-B positive patients were aligned with HIV-1 reference sequences (https://www.ncbi.nlm.nih.gov/) by using MAFFT alignment and edited by using Bioedit software. A maximum likelihood (ML) phylogenetic tree was performed by MEGA7 and was visualised by using FigTree v1.4.3. Of 129 migrants, 35 were born in Europe (28 in Eastern Europe), 70 in the Americas (67 in South America), 15 in Africa and nine in Asia; 76.4% were men who have sex with men (MSM). The serotype HIV-1-B prevailed (89.9%), followed by -C, -F1, -D and -A. Compared with 116 HIV-B patients, the 13 with HIV-non-B showed lower Nadir of CD4+ cell/mmc (P = 0.043), more frequently had sub Saharan origin (38.5 vs. 1.72%, P = 0.0001) and less frequently were MSM (40 vs. 74.5%, P = 0.02). The ML phylogenetic tree of the 116 HIV-1 subtype-B positive patients showed 13 statistically supported nodes (bootstrap > 70%). Most of the sequences included in these nodes have been isolated from male patients from the Americas and the most common risk factor was MSM. The low number of HIV-1 non-B subtype patients did not allow to perform this analysis. These results suggest a shift of HIV-1 prevention projects' focus and a continuous monitoring of HIV-1 molecular epidemiology among entry populations. Prevention efforts based on HIV molecular epidemiology may improve public health surveillance setting.
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Abongwa LE, Nyamache AK, Torimiro JN, Okemo P, Charles F. Human immunodeficiency virus type 1 ((HIV-1) subtypes in the northwest region, Cameroon. Virol J 2019; 16:103. [PMID: 31416460 PMCID: PMC6694531 DOI: 10.1186/s12985-019-1209-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/05/2019] [Indexed: 12/01/2022] Open
Abstract
Background The high genetic diversity of HIV-1 has been shown to influence the global distribution, disease progression, treatment success, and the development of an effective vaccine. Despite the low HIV prevalence in Cameroon, all the major HIV subtypes alongside several circulating recombinant forms (CRFs) and unique recombinant forms (URFs) have been reported in Cameroon. To date, HIV-1 diversity in some parts of Cameroon has been largely studied however, information on circulating HIV-1 subtypes in the Northwest region (NWR) of Cameroon is dearth. Therefore the aim of this study was to determine the current circulating HIV-1 subtypes among adults in the NWR of Cameroon. Methods The genetic analysis of the reverse transcriptase region of the pol gene was performed on 81 samples. The samples were collected from drug naïve patients aged between 18 and 61 years residing within the rural and urban towns in the NWR during the period between February and April 2016. Viral RNA was extracted from plasma, reverse-transcribed, further amplified by nested-PCR before sequencing using an in-house protocol. Generated sequences were then phylogenetically analyzed together with references using MEGA 7. Results Phylogenetic analysis revealed a broad viral diversity including CRF02 _AG (74.1%), F2 (7.4%), D (7.4%), G (3.7%), A1 (1.2%), CRF22_01A1 (2.5%), CRF06_cpx (1.2%), CRF09_cpx (1.2%), CRF11_cpx (1.2%). Three close epidemic clusters were found among F2 (1) and CRF02_AG (2) variants. For the first time we are reporting the CRF22_01A1 subtype in this region. Conclusion Our findings update HIV-1 subtypes information in Cameroon and uphold previous studies that CRF02_AG is the most prevalent subtype. This CRF02_AG subtype may have important public health, research, and clinical consequences.
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Affiliation(s)
- Lem Edith Abongwa
- Department of Biochemistry, Biotechnology, and Microbiology, School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya. .,Department of Biological Sciences, Faculty of Science, University of Bamenda, Northwest, Region, Bamenda, Cameroon. .,Laboratory of Molecular Biology, Chantal Biya International Center for Research on the Prevention and Management of HIV / AIDS (CIRCB), Yaounde, Cameroon.
| | - Anthony Kebira Nyamache
- Department of Biochemistry, Biotechnology, and Microbiology, School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya
| | - Judith Ndongo Torimiro
- Laboratory of Molecular Biology, Chantal Biya International Center for Research on the Prevention and Management of HIV / AIDS (CIRCB), Yaounde, Cameroon.,Department of Biochemistry, Faculty of Medicine and Biomedical Science, University of Yaounde I, Yaounde, Cameroon
| | - Paul Okemo
- Department of Biochemistry, Biotechnology, and Microbiology, School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya
| | - Fokunang Charles
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde, Cameroon
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Ledwaba J, Sayed Y, Pillay V, Morris L, Hunt G. Low Frequency of Protease Inhibitor Resistance Mutations and Insertions in HIV-1 Subtype C Protease Inhibitor-Naïve Sequences. AIDS Res Hum Retroviruses 2019; 35:673-678. [PMID: 30793914 DOI: 10.1089/aid.2019.0012] [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] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) protease sequences from 2,225 protease inhibitor (PI)-naïve HIV-1 subtype C-infected individuals collected over a 14-year period were analyzed for polymorphisms. Over 50% of sequences differed from an HIV-1 subtype B consensus sequence at 8 of the 99 amino acids at residues 12, 15, 19, 36, 41, 69, 89, and 93, but not in the functionally important regions. The frequency of primary resistance and accessory mutations occurred in <1% of the sequences. Of note, 11 sequences (0.5%) harbored amino acid insertions between residues 36 and 39, located in the elbow of the flap region. The insertions were found throughout the 13-year period. Occurrence of insertions in subtype C viruses is rare and viruses remain sensitive to currently used PIs (lopinavir/r, atazanavir/r, and darunavir/r). However, ongoing characterization of isolates is required to identify changes that may impact PI treatment since PIs are part of standard SA regimens.
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Affiliation(s)
- Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Visva Pillay
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Shadabi E, Liang B, Plummer F, Luo M. Identification and Characterization of Positively Selected Mutations in Nef of Four HIV-1 Major Subtypes from Los Alamos National Laboratory. Curr HIV Res 2019; 16:130-142. [PMID: 29600767 DOI: 10.2174/1570162x16666180330140807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/07/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Human immunodeficiency virus-1 (HIV-1) mutates rapidly to escape host immune pressure. This results in the generation of positively selected mutations (PSM) throughout the viral genome. Escape mutations in Nef, one of the accessory proteins of HIV-1, which plays an important role in viral pathogenicity have previously been identified in several large cohort studies, but the evolution of PSMs overtime in various HIV-1 subtypes remains unknown. METHODS 161 clade A1, 3093 clade B, 647 clade C and 115 clade D HIV-1 nef sequences were obtained from the HIV Database of Los Alamos National Laboratory and aligned using MEGA 6.0. The sequences from each clade were grouped based on the year of collection. Quasi analysis was used to identify PSMs and the number and locations of PSMs were compared among different subtypes. RESULTS PSMs for all four subtypes were distributed across the sequence of Nef, and conserved residues F90, W113, PxxPxR (a.a 72-77) remain unaltered overtime. The frequency of PSMs was stable among subtype B sequences but increased overtime for other subtypes. Phylogenetic analysis shows that sequences containing PSMs tend to cluster together at both inter and intra- subtype levels. CONCLUSION Identification of PSMs and their changes overtime within various subtypes of HIV-1 is important in defining global viral evolutionary patterns that can provide insights for designing therapeutic strategies.
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Affiliation(s)
- Elnaz Shadabi
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Binhua Liang
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Frank Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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13
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Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Fleminger I, Kirtley S, Williams B, Gouws-Williams E, Ghys PD. Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis. THE LANCET. INFECTIOUS DISEASES 2018; 19:143-155. [PMID: 30509777 DOI: 10.1016/s1473-3099(18)30647-9] [Citation(s) in RCA: 230] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/26/2018] [Accepted: 10/12/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. METHODS We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. We grouped countries into 14 regions and analysed data for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164. FINDINGS This systematic review and global survey yielded 2203 datasets with 383 519 samples from 116 countries in 1990-2015. Globally, subtype C accounted for 46·6% (16 280 897/34 921 639 of PLHIV) of all HIV-1 infections in 2010-15. Subtype B was responsible for 12·1% (4 235 299/34 921 639) of infections, followed by subtype A (10·3%; 3 587 003/34 921 639), CRF02_AG (7·7%; 2 705 110/34 921 639), CRF01_AE (5·3%; 1 840 982/34 921 639), subtype G (4·6%; 1 591 276/34 921 639), and subtype D (2·7%; 926 255/34 921 639). Subtypes F, H, J, and K combined accounted for 0·9% (311 332/34 921 639) of infections. Other CRFs accounted for 3·7% (1 309 082/34 921 639), bringing the proportion of all CRFs to 16·7% (5 844 113/34 921 639). URFs constituted 6·1% (2 134 405/34 921 639), resulting in recombinants accounting for 22·8% (7 978 517/34 921 639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005-15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time. INTERPRETATION Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines. FUNDING None.
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Affiliation(s)
- Joris Hemelaar
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK.
| | - Ramyiadarsini Elangovan
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jason Yun
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Leslie Dickson-Tetteh
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Isabella Fleminger
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Shona Kirtley
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Brian Williams
- South African Centre for Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | | | - Peter D Ghys
- Strategic Information Department, UNAIDS, Geneva, Switzerland
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HIV-1 second-line failure and drug resistance at high-level and low-level viremia in Western Kenya. AIDS 2018; 32:2485-2496. [PMID: 30134290 DOI: 10.1097/qad.0000000000001964] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Characterize failure and resistance above and below guidelines-recommended 1000 copies/ml virologic threshold, upon second-line failure. DESIGN Cross-sectional study. METHODS Kenyan adults on lopinavir/ritonavir-based second-line were enrolled at AMPATH (Academic Model Providing Access to Healthcare). Charts were reviewed for demographic/clinical characteristics and CD4/viral load were obtained. Participants with detectable viral load had a second visit and pol genotyping was attempted in both visits. Accumulated resistance was defined as mutations in the second, not the first visit. Low-level viremia (LLV) was detectable viral load less than 1000 copies/ml. Failure and resistance associations were evaluated using logistic and Poisson regression, Fisher Exact and t-tests. RESULTS Of 394 participants (median age 42, 60% women, median 1.9 years on second-line) 48% had detectable viral load; 21% had viral load more than 1000 copies/ml, associated with younger age, tuberculosis treatment, shorter time on second-line, lower CD4count/percentage, longer first-line treatment interruption and pregnancy. In 105 sequences from the first visit (35 with LLV), 79% had resistance (57% dual-class, 7% triple-class; 46% with intermediate-to-high-level resistance to ≥1 future drug option). LLV was associated with more overall and NRTI-associated mutations and with predicted resistance to more next-regimen drugs. In 48 second-visit sequences (after median 55 days; IQR 28-33), 40% accumulated resistance and LLV was associated with more mutation accumulation. CONCLUSION High resistance upon second-line failure exists at levels above and below guideline-recommended virologic-failure threshold, impacting future treatment options. Optimization of care should include increased viral load monitoring, resistance testing and third-line ART access, and consideration of lowering the virologic failure threshold, though this demands further investigation.
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15
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Brenner BG, Ibanescu RI, Hardy I, Roger M. Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in "Real-World" Settings. Viruses 2017; 10:v10010010. [PMID: 29283390 PMCID: PMC5795423 DOI: 10.3390/v10010010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 12/15/2022] Open
Abstract
HIV continues to spread among vulnerable heterosexual (HET), Men-having-Sex with Men (MSM) and intravenous drug user (IDU) populations, influenced by a complex array of biological, behavioral and societal factors. Phylogenetics analyses of large sequence datasets from national drug resistance testing programs reveal the evolutionary interrelationships of viral strains implicated in the dynamic spread of HIV in different regional settings. Viral phylogenetics can be combined with demographic and behavioral information to gain insights on epidemiological processes shaping transmission networks at the population-level. Drug resistance testing programs also reveal emergent mutational pathways leading to resistance to the 23 antiretroviral drugs used in HIV-1 management in low-, middle- and high-income settings. This article describes how genotypic and phylogenetic information from Quebec and elsewhere provide critical information on HIV transmission and resistance, Cumulative findings can be used to optimize public health strategies to tackle the challenges of HIV in “real-world” settings.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
| | - Ruxandra-Ilinca Ibanescu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
| | - Isabelle Hardy
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC H2X 0A9, Canada.
| | - Michel Roger
- Département de Microbiologie et d'Immunologie et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC H2X 0A9, Canada.
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16
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Nagata S, Imai J, Makino G, Tomita M, Kanai A. Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation. Front Microbiol 2017; 8:2151. [PMID: 29163435 PMCID: PMC5666293 DOI: 10.3389/fmicb.2017.02151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/20/2017] [Indexed: 11/15/2022] Open
Abstract
RNA viruses have been used as model systems to understand the patterns and processes of molecular evolution because they have high mutation rates and are genetically diverse. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immune deficiency syndrome, is highly genetically diverse, and is classified into several groups and subtypes. However, it has been difficult to use its diverse sequences to establish the overall phylogenetic relationships of different strains or the trends in sequence conservation with the construction of phylogenetic trees. Our aims were to systematically characterize HIV-1 subtype evolution and to identify the regions responsible for HIV-1 subtype differentiation at the amino acid level in the Pol protein, which is often used to classify the HIV-1 subtypes. In this study, we systematically characterized the mutation sites in 2,052 Pol proteins from HIV-1 group M (144 subtype A; 1,528 subtype B; 380 subtype C), using sequence similarity networks. We also used spectral clustering to group the sequences based on the network graph structures. A stepwise analysis of the cluster hierarchies allowed us to estimate a possible evolutionary pathway for the Pol proteins. The subtype A sequences also clustered according to when and where the viruses were isolated, whereas both the subtype B and C sequences remained as single clusters. Because the Pol protein has several functional domains, we identified the regions that are discriminative by comparing the structures of the domain-based networks. Our results suggest that sequence changes in the RNase H domain and the reverse transcriptase (RT) connection domain are responsible for the subtype classification. By analyzing the different amino acid compositions at each site in both domain sequences, we found that a few specific amino acid residues (i.e., M357 in the RT connection domain and Q480, Y483, and L491 in the RNase H domain) represent the differences among the subtypes. These residues were located on the surface of the RT structure and in the vicinity of the amino acid sites responsible for RT enzymatic activity or function.
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Affiliation(s)
- Shohei Nagata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Junnosuke Imai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Gakuto Makino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
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17
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Vasavi C, Tamizhselvi R, Munusami P. Drug Resistance Mechanism of L10F, L10F/N88S and L90M mutations in CRF01_AE HIV-1 protease: Molecular dynamics simulations and binding free energy calculations. J Mol Graph Model 2017. [DOI: 10.1016/j.jmgm.2017.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Ghafari S, Memarnejadian A, Samarbaf-Zadeh A, Mostafavi E, Makvandi M, Salmanzadeh S, Ghadiri A, Jordan MR, Mousavi E, Jahanbakhsh F, Azadmanesh K. Prevalence of HIV-1 transmitted drug resistance in recently infected, treatment-naïve persons in the Southwest of Iran, 2014-2015. Arch Virol 2017; 162:2737-2745. [PMID: 28589513 DOI: 10.1007/s00705-017-3431-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/22/2017] [Indexed: 10/19/2022]
Abstract
The emergence and transmission of drug resistant HIV mutants is a major concern, especially in resource-limited countries with expanding antiretroviral therapy. Studies have recently reported the prevalence of HIV-1 transmitted drug resistance (TDR) mutations in certain Iranian cities; however, no information is currently available about the level of TDR, as well as the nature of the circulating HIV-1 subtypes, in the Southwestern bordering province of Iran, Khuzestan. Herein, we used a WHO-recommended TDR survey method to classify the prevalence of TDR in indigenous people of Khuzestan province. For this purpose, between March 2014 and February 2015, blood samples were collected from 52 newly diagnosed, antiretroviral treatment-naïve, HIV-1 infected persons aged from 18 to 30 years. TDR mutations were determined by sequencing the protease (PR) and reverse transcriptase (RT) genes and interpreted using the WHO drug resistance mutations surveillance list. HIV-1 subtypes were characterized by sequencing the PR-RT, C2-V5, and p17 regions of the pol, env and gag genes, respectively. Two participants had non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations, specifically K103N in one individual and K101EK/K103KN/G190AG in the other. No nucleoside reverse transcriptase inhibitor (NRTI) or major protease inhibitor (PI) mutations were identified. HIV-1 subtyping revealed that all participants were infected with HIV-1 CRF35_AD. According to the WHO sequential sampling method, the prevalence of HIV-1 TDR in the sampling area (Khuzestan province) was classified as moderate for NNRTIs and low for NRTIs and PIs. This is the first HIV-1 drug resistance threshold survey in the Khuzestan province of Iran and shows a predominance of NNRTI TDR mutations in this area.
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Affiliation(s)
- Shokouh Ghafari
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Alireza Samarbaf-Zadeh
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Ehsan Mostafavi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.,Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
| | - Manoochehr Makvandi
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shokrolah Salmanzadeh
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ata Ghadiri
- Cellular and Molecular Research Center, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Elham Mousavi
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Titanji BK, Pillay D, Jolly C. Combination antiretroviral therapy and cell-cell spread of wild-type and drug-resistant human immunodeficiency virus-1. J Gen Virol 2017; 98:821-834. [PMID: 28141491 PMCID: PMC5657029 DOI: 10.1099/jgv.0.000728] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) disseminates between T cells either by cell-free infection or by highly efficient direct cell–cell spread. The high local multiplicity that characterizes cell–cell infection causes variability in the effectiveness of antiretroviral drugs applied as single agents. Whereas protease inhibitors (PIs) are effective inhibitors of HIV-1 cell–cell and cell-free infection, some reverse transcriptase inhibitors (RTIs) show reduced potency; however, antiretrovirals are not administered as single agents and are used clinically as combination antiretroviral therapy (cART). Here we explored the efficacy of PI- and RTI-based cART against cell–cell spread of wild-type and drug-resistant HIV-1 strains. Using a quantitative assay to measure cell–cell spread of HIV-1 between T cells, we evaluated the efficacy of different clinically relevant drug combinations. We show that combining PIs and RTIs improves the potency of inhibition of HIV-1 and effectively blocks both cell-free and cell–cell spread. Combining drugs that alone are poor inhibitors of cell–cell spread markedly improves HIV-1 inhibition, demonstrating that clinically relevant combinations of ART can inhibit this mode of HIV-1 spread. Furthermore, comparison of wild-type and drug-resistant viruses reveals that PI- and RTI-resistant viruses have a replicative advantage over wild-type virus when spreading by cell–cell means in the presence of cART, suggesting that in the context of inadequate drug combinations or drug resistance, cell–cell spread could potentially allow for ongoing viral replication.
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Affiliation(s)
- Boghuma Kabisen Titanji
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.,Department of Medicine, Emory University School of Medicine, Atlanta, USA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.,Africa Centre for Health and Population Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa. AIDS 2016; 30:2577-2589. [PMID: 27603287 DOI: 10.1097/qad.0000000000001233] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVE In resource-limited countries, antiretroviral therapy (ART) has been scaled up, but individual monitoring is still suboptimal. Here, we studied whether or not ART had an impact on the frequency and selection of drug resistance mutations (DRMs) under these settings. We also examined whether differences exist between HIV-1 genetic variants. DESIGN A total of 3736 sequences from individuals failing standard first-line ART (n = 1599, zidovudine/stavudine + lamivudine + neviparine/efavirenz) were analyzed and compared with sequences from reverse transcriptase inhibitor (RTI)-naive individuals (n = 2137) from 10 West and Central African countries. METHODS Fisher exact tests and corrections for multiple comparisons were used to assess the significance of associations. RESULTS All RTI-DRM from the 2015 International Antiviral Society list, except F227C, and nine mutations from other expert lists were observed to confer extensive resistance and cross-resistance. Five additional independently selected mutations (I94L, L109I, V111L, T139R and T165L) were statistically associated with treatment. The proportion of sequences with multiple mutations and the frequency of all thymidine analog mutations, M184V, certain NNRTIS, I94L and L109I showed substantial increase with time on ART. Only one nucleoside and two nonnucleoside RTI-DRMs differed by subtype/circulating recombinant form. CONCLUSION This study validates the global robustness of the actual DRM repertoire, in particular for circulating recombinant form 02 predominating in West and Central Africa, despite our finding of five additional selected mutations. However, long-term ART without virological monitoring clearly leads to the accumulation of mutations and the emergence of additional variations, which limit drug options for treatment and can be transmitted. Improved monitoring and optimization of ART are necessary for the long-term effectiveness of ART.
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21
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Lam EP, Moore CL, Gotuzzo E, Nwizu C, Kamarulzaman A, Chetchotisakd P, van Wyk J, Teppler H, Kumarasamy N, Molina JM, Emery S, Cooper DA, Boyd MA. Antiretroviral Resistance After First-Line Antiretroviral Therapy Failure in Diverse HIV-1 Subtypes in the SECOND-LINE Study. AIDS Res Hum Retroviruses 2016; 32:841-50. [PMID: 27346600 DOI: 10.1089/aid.2015.0331] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigate mutations and correlates according to HIV-1 subtype after virological failure (VF) of standard first-line antiretroviral therapy (ART) (non-nucleoside/nucleotide reverse transcriptase inhibitor [NNRTI] +2 nucleoside/nucleotide reverse transcriptase inhibitor [N(t)RTI]). SECOND-LINE study participants were assessed at baseline for HIV-1 subtype, demographics, HIV-1 history, ART exposure, viral load (VL), CD4(+) count, and genotypic ART resistance. We used backward stepwise multivariate regression (MVR) to assess associations between baseline variables and presence of ≥3 N(t)RTI mutations, ≥1 NNRTI mutation, ≥3 thymidine analog-N(t)RTI [ta-N(t)RTI] mutations (TAMs), the K65/K70 mutation, and predicted etravirine (ETV)/rilpivirine (RPV) activity. The inclusion p-value for MVR was p < .2. The exclusion p-value from stepwise elimination was p > .05. Of 541 participants, 491 (91%) had successfully characterized baseline viral isolates. Subtype distribution: B (n = 123, 25%), C (n = 202, 41%), CRF01_AE (n = 109, 22%), G (n = 25, 5%), and CRF02_AG (n = 27, 5%). Baseline CD4(+) 200-394 cells/mm(3) were associated with <3 N(t)RTI mutations (OR = 0.47; 95% CI 0.29-0.77; p = .003), absence of the K65/K70 mutation (OR = 0.43; 95% CI 0.26-0.73; p = .002), and higher ETV sensitivity (OR = 0.52; 95% CI 0.35-0.78; p = .002). Recent tenofovir (TDF) use was associated with K65/K70 mutations (OR = 8.91; 95% CI 5.00-15.85; p < .001). Subtype CRF01_AE was associated with ≥3 N(t)RTI mutations (OR = 2.34; 95% CI 1.31-4.17; p = .004) and higher RPV resistance (OR = 2.13; 95% CI 1.30-3.49; p = .003), and subtype C was associated with <3 TAMs (OR = 0.45; 95% CI 0.21-0.99; p = .015). Subtypes CRF01_AE (OR = 2.46; 95% CI 1.26-4.78; p = .008) and G (OR = 4.77; 95% CI 1.44-15.76; p = .01) were associated with K65/K70 mutations. Higher VL at confirmed first-line VF was associated with ≥3 N(t)RTI mutations (OR = 1.39; 95% CI 1.07-1.78; p = .013) and ≥3 TAMs (OR = 1.62; 95% CI 1.15-2.29; p = .006). The associations of first-line resistance mutations across the HIV-1 subtypes in this study are consistent with knowledge derived from subtype B, with some exceptions. Patterns of resistance after failure of a first-line ta-N(t)RTI regimen support using TDF in N(t)RTI-containing second-line regimens, or using N(t)RTI-sparing regimens.
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Affiliation(s)
- Edward P. Lam
- The Kirby Institute UNSW Australia, Sydney, Australia
| | | | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano, Heredia, Lima, Peru
| | - Chidi Nwizu
- Center for Clinical Care and Clinical Research in Nigeria, Abuja, Nigeria
| | - Adeeba Kamarulzaman
- Clinical Investigations Centre, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | | - Jean-Michel Molina
- Department of Clinical Infectious Diseases, Hôpital Saint-Louis, Paris, France
| | - Sean Emery
- The Kirby Institute UNSW Australia, Sydney, Australia
| | | | - Mark A. Boyd
- The Kirby Institute UNSW Australia, Sydney, Australia
- University of Adelaide, Lyell McEwin Hospital, Adelaide, South Australia, Australia
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Liu Z, Huang X, Hu L, Pham L, Poole KM, Tang Y, Mahon BP, Tang W, Li K, Goldfarb NE, Dunn BM, McKenna R, Fanucci GE. Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution. J Biol Chem 2016; 291:22741-22756. [PMID: 27576689 DOI: 10.1074/jbc.m116.747568] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multidrug resistance to current Food and Drug Administration-approved HIV-1 protease (PR) inhibitors drives the need to understand the fundamental mechanisms of how drug pressure-selected mutations, which are oftentimes natural polymorphisms, elicit their effect on enzyme function and resistance. Here, the impacts of the hinge-region natural polymorphism at residue 35, glutamate to aspartate (E35D), alone and in conjunction with residue 57, arginine to lysine (R57K), are characterized with the goal of understanding how altered salt bridge interactions between the hinge and flap regions are associated with changes in structure, motional dynamics, conformational sampling, kinetic parameters, and inhibitor affinity. The combined results reveal that the single E35D substitution leads to diminished salt bridge interactions between residues 35 and 57 and gives rise to the stabilization of open-like conformational states with overall increased backbone dynamics. In HIV-1 PR constructs where sites 35 and 57 are both mutated (e.g. E35D and R57K), x-ray structures reveal an altered network of interactions that replace the salt bridge thus stabilizing the structural integrity between the flap and hinge regions. Despite the altered conformational sampling and dynamics when the salt bridge is disrupted, enzyme kinetic parameters and inhibition constants are similar to those obtained for subtype B PR. Results demonstrate that these hinge-region natural polymorphisms, which may arise as drug pressure secondary mutations, alter protein dynamics and the conformational landscape, which are important thermodynamic parameters to consider for development of inhibitors that target for non-subtype B PR.
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Affiliation(s)
- Zhanglong Liu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Xi Huang
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Lingna Hu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Linh Pham
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Katye M Poole
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Yan Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Brian P Mahon
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Wenxing Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Kunhua Li
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Nathan E Goldfarb
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Ben M Dunn
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Robert McKenna
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Gail E Fanucci
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
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Huang A, Hogan JW, Luo X, DeLong A, Saravanan S, Wu Y, Sirivichayakul S, Kumarasamy N, Zhang F, Phanuphak P, Diero L, Buziba N, Istrail S, Katzenstein DA, Kantor R. Global Comparison of Drug Resistance Mutations After First-Line Antiretroviral Therapy Across Human Immunodeficiency Virus-1 Subtypes. Open Forum Infect Dis 2016; 3:ofv158. [PMID: 27419147 PMCID: PMC4943563 DOI: 10.1093/ofid/ofv158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/19/2015] [Indexed: 12/02/2022] Open
Abstract
Background. Human immunodeficiency virus (HIV)-1 drug resistance mutations (DRMs) often accompany treatment failure. Although subtype differences are widely studied, DRM comparisons between subtypes either focus on specific geographic regions or include populations with heterogeneous treatments. Methods. We characterized DRM patterns following first-line failure and their impact on future treatment in a global, multi-subtype reverse-transcriptase sequence dataset. We developed a hierarchical modeling approach to address the high-dimensional challenge of modeling and comparing frequencies of multiple DRMs in varying first-line regimens, durations, and subtypes. Drug resistance mutation co-occurrence was characterized using a novel application of a statistical network model. Results. In 1425 sequences, 202 subtype B, 696 C, 44 G, 351 circulating recombinant forms (CRF)01_AE, 58 CRF02_AG, and 74 from other subtypes mutation frequencies were higher in subtypes C and CRF01_AE compared with B overall. Mutation frequency increased by 9%-20% at reverse transcriptase positions 41, 67, 70, 184, 215, and 219 in subtype C and CRF01_AE vs B. Subtype C and CRF01_AE exhibited higher predicted cross-resistance (+12%-18%) to future therapy options compared with subtype B. Topologies of subtype mutation networks were mostly similar. Conclusions. We find clear differences in DRM outcomes following first-line failure, suggesting subtype-specific ecological or biological factors that determine DRM patterns.
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Affiliation(s)
| | | | - Xi Luo
- Brown University , Providence, Rhode Island
| | | | | | - Yasong Wu
- National Centre for AIDS/STD Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing Ditan Hospital, Capital Medical University , China
| | | | | | - Fujie Zhang
- National Centre for AIDS/STD Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing Ditan Hospital, Capital Medical University , China
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Comparative analysis of drug resistance mutations in the human immunodeficiency virus reverse transcriptase gene in patients who are non-responsive, responsive and naive to antiretroviral therapy. Arch Virol 2016; 161:1101-13. [PMID: 26801790 DOI: 10.1007/s00705-016-2760-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/11/2016] [Indexed: 11/27/2022]
Abstract
Drug resistance mutations in the Pol gene of human immunodeficiency virus 1 (HIV-1) are one of the critical factors associated with antiretroviral therapy (ART) failure in HIV-1 patients. The issue of resistance to reverse transcriptase inhibitors (RTIs) in HIV infection has not been adequately addressed in the Indian subcontinent. We compared HIV-1 reverse transcriptase (RT) gene sequences to identify mutations present in HIV-1 patients who were ART non-responders, ART responders and drug naive. Genotypic drug resistance testing was performed by sequencing a 655-bp region of the RT gene from 102 HIV-1 patients, consisting of 30 ART-non-responding, 35 ART-responding and 37 drug-naive patients. The Stanford HIV Resistance Database (HIVDBv 6.2), IAS-USA mutation list, ANRS_09/2012 algorithm, and Rega v8.02 algorithm were used to interpret the pattern of drug resistance. The majority of the sequences (96 %) belonged to subtype C, and a few of them (3.9 %) to subtype A1. The frequency of drug resistance mutations observed in ART-non-responding, ART-responding and drug-naive patients was 40.1 %, 10.7 % and 20.58 %, respectively. It was observed that in non-responders, multiple mutations were present in the same patient, while in responders, a single mutation was found. Some of the drug-naive patients had more than one mutation. Thymidine analogue mutations (TAMs), however, were found in non-responders and naive patients but not in responders. Although drug resistance mutations were widely distributed among ART non-responders, the presence of resistance mutations in the viruses of drug-naive patients poses a big concern in the absence of a genotyping resistance test.
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25
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Avi R, Pauskar M, Karki T, Kallas E, Jõgeda EL, Margus T, Huik K, Lutsar I. Prevalence of drug resistance mutations in HAART patients infected with HIV-1 CRF06_cpx in Estonia. J Med Virol 2015; 88:448-54. [PMID: 26291050 DOI: 10.1002/jmv.24361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2015] [Indexed: 11/08/2022]
Abstract
HIV-1 drug resistance mutations (DRMs) and substitutions were assessed after the failure of the first line non-nucleoside reverse transcriptase inhibitors (NNRTIs) + 2 nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) treatment regimens (efavirenz [EFV] + lamivudine[3TC] + zidovudine [ZDV] vs. EFV + 3TC + ddI) among the HIV-1 CRF06_cpx infected subjects in Estonia. HIV-1 genomic RNA was sequenced; DRMs and amino acid substitutions were compared in 44 treatment naïve and 45 first-line NNRTI + 2 NRTI treatment failed patients consisting of EFV + 3TC + ZDV (n = 17) and EFV + 3TC + didanosine[ddI] (n = 21) therapy failed sub-populations. At least one DRM was found in 78% of treatment experienced patients. The most common NRTI mutations were M184V (80%), L74V (31%), L74I (17%), K219E (9%), and M184I (9%), NNRTI mutations were K103N (83%), P225H (14%), L100I (11%), and Y188L (11%), reflecting generally the similar pattern of DRMs to that seen in treatment failed subtype B viruses. Sub-population analysis revealed that EFV + 3TC + ddI failed patients had more DRMs compared to EFV + 3TC + ZDV failed patients, especially the ddI DRM L74IV and several additional NNRTI DRMs. Additionally, CRF06_cpx specific mutation E179V and substitutions R32K, K122E, and V200AE were also detected in treatment experienced population. After the failure of the first-line EFV + 3TC + ddI therapy HIV-1 CRF06_cpx viruses develop additional NRTI and NNRTI mutations compared to EFV + 3TC + ZDV regimen. Therefore the usage of EFV + 3TC + ddI in this subtype decreases the options for next regimens containing abacavir, and NNRTI class agents.
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Affiliation(s)
- Radko Avi
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Merit Pauskar
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Tõnis Karki
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Eveli Kallas
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Ene-Ly Jõgeda
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Tõnu Margus
- Department of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kristi Huik
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Irja Lutsar
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
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Thirunavukarasu D, Udhaya V, Iqbal HS, Umaarasu T. Patterns of HIV-1 Drug-Resistance Mutations among Patients Failing First-Line Antiretroviral Treatment in South India. J Int Assoc Provid AIDS Care 2015; 15:261-8. [PMID: 26385878 DOI: 10.1177/2325957415603508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Although highly active antiretroviral therapy has improved the quality of life among HIV-infected people in India, the emergence of drug resistance along with the limited access and affordability to routine monitoring continues to be a challenge worldwide. METHODS The frequency and patterns of HIV-1 drug-resistance mutations among the first-line failing HIV-infected patients attending a hospital in Salem, Tamil Nadu, India, were genotypically analyzed using the online Stanford HIV Database. RESULTS Of the study patients followed up for 6 months, 23 patients failed first-line therapy and the mutation of I135R/T/V/X, L178 I/M, M184V/I, D67N, K70R, and K103N was most common. Phylogenetic analysis revealed that most of these patients belonged to HIV subtype C. CONCLUSION The study documents the frequency of nucleoside reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor mutations that are prevalent in the first-line failing HIV-infected patients of South Indian region and adds up to the data for developing future algorithms to study the drug-resistance mutations of HIV subtype C. Thus, the results of the study call for the need for rational approach for selecting and for frequent viral monitoring to be performed to detect failure, followed by genotyping.
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Affiliation(s)
| | - Visvanathan Udhaya
- Department of Microbiology, Faculty of Medicine, Annamalai University, Chidambaram, Tamil Nadu, India
| | | | - Thirunavukarasu Umaarasu
- Department of Microbiology, Vivekanandha Dental College for Women, Tiruchengode, Tamil Nadu, India
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Zhang L, Wang J, Coetzer M, Angione S, Kantor R, Tripathi A. One-Step Ligation on RNA Amplification for the Detection of Point Mutations. J Mol Diagn 2015; 17:679-88. [PMID: 26322949 DOI: 10.1016/j.jmoldx.2015.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 06/16/2015] [Accepted: 07/01/2015] [Indexed: 12/16/2022] Open
Abstract
The detection of point mutations is required in the diagnosis of many human diseases. The conformal specificity of DNA ligases was elegantly used to distinguish single-nucleotide mismatches. However, to detect point mutations in RNA retroviruses, conventional ligase-mediated approaches require the reverse transcription of viral genomes before separate ligation and amplification steps. We developed one-step ligation on RNA amplification (LRA) for the direct detection of RNA point mutations. The process combines the ligase-mediated joining of two oligonucleotides and subsequent hot start amplification into a single-tube reaction. We report that modifications to the structure of the oligonucleotide ligation probes improve the rate of ligation and the specificity of mutation detection on RNA. We applied LRA to the detection of a common, clinically relevant HIV-1 reverse transcriptase drug-resistant point mutation, K103N, and compared it with allele-specific PCR and pyrosequencing. LRA achieved a limit of specific quantitation of 1:100 (1%), and a limit of specific detection for mutant K103N RNA transcripts among excess wild-type strands of 1:10,000 (0.01%). LRA also exhibited good detection threshold of 5 × 10(2) copies/μL K103N RNA transcripts. LRA is a novel point mutation detection method, with potential utilization in HIV drug resistance detection and early diagnostics of genetic disorders associated with other infectious diseases and cancer.
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Affiliation(s)
- Lei Zhang
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island
| | - Jingjing Wang
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island
| | - Mia Coetzer
- Division of Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Stephanie Angione
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island
| | - Rami Kantor
- Division of Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Anubhav Tripathi
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island.
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Grossman Z, Avidor B, Mor Z, Chowers M, Levy I, Shahar E, Riesenberg K, Sthoeger Z, Maayan S, Shao W, Lorber M, Olstein-Pops K, Elbirt D, Elinav H, Asher I, Averbuch D, Istomin V, Gottesman BS, Kedem E, Girshengorn S, Kra-Oz Z, Shemer Avni Y, Radian Sade S, Turner D, Maldarelli F. A Population-Structured HIV Epidemic in Israel: Roles of Risk and Ethnicity. PLoS One 2015; 10:e0135061. [PMID: 26302493 PMCID: PMC4547742 DOI: 10.1371/journal.pone.0135061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/17/2015] [Indexed: 11/30/2022] Open
Abstract
Background HIV in Israel started with a subtype-B epidemic among men who have sex with men, followed in the 1980s and 1990s by introductions of subtype C from Ethiopia (predominantly acquired by heterosexual transmission) and subtype A from the former Soviet Union (FSU, most often acquired by intravenous drug use). The epidemic matured over the last 15 years without additional large influx of exogenous infections. Between 2005 and 2013 the number of infected men who have sex with men (MSM) increased 2.9-fold, compared to 1.6-fold and 1.3-fold for intravenous drug users (IVDU) and Ethiopian-origin residents. Understanding contemporary spread is essential for effective public health planning. Methods We analyzed demographic and virologic data from 1,427 HIV-infected individuals diagnosed with HIV-I during 1998–2012. HIV phylogenies were reconstructed with maximum-likelihood and Bayesian methods. Results Subtype-B viruses, but not A or C, demonstrated a striking number of large clusters with common ancestors having posterior probability ≥0.95, including some suggesting presence of transmission networks. Transmitted drug resistance was highest in subtype B (13%). MSM represented a frequent risk factor in cross-ethnic transmission, demonstrated by the presence of Israeli-born with non-B virus infections and FSU immigrants with non-A subtypes. Conclusions Reconstructed phylogenetic trees demonstrated substantial grouping in subtype B, but not in non-MSM subtype-A or in subtype-C, reflecting differences in transmission dynamics linked to HIV transmission categories. Cross-ethnic spread occurred through multiple independent introductions, with MSM playing a prevalent role in the transmission of the virus. Such data provide a baseline to track epidemic trends and will be useful in informing and quantifying efforts to reduce HIV transmission.
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Affiliation(s)
- Zehava Grossman
- School of Public Health, Tel-Aviv University, Tel-Aviv, Israel
- National Cancer Institute, Frederick, MD, United States of America
- * E-mail:
| | - Boaz Avidor
- Crusaid Kobler AIDS Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Laboratory of Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Zohar Mor
- Ramla Department of Health, Ministry of Health, Ramla, Israel
| | | | - Itzchak Levy
- Infectious Diseases Unit, Sheba Medical Center, Ramat-Gan, Israel
| | | | | | | | | | - Wei Shao
- Advanced Biomedical Computing Center, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
| | | | | | | | | | | | | | | | | | | | - Shirley Girshengorn
- Crusaid Kobler AIDS Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Laboratory of Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | | | | | - Dan Turner
- Crusaid Kobler AIDS Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Frank Maldarelli
- National Cancer Institute, Frederick, MD, United States of America
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Comparison of susceptibility of HIV-1 variants to antiretroviral drugs by genotypic and recombinant virus phenotypic analyses. Int J Infect Dis 2015; 37:86-92. [PMID: 26117343 DOI: 10.1016/j.ijid.2015.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/28/2015] [Accepted: 06/20/2015] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE This study utilized genotypic and in-house recombinant virus phenotypic assays to examine HIV-1 variant susceptibility to antiretroviral (ARV) drugs; comparisons were made between the analyses. METHODS A nested PCR was employed to amplify the HIV-1 gag-pol gene, which comprised the entire PR gene (codons 1-99) and the former RT gene (codons 1-312). Genetic resistance was determined by submitting the sequences to the Stanford University Network HIV-1 Database. Phenotypic susceptibilities to six ARV drugs were measured using a high-throughput, multi-cycle, recombinant virus phenotypic assay. Results were expressed in terms of the IC50 (half maximal inhibitory concentration) and fold-change values. The relationship between phenotypic drug resistance and genetic polymorphisms was determined. RESULTS Nineteen fragment sequences for which recombinant viruses were successfully constructed were translated and compared with the consensus B sequences in the Stanford University Network HIV-1 Database. No recognizable genotypic resistance-associated mutations were noted, except in one sample. Each homologous replication-competent recombinant viral fold-change in the presence of six ARV drugs used widely in China was measured. According to the clinical and statistical criteria, 16 of the 19 samples were susceptible to the six drugs tested. The majority of phenotypic and genotypic results obtained were in agreement, with a concordance rate of 97.4%. Both phenotypic and genotypic assays suggested that sample HN2009001 was resistant to all drugs tested. All phenotypic and genotypic results obtained regarding the susceptibility of the 19 recombinant viruses to nucleoside reverse transcriptase inhibitors (NRTIs) were in agreement. With regard to the genotypic results for the non-nucleoside reverse transcriptase inhibitors (NNRTIs), 7.9% (3/38) were inconsistent with the phenotypic results. CONCLUSIONS The in-house recombinant virus phenotypic assay was able to provide a straightforward quantitative assessment of resistance. In most cases, the genotypic and novel phenotypic assays yielded similar results. The disparity in HIV-1 susceptibility indicates a need to further investigate the clinical outcomes of antiretroviral therapy in certain individuals.
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Kantor R, Smeaton L, Vardhanabhuti S, Hudelson SE, Wallis CL, Tripathy S, Morgado MG, Saravanan S, Balakrishnan P, Reitsma M, Hart S, Mellors JW, Halvas E, Grinsztejn B, Hosseinipour MC, Kumwenda J, La Rosa A, Lalloo UG, Lama JR, Rassool M, Santos BR, Supparatpinyo K, Hakim J, Flanigan T, Kumarasamy N, Campbell TB, Eshleman SH. Pretreatment HIV Drug Resistance and HIV-1 Subtype C Are Independently Associated With Virologic Failure: Results From the Multinational PEARLS (ACTG A5175) Clinical Trial. Clin Infect Dis 2015; 60:1541-9. [PMID: 25681380 PMCID: PMC4425827 DOI: 10.1093/cid/civ102] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Evaluation of pretreatment HIV genotyping is needed globally to guide treatment programs. We examined the association of pretreatment (baseline) drug resistance and subtype with virologic failure in a multinational, randomized clinical trial that evaluated 3 antiretroviral treatment (ART) regimens and included resource-limited setting sites. METHODS Pol genotyping was performed in a nested case-cohort study including 270 randomly sampled participants (subcohort), and 218 additional participants failing ART (case group). Failure was defined as confirmed viral load (VL) >1000 copies/mL. Cox proportional hazards models estimated resistance-failure association. RESULTS In the representative subcohort (261/270 participants with genotypes; 44% women; median age, 35 years; median CD4 cell count, 151 cells/µL; median VL, 5.0 log10 copies/mL; 58% non-B subtypes), baseline resistance occurred in 4.2%, evenly distributed among treatment arms and subtypes. In the subcohort and case groups combined (466/488 participants with genotypes), used to examine the association between resistance and treatment failure, baseline resistance occurred in 7.1% (9.4% with failure, 4.3% without). Baseline resistance was significantly associated with shorter time to virologic failure (hazard ratio [HR], 2.03; P = .035), and after adjusting for sex, treatment arm, sex-treatment arm interaction, pretreatment CD4 cell count, baseline VL, and subtype, was still independently associated (HR, 2.1; P = .05). Compared with subtype B, subtype C infection was associated with higher failure risk (HR, 1.57; 95% confidence interval [CI], 1.04-2.35), whereas non-B/C subtype infection was associated with longer time to failure (HR, 0.47; 95% CI, .22-.98). CONCLUSIONS In this global clinical trial, pretreatment resistance and HIV-1 subtype were independently associated with virologic failure. Pretreatment genotyping should be considered whenever feasible. CLINICAL TRIALS REGISTRATION NCT00084136.
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Affiliation(s)
- Rami Kantor
- Divisionof Infectious Diseases, Department of Medicine, Brown University, Providence, Rhode Island
| | - Laura Smeaton
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Harvard University, Boston, Massachusetts
| | - Saran Vardhanabhuti
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Harvard University, Boston, Massachusetts
| | - Sarah E. Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Mariza G. Morgado
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | | | - Marissa Reitsma
- Divisionof Infectious Diseases, Department of Medicine, Brown University, Providence, Rhode Island
| | - Stephen Hart
- Frontier Science and Technology Research Foundation, Amherst, New York
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Elias Halvas
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Beatriz Grinsztejn
- Instituto de Pesquisa Clinica Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | | | - Johnstone Kumwenda
- Department of Internal Medicine, University of Malawi, College of Medicine, Blantyre
| | - Alberto La Rosa
- Asociacion Civil Impacta Salud y Educacion, Barranco, Lima, Peru
| | | | - Javier R. Lama
- Asociacion Civil Impacta Salud y Educacion, Barranco, Lima, Peru
| | - Mohammed Rassool
- Department of Medicine, University of Witwatersrand; Helen Joseph Hospital, Themba Lethu Clinic, Johannesburg, South Africa
| | - Breno R. Santos
- Serviço de Infectologia, Hospital Nossa Senhora da Conceição, Porto Alegre, Brazil
| | - Khuanchai Supparatpinyo
- Research Institute for Health Sciences and Faculty of Medicine, Chiang Mai University, Thailand
| | - James Hakim
- Department of Medicine, University of Zimbabwe, Harare
| | - Timothy Flanigan
- Divisionof Infectious Diseases, Department of Medicine, Brown University, Providence, Rhode Island
| | | | - Thomas B. Campbell
- Division of Infectious Diseases, Department of Medicine, University of Colorado Denver, Aurora
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Diallo K, Zheng DP, Rottinghaus EK, Bassey O, Yang C. Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria. AIDS Res Hum Retroviruses 2015; 31:564-75. [PMID: 25582324 DOI: 10.1089/aid.2014.0168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Studying the genetic diversity and natural polymorphisms of HIV-1 would benefit our understanding of HIV drug resistance (HIVDR) development and predict treatment outcomes. In this study, we have characterized the HIV-1 genetic diversity and natural polymorphisms at the 5' region of the pol gene encompassing the protease (PR) and reverse transcriptase (RT) from 271 plasma specimens collected in 2008 from HIV-1-infected patients who were eligible for initiating antiretroviral therapy in Abuja (Nigeria). The analysis indicated that the predominant subtype was subtype G (31.0%), followed by CRF02-AG (19.2 %), CRF43-02G (18.5%), and A/CRF36-cpx (11.4%); the remaining (19.9%) were other subtypes and circulating (CRF) and unique (URF) recombinant forms. Recombinant viruses (68.6%) were the major viral strains in the region. Eighty-four subtype G sequences were further mainly classified into two major and two minor clusters; sequences in the two major clusters were closely related to the HIV-1 strains in two of the three major subtype G clusters detected worldwide. Those in the two minor clusters appear to be new subtype G strains circulating only in Abuja. The pretreatment DR prevalence was <3%; however, numerous natural polymorphisms were present. Eleven polymorphic mutations (G16E, K20I, L23P, E35D, M36I, N37D/S/T, R57K, L63P, and V82I) were detected in the PR that were subtype or CRF specific while only three mutations (D123N, I135T, and I135V) were identified in the RT. Overall, this study indicates an evolving HIV-1 epidemic in Abuja with recombinant viruses becoming the dominant strains and the emergence of new subtype G strains; pretreatment HIVDR was low and the occurrence of natural polymorphism in the PR region was subtype or CRF dependent.
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Affiliation(s)
- Karidia Diallo
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Du-Ping Zheng
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Erin K. Rottinghaus
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Orji Bassey
- Centers for Disease Control and Prevention, Abuja, Nigeria
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
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Rogo T, DeLong AK, Chan P, Kantor R. Antiretroviral treatment failure, drug resistance, and subtype diversity in the only pediatric HIV clinic in Rhode Island. Clin Infect Dis 2015; 60:1426-35. [PMID: 25637585 PMCID: PMC4415056 DOI: 10.1093/cid/civ058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/21/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Drug resistance development in the human immunodeficiency virus (HIV)-infected pediatric population in the United States can impact long-term antiretroviral therapy (ART) efficacy. Limited formularies and adherence constraints in children jeopardize lifelong-needed ART. METHODS We examined treatment failure, drug resistance, and their correlates in ART-naive and ART-experienced children attending the pediatric HIV clinic in Rhode Island between 1991 and 2012. Pol sequences were obtained for phylogenetic, subtype, and resistance analyses. Associations between selected covariates and virologic failure and resistance were evaluated using generalized additive models and Fisher exact tests. RESULTS Data were available for all 56 clinic-attending children. At diagnosis, 33% were aged <1 year, 31% aged 1-4 years, and 37% aged ≥ 5 years; 54% were male, 73% black or Hispanic, 55% US-born, 20% refugees, and 64% perinatally infected. Of 44 ART-experienced children, 57% had virologic failure, most never virologically suppressed. Failure was associated with missed appointments (P = .05) and missed doses (P < .01). Of 40 children with available genotypes, 35% were infected with non-B subtypes; 6% of ART-naive children had resistance; and 73% of ART-experienced children had ≥ 1 major mutation: (16% conferring triple-class, 47% dual-class, and 37% single-class resistance). An epidemiologically confirmed resistance transmission from a perinatally infected teenage male to a newly infected teenage female was demonstrated. CONCLUSIONS We report high HIV type 1 diversity, extensive drug resistance among ART-experienced children, and horizontal transmission of resistance in the Rh ode Island pediatric HIV clinic. As HIV-infected children mature into adulthood, close monitoring of ART, adherence, and diagnosis disclosure are essential to optimize patient care.
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Affiliation(s)
| | | | - Philip Chan
- Division of Infectious Diseases, Brown University, Providence, Rhode Island
| | - Rami Kantor
- Division of Infectious Diseases, Brown University, Providence, Rhode Island
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Bártolo I, Zakovic S, Martin F, Palladino C, Carvalho P, Camacho R, Thamm S, Clemente S, Taveira N. HIV-1 diversity, transmission dynamics and primary drug resistance in Angola. PLoS One 2014; 9:e113626. [PMID: 25479241 PMCID: PMC4257534 DOI: 10.1371/journal.pone.0113626] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/29/2014] [Indexed: 11/30/2022] Open
Abstract
Objectives To assess HIV-1 diversity, transmission dynamics and prevalence of transmitted drug resistance (TDR) in Angola, five years after ART scale-up. Methods Population sequencing of the pol gene was performed on 139 plasma samples collected in 2009 from drug-naive HIV-1 infected individuals living in Luanda. HIV-1 subtypes were determined using phylogenetic analysis. Drug resistance mutations were identified using the Calibrated Population Resistance Tool (CPR). Transmission networks were determined using phylogenetic analysis of all Angolan sequences present in the databases. Evolutionary trends were determined by comparison with a similar survey performed in 2001. Results 47.1% of the viruses were pure subtypes (all except B), 47.1% were recombinants and 5.8% were untypable. The prevalence of subtype A decreased significantly from 2001 to 2009 (40.0% to 10.8%, P = 0.0019) while the prevalence of unique recombinant forms (URFs) increased>2-fold (40.0% to 83.1%, P<0.0001). The most frequent URFs comprised untypable sequences with subtypes H (U/H, n = 7, 10.8%), A (U/A, n = 6, 9.2%) and G (G/U, n = 4, 6.2%). Newly identified U/H recombinants formed a highly supported monophyletic cluster suggesting a local and common origin. TDR mutation K103N was found in one (0.7%) patient (1.6% in 2001). Out of the 364 sequences sampled for transmission network analysis, 130 (35.7%) were part of a transmission network. Forty eight transmission clusters were identified; the majority (56.3%) comprised sequences sampled in 2008–2010 in Luanda which is consistent with a locally fuelled epidemic. Very low genetic distance was found in 27 transmission pairs sampled in the same year, suggesting recent transmission events. Conclusions Transmission of drug resistant strains was still negligible in Luanda in 2009, five years after the scale-up of ART. The dominance of small and recent transmission clusters and the emergence of new URFs are consistent with a rising HIV-1 epidemics mainly driven by heterosexual transmission.
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Affiliation(s)
- Inês Bártolo
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Suzana Zakovic
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Francisco Martin
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Claudia Palladino
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia Carvalho
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
| | - Ricardo Camacho
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sven Thamm
- Abbott GmbH & Co. KG, Wiesbaden, Germany
| | - Sofia Clemente
- Hospital da Divina Providência, Serviço de Doenças Infecciosas, Luanda, Angola
| | - Nuno Taveira
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
- * E-mail:
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HIV diversity and drug resistance from plasma and non-plasma analytes in a large treatment programme in western Kenya. J Int AIDS Soc 2014; 17:19262. [PMID: 25413893 PMCID: PMC4238965 DOI: 10.7448/ias.17.1.19262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Antiretroviral resistance leads to treatment failure and resistance transmission. Resistance data in western Kenya are limited. Collection of non-plasma analytes may provide additional resistance information. METHODS We assessed HIV diversity using the REGA tool, transmitted resistance by the WHO mutation list and acquired resistance upon first-line failure by the IAS-USA mutation list, at the Academic Model Providing Access to Healthcare (AMPATH), a major treatment programme in western Kenya. Plasma and four non-plasma analytes, dried blood-spots (DBS), dried plasma-spots (DPS), ViveST(TM)-plasma (STP) and ViveST-blood (STB), were compared to identify diversity and evaluate sequence concordance. RESULTS Among 122 patients, 62 were treatment-naïve and 60 treatment-experienced; 61% were female, median age 35 years, median CD4 182 cells/µL, median viral-load 4.6 log10 copies/mL. One hundred and ninety-six sequences were available for 107/122 (88%) patients, 58/62 (94%) treatment-naïve and 49/60 (82%) treated; 100/122 (82%) plasma, 37/78 (47%) attempted DBS, 16/45 (36%) attempted DPS, 14/44 (32%) attempted STP from fresh plasma and 23/34 (68%) from frozen plasma, and 5/42 (12%) attempted STB. Plasma and DBS genotyping success increased at higher VL and shorter shipment-to-genotyping time. Main subtypes were A (62%), D (15%) and C (6%). Transmitted resistance was found in 1.8% of plasma sequences, and 7% combining analytes. Plasma resistance mutations were identified in 91% of treated patients, 76% NRTI, 91% NNRTI; 76% dual-class; 60% with intermediate-high predicted resistance to future treatment options; with novel mutation co-occurrence patterns. Nearly 88% of plasma mutations were identified in DBS, 89% in DPS and 94% in STP. Of 23 discordant mutations, 92% in plasma and 60% in non-plasma analytes were mixtures. Mean whole-sequence discordance from frozen plasma reference was 1.1% for plasma-DBS, 1.2% plasma-DPS, 2.0% plasma-STP and 2.3% plasma-STB. Of 23 plasma-STP discordances, one mutation was identified in plasma and 22 in STP (p<0.05). Discordance was inversely significantly related to VL for DBS. CONCLUSIONS In a large treatment programme in western Kenya, we report high HIV-1 subtype diversity; low plasma transmitted resistance, increasing when multiple analytes were combined; and high-acquired resistance with unique mutation patterns. Resistance surveillance may be augmented by using non-plasma analytes for lower-cost genotyping in resource-limited settings.
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Singh K, Flores JA, Kirby KA, Neogi U, Sonnerborg A, Hachiya A, Das K, Arnold E, McArthur C, Parniak M, Sarafianos SG. Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors. Viruses 2014; 6:3535-62. [PMID: 25254383 PMCID: PMC4189038 DOI: 10.3390/v6093535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
Human immunodeficiency virus (HIV) causes approximately 2.5 million new infections every year, and nearly 1.6 million patients succumb to HIV each year. Several factors, including cross-species transmission and error-prone replication have resulted in extraordinary genetic diversity of HIV groups. One of these groups, known as group M (main) contains nine subtypes (A-D, F-H and J-K) and causes ~95% of all HIV infections. Most reported data on susceptibility and resistance to anti-HIV therapies are from subtype B HIV infections, which are prevalent in developed countries but account for only ~12% of all global HIV infections, whereas non-B subtype HIV infections that account for ~88% of all HIV infections are prevalent primarily in low and middle-income countries. Although the treatments for subtype B infections are generally effective against non-B subtype infections, there are differences in response to therapies. Here, we review how polymorphisms, transmission efficiency of drug-resistant strains, and differences in genetic barrier for drug resistance can differentially alter the response to reverse transcriptase-targeting therapies in various subtypes.
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Affiliation(s)
- Kamalendra Singh
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Jacqueline A Flores
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Karen A Kirby
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Atsuko Hachiya
- Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization, Nagoya Medical Center, Nagoya 460-0001, Japan.
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Carole McArthur
- Department of Oral and Craniofacial Science , School of Dentistry, University of Missouri, Kansas City, MO 64108, USA.
| | - Michael Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Stefan G Sarafianos
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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High prevalence of subtype F in newly diagnosed HIV-1 persons in northwest Spain and evidence for impaired treatment response. AIDS 2014; 28:1837-40. [PMID: 24871456 DOI: 10.1097/qad.0000000000000326] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HIV-1 non-B subtype variants were found in 37.8% of 296 newly diagnosed persons in northwest Spain over the past 5 years. Subtype F was the most prevalent non-B subtype (29.6%) and displayed preferential transmission among MSM. Virologic response rates to antiretroviral therapy were lower among F subtypes compared to B subtypes at weeks 24 (31% vs. 78.3%), 48 (51.7% vs. 85.2%), and 96 (61.1% vs. 94.3%) of therapy. Subtype F was independently associated with virological response at 24 weeks.
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Kiwelu IE, Novitsky V, Kituma E, Margolin L, Baca J, Manongi R, Sam N, Shao J, McLane MF, Kapiga SH, Essex M. HIV-1 pol diversity among female bar and hotel workers in Northern Tanzania. PLoS One 2014; 9:e102258. [PMID: 25003939 PMCID: PMC4087014 DOI: 10.1371/journal.pone.0102258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/16/2014] [Indexed: 11/18/2022] Open
Abstract
A national ART program was launched in Tanzania in October 2004. Due to the existence of multiple HIV-1 subtypes and recombinant viruses co-circulating in Tanzania, it is important to monitor rates of drug resistance. The present study determined the prevalence of HIV-1 drug resistance mutations among ART-naive female bar and hotel workers, a high-risk population for HIV-1 infection in Moshi, Tanzania. A partial HIV-1 pol gene was analyzed by single-genome amplification and sequencing in 45 subjects (622 pol sequences total; median number of sequences per subject, 13; IQR 5-20) in samples collected in 2005. The prevalence of HIV-1 subtypes A1, C, and D, and inter-subtype recombinant viruses, was 36%, 29%, 9% and 27%, respectively. Thirteen different recombination patterns included D/A1/D, C/A1, A1/C/A1, A1/U/A1, C/U/A1, C/A1, U/D/U, D/A1/D, A1/C, A1/C, A2/C/A2, CRF10_CD/C/CRF10_CD and CRF35_AD/A1/CRF35_AD. CRF35_AD was identified in Tanzania for the first time. All recombinant viruses in this study were unique, suggesting ongoing recombination processes among circulating HIV-1 variants. The prevalence of multiple infections in this population was 16% (n = 7). Primary HIV-1 drug resistance mutations to RT inhibitors were identified in three (7%) subjects (K65R plus Y181C; N60D; and V106M). In some subjects, polymorphisms were observed at the RT positions 41, 69, 75, 98, 101, 179, 190, and 215. Secondary mutations associated with NNRTIs were observed at the RT positions 90 (7%) and 138 (6%). In the protease gene, three subjects (7%) had M46I/L mutations. All subjects in this study had HIV-1 subtype-specific natural polymorphisms at positions 36, 69, 89 and 93 that are associated with drug resistance in HIV-1 subtype B. These results suggested that HIV-1 drug resistance mutations and natural polymorphisms existed in this population before the initiation of the national ART program. With increasing use of ARV, these results highlight the importance of drug resistance monitoring in Tanzania.
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Affiliation(s)
- Ireen E. Kiwelu
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Elimsaada Kituma
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - Lauren Margolin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Jeannie Baca
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rachel Manongi
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - Noel Sam
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - John Shao
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
| | - Mary F. McLane
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Saidi H. Kapiga
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Megens S, Laethem KV. HIV-1 genetic variation and drug resistance development. Expert Rev Anti Infect Ther 2014; 11:1159-78. [PMID: 24151833 DOI: 10.1586/14787210.2013.844649] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Up until 10 years ago, basic and clinical HIV-1 research was mainly performed on HIV-1 subtype B that predominated in resource-rich settings. Over the past decade, HIV-1 care and therapy has been scaled up substantially in Latin America, Africa and Asia. These regions are largely dominated by non-B subtype infections, and especially the African continent is affected by the HIV pandemic. Insight on the potency of antiviral drugs and regimens as well as on the emergence of drug resistance in non-B subtypes was lacking triggering research in this field, also partly driven by the introduction and spreading of HIV-1 non-B subtypes in Europe. The scope of this article was to review and discuss the state-of-the-art on the impact of HIV-1 genetic variation on the in vitro activity of antiviral drugs and in vivo response to antiviral therapy; as well as on the in vitro and in vivo emergence of drug resistance.
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Affiliation(s)
- Sarah Megens
- Department Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Wang W, Yao N, Ju B, Dong Z, Cong Z, Jiang H, Qin C, Wei Q. A simian-human immunodeficiency virus carrying the rt gene from Chinese CRF01_AE strain of HIV is sensitive to nucleoside reverse transcriptase inhibitors and has a highly genetic stability in vivo. Microbes Infect 2014; 16:461-71. [PMID: 24709063 DOI: 10.1016/j.micinf.2014.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/14/2014] [Accepted: 03/27/2014] [Indexed: 11/16/2022]
Abstract
Human immunodeficiency virus (HIV)-1 subtype CRF01_AE is one of the major HIV-1 subtypes that dominate the global epidemic. However, its drug resistance, associated mutations, and viral fitness have not been systemically studied, because available chimeric simian-HIVs (SHIVs) usually express the HIV-1 reverse transcriptase (rt) gene of subtype B HIV-1, which is different from subtype CRF01_AE HIV-1. In this study, a recombinant plasmid, pRT-SHIV/AE, was constructed to generate a chimeric RT-SHIV/AE by replacing the rt gene of simian immunodeficiency virus (SIVmac239) with the counterpart of Chinese HIV-1 subtype CRF01_AE. The infectivity, replication capacity, co-receptor tropism, drug sensitivity, and genetic stability of RT-SHIV/AE were characterized. The new chimeric RT-SHIV/AE effectively infected and replicated in human T cell line and rhesus peripheral blood mononuclear cells (rhPBMC). The rt gene of RT-SHIV/AE lacked the common mutation (T215I) associated with drug resistance. RT-SHIV-AE retained infectivity and immunogenicity, similar to that of its counterpart RT-SHIV/TC virus following intravenous inoculation in Chinese rhesus macaque. RT-SHIV-AE was more sensitive to nucleoside reverse transcriptase inhibitors (NRTIs) than the RT-SHIV/TC. RT-SHIV/AE was genetically stable in Chinese rhesus macaque. The new chimeric RT-SHIV/AE may be a valuable tool for evaluating the efficacy of the rt-based antiviral drugs against the subtype CRF01_AE HIV-1.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Beijing 100021, PR China; Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Beijing 100021, PR China; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China; Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China
| | - Nan Yao
- Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China
| | - Bin Ju
- Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China
| | - Zhihui Dong
- Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China
| | - Zhe Cong
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Beijing 100021, PR China; Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Beijing 100021, PR China; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China; Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China
| | - Hong Jiang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Beijing 100021, PR China; Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Beijing 100021, PR China; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China; Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China
| | - Chuan Qin
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Beijing 100021, PR China; Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Beijing 100021, PR China; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China; Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China.
| | - Qiang Wei
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Beijing 100021, PR China; Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Beijing 100021, PR China; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China; Comparative Medical Center, Peking Union Medical College, No. 5 Panjiayuan Nanli, Chaoyang District, Beijing 100021, PR China.
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Sui H, Gui T, Jia L, Guo W, Han J, Liu Y, Bao Z, Li H, Li J, Li L. Different frequencies of drug resistance mutations among HIV-1 subtypes circulating in China: a comprehensive study. PLoS One 2014; 9:e91803. [PMID: 24663120 PMCID: PMC3963863 DOI: 10.1371/journal.pone.0091803] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/13/2014] [Indexed: 12/12/2022] Open
Abstract
The rapid spreading of HIV drug resistance is threatening the overall success of free HAART in China. Much work has been done on drug-resistant mutations, however, most of which were based on subtype B. Due to different genetic background, subtypes difference would have an effect on the development of drug-resistant mutations, which has already been proved by more and more studies. In China, the main epidemic subtypes are CRF07_BC, CRF08_BC, Thai B and CRF01_AE. The depiction of drug resistance mutations in those subtypes will be helpful for the selection of regimens for Chinese. In this study, the distributions difference of amino acids at sites related to HIV drug resistance were compared among subtype B, CRF01_AE, CRF07_BC and CRF08_BC strains prevalent in China. The amino acid composition of sequences belonging to different subtypes, which were obtained from untreated and treated individuals separately, were also compared. The amino acids proportions of 19 sites in RT among subtype B, CRF01_AE and CRF08_BC have significant difference in drug resistance groups (chi-square test, p<0.05). Genetic barriers analysis revealed that sites 69, 138, 181, 215 and 238 were significantly different among subtypes (Kruskal Wallis test, p<0.05). All subtypes shared three highest prevalent drug resistance sites 103, 181 and 184 in common. Many drug resistant sites in protease show surprising high proportions in almost all subtypes in drug-naïve patients. This is the first comprehensive study in China on different development of drug resistance among different subtypes. The detailed data will lay a foundation for HIV treatment regimens design and improve HIV therapy in China.
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Affiliation(s)
- Hongshuai Sui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Clinical Laboratory of Beidaihe 281 hospital, Qinhuangdao, Hebei province, China
| | - Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Guo
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (JL); (LL)
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (JL); (LL)
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Mulu A, Lange T, Liebert UG, Maier M. Clade homogeneity and Pol gene polymorphisms in chronically HIV-1 infected antiretroviral treatment naive patients after the roll out of ART in Ethiopia. BMC Infect Dis 2014; 14:158. [PMID: 24655349 PMCID: PMC3976149 DOI: 10.1186/1471-2334-14-158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/18/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Despite the increasing use of antiretroviral treatment (ART) recent data on frequency and pattern of drug resistance mutations in Ethiopia is not available. Furthermore with increasing mobility of people HIV-1 subtypes other than the predominant subtype C may likely be introduced from the neighbouring countries. This study was aimed to determine the molecular characterization and pre-antiretroviral treatment resistance mutations among HIV-1 chronically infected ART naïve patients after the roll out of ART in Ethiopia. METHODS Viral RNA was determined in 160 baseline plasma samples. The entire PR and the first 335 codons (76%) of the RT regions of the pol gene of the HIV-1 genome (N = 160) were amplified and sequenced using an in-house assay. Genotypic drug resistance was defined as the presence of one or more resistance-related mutations as specified by the consensus mutation of Stanford University HIVDB and the International Antiviral Society (IAS) mutation lists. RESULTS A predominance of HIV-1 subtype C (98.7%) was observed. The level of drug resistance is found to be 5.6% and 13.1% according to the Stanford University HIVDB drug resistance interpretation algorithms and the International Antiviral Society mutation lists, respectively. Mutations conferring simultaneous resistance to NRTIs and NNRTIs were not detected and no major PR mutation was found. However, a high rate of polymorphic changes both in PR and RT regions were observed. Moreover, twenty four (15%) monophyletic transmission clusters with bootstrap value of 99% were found. CONCLUSIONS Strong evidence for consistent HIV-1C clade homogeneity and low influx of other variant into the country was found. The level of drug resistance observed in chronically infected treatment naïve patients which exceeds the WHO estimates suggests the need for incorporation of HIV-1 drug resistance testing prior to ART initiation. The occurrence of monophyletic transmission clusters affecting (24/160) individuals indicates their potential risk related practice. Thus, an intensified public health intervention program and monitoring of HIV drug resistance testing appears indispensible.
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Affiliation(s)
- Andargachew Mulu
- Institute of Virology, Leipzig University Leipzig, Germany
- Department of Microbiology, College of Medicine and Health Sciences, University of Gondar Gondar, Ethiopia
| | - Thomas Lange
- Institute of Virology, Leipzig University Leipzig, Germany
| | | | - Melanie Maier
- Institute of Virology, Leipzig University Leipzig, Germany
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Mata-Munguía C, Escoto-Delgadillo M, Torres-Mendoza B, Flores-Soto M, Vázquez-Torres M, Gálvez-Gastelum F, Viniegra-Osorio A, Castillero-Manzano M, Vázquez-Valls E. Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis. BMC Bioinformatics 2014; 15:72. [PMID: 24629078 PMCID: PMC4003850 DOI: 10.1186/1471-2105-15-72] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 03/05/2014] [Indexed: 11/22/2022] Open
Abstract
Background The correlations of genotypic and phenotypic tests with treatment, clinical history and the significance of mutations in viruses of HIV-infected patients are used to establish resistance mutations to protease inhibitors (PIs). Emerging mutations in human immunodeficiency virus type 1 (HIV-1) protease confer resistance to PIs by inducing structural changes at the ligand interaction site. The aim of this study was to establish an in silico structural relationship between natural HIV-1 polymorphisms and unusual HIV-1 mutations that confer resistance to PIs. Results Protease sequences isolated from 151 Mexican HIV-1 patients that were naïve to, or subjected to antiretroviral therapy, were examined. We identified 41 unrelated resistance mutations with a prevalence greater than 1%. Among these mutations, nine exhibited positive selection, three were natural polymorphisms (L63S/V/H) in a codon associated with drug resistance, and six were unusual mutations (L5F, D29V, L63R/G, P79L and T91V). The D29V mutation, with a prevalence of 1.32% in the studied population, was only found in patients treated with antiretroviral drugs. Using in silico modelling, we observed that D29V formed unstable protease complexes when were docked with lopinavir, saquinavir, darunavir, tipranavir, indinavir and atazanavir. Conclusions The structural correlation of natural polymorphisms and unusual mutations with drug resistance is useful for the identification of HIV-1 variants with potential resistance to PIs. The D29V mutation likely confers a selection advantage in viruses; however, in silico, presence of this mutation results in unstable enzyme/PI complexes, that possibly induce resistance to PIs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Eduardo Vázquez-Valls
- Laboratorio de Inmunodeficiencias y Retrovirus Humanos, Centro de Investigación Biomédica de Occidente, CMNO, IMSS, Guadalajara 44340, México.
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Kantor R. Research components of the Brown Kenya Program: a personal and professional perspective. RHODE ISLAND MEDICAL JOURNAL (2013) 2013; 96:16-9. [PMID: 24087816 PMCID: PMC8579719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Rami Kantor
- Director of Research for the Brown Kenya Program and an Associate Professor of Medicine at the Alpert Medical School at Brown University. He is an infectious disease specialist
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Treatment failure and drug resistance is more frequent in HIV-1 subtype D versus subtype A-infected Ugandans over a 10-year study period. AIDS 2013; 27:1899-909. [PMID: 23727942 DOI: 10.1097/qad.0b013e3283610ec7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine the impact of HIV-1 subtype on treatment outcomes and the emergence of drug resistance in the resource limited setting of Kampala, Uganda. DESIGN The Joint Clinical Research Centre (JCRC) in Kampala, Uganda has provided over 2000 drug-resistant genotypes (DRGs) over the past 10 years as standard of care for patients failing therapy and 1403 from treatment-naive and experienced patients over the past 10 years have been analyzed for this study. METHOD Viral loads, CD4 cell count, treatment histories and other relevant clinical data was compared with the infecting HIV-1 subtype and DRGs of Ugandan patients failing treatment. RESULTS Patients failing HAART with DRGs (n = 937) were more frequently infected with subtype D than expected on the basis of the subtype distribution in the treatment-naive population (n = 655) in Kampala (P < 0.001). Higher proportions of treatment failures among subtype D-infected patients were driven by resistance to nucleoside reverse transcriptase inhibitors (NRTI) (P < 0.0002) more than to non-NRTIs (P > 0.04) or protease inhibitors. CONCLUSION Higher rates of treatment failure among subtype D as compared with subtype A-infected Ugandans was analogous to the faster disease progression in subtype D-infected patients. The mechanism(s) by which drug resistance may emerge faster in subtype D HIV-1 may relate to higher replicative fitness and increased propensity for a CXCR4 tropism.
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Santoro MM, Perno CF. HIV-1 Genetic Variability and Clinical Implications. ISRN MICROBIOLOGY 2013; 2013:481314. [PMID: 23844315 PMCID: PMC3703378 DOI: 10.1155/2013/481314] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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Affiliation(s)
- Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- INMI L Spallanzani Hospital, Antiretroviral Therapy Monitoring Unit, Via Portuense 292, 00149 Rome, Italy
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Invernizzi CF, Coutsinos D, Oliveira M, Schildknecht RS, Xu H, Gaseitsiwe S, Moisi D, Brenner BG, Wainberg MA. The preferential selection of K65R in HIV-1 subtype C is attenuated by nucleotide polymorphisms at thymidine analogue mutation sites. J Antimicrob Chemother 2013; 68:2192-6. [PMID: 23749954 DOI: 10.1093/jac/dkt204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We recently reported the preferential selection of the K65R resistance mutation in subtype C HIV-1 compared with subtype B and showed the underlying mechanism to be dependent on subtype C-specific silent nucleotide polymorphisms, i.e. genomic mutations that change the genotype but not the phenotype. The number of clinical reports demonstrating elevated numbers of K65R nevertheless suggests the existence of factors limiting the increased incidence of K65R mutations. Thus, we investigated the contributions of subtype C-specific silent nucleotide polymorphisms at thymidine analogue mutation (TAM) sites 70, 210 and/or 219 that might reduce the previously described preferential selection of K65R in subtype C HIV-1 associated with subtype C-specific nucleotide polymorphisms at sites 64/65. METHODS Cell culture drug selections were performed with various drugs in MT2 cells. RESULTS The use of nucleoside/nucleotide reverse transcriptase inhibitors [N(t)RTIs] as single drugs or in combination confirmed the more frequent selection of K65R by multiple N(t)RTIs in a subtype B virus that contained the 64/65 nucleotide polymorphisms of subtype C than in a wild-type subtype B virus. This effect was attenuated in the presence of several silent TAM nucleotide polymorphisms, except when stavudine was employed in the selection protocol. CONCLUSIONS These results further demonstrate that stavudine can preferentially select for K65R in subtype C virus and also provide a basis for understanding the importance of silent nucleotide polymorphisms in regard to altered HIV drug resistance profiles.
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Affiliation(s)
- Cédric F Invernizzi
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
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Huang A, Kantor R, DeLong A, Schreier L, Istrail S. QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads. In Silico Biol 2013; 11:193-201. [PMID: 23202421 PMCID: PMC5530257 DOI: 10.3233/isb-2012-0454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Next generation sequencing technologies have recently been applied to characterize mutational spectra of the heterogeneous population of viral genotypes (known as a quasispecies) within HIV-infected patients. Such information is clinically relevant because minority genetic subpopulations of HIV within patients enable viral escape from selection pressures such as the immune response and antiretroviral therapy. However, methods for quasispecies sequence reconstruction from next generation sequencing reads are not yet widely used and remains an emerging area of research. Furthermore, the majority of research methodology in HIV has focused on 454 sequencing, while many next-generation sequencing platforms used in practice are limited to shorter read lengths relative to 454 sequencing. Little work has been done in determining how best to address the read length limitations of other platforms. The approach described here incorporates graph representations of both read differences and read overlap to conservatively determine the regions of the sequence with sufficient variability to separate quasispecies sequences. Within these tractable regions of quasispecies inference, we use constraint programming to solve for an optimal quasispecies subsequence determination via vertex coloring of the conflict graph, a representation which also lends itself to data with non-contiguous reads such as paired-end sequencing. We demonstrate the utility of the method by applying it to simulations based on actual intra-patient clonal HIV-1 sequencing data.
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Affiliation(s)
- Austin Huang
- Division of Infectious Disease, Computer Science Department, Brown University, Box 1910, Providence, RI 02912, USA.
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Anta L, Blanco JL, Llibre JM, García F, Pérez-Elías MJ, Aguilera A, Pérez-Romero P, Caballero E, Vidal C, Cañizares A, Gutiérrez F, Dalmau D, Iribarren JA, Soriano V, de Mendoza C. Resistance to the most recent protease and non-nucleoside reverse transcriptase inhibitors across HIV-1 non-B subtypes. J Antimicrob Chemother 2013; 68:1994-2002. [PMID: 23629015 DOI: 10.1093/jac/dkt146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Limited data are available on resistance to etravirine, rilpivirine, darunavir and tipranavir in patients infected with HIV-1 non-B subtypes, in which natural polymorphisms at certain positions could influence the barrier and/or pathways to drug resistance. METHODS FASTA format sequences from the reverse transcriptase and protease genes recorded within the Spanish Drug Resistance database (ResRIS) were examined. RESULTS From 8272 genotypes derived from 5930 different HIV-1 patients included in ResRIS, 5276 genotypes had complete treatment information. Overall, 85% were from antiretroviral-experienced subjects and 7.5% belonged to HIV-1 non-B subtypes: CRF02_AG, C, F and G being the most prevalent variants. For etravirine, only G190A was more prevalent in B than non-B subtypes, whereas V90I and V179E were more frequent in non-B than B subtypes. For rilpivirine, V108I and Y188I were more frequent in B than non-B subtypes, whereas V90I was more prevalent in non-B subtypes. Despite these differences, the overall prevalence of resistance did not differ significantly when comparing etravirine or rilpivirine in B versus non-B subtypes (11.3% versus 7.4%, P = 0.13, and 10.5% versus 7.4%, P = 0.23, respectively). Despite more frequent natural polymorphisms in non-B than B subtypes at tipranavir resistance positions, the prevalence of tipranavir resistance was greater in B than non-B subtypes (11% versus 4.3%, P = 0.004), reflecting a greater antiretroviral exposure in the former. Darunavir resistance did not differ significantly when comparing B and non-B subtypes (5.8% versus 5.5%, P = 0.998). CONCLUSIONS The rate of resistance to the most recently approved protease and non-nucleoside reverse transcriptase inhibitors is low in antiretroviral-experienced patients, regardless of the HIV-1 subtype.
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Morabito K, Kantor R, Tai W, Schreier L, Tripathi A. Detection of HIV-1 minority variants containing the K103N drug-resistance mutation using a simple method to amplify RNA targets (SMART). J Mol Diagn 2013; 15:401-12. [PMID: 23541840 DOI: 10.1016/j.jmoldx.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 01/30/2013] [Accepted: 02/12/2013] [Indexed: 11/26/2022] Open
Abstract
The simple method for amplifying RNA targets (SMART) was used to detect K103N, a common HIV-1 reverse transcriptase drug-resistance mutation. Novel amplifiable SMART probes served as reporter molecules for RNA sequences that are captured and separated on a microfluidic platform under zero-flow conditions. Assays were performed both off chip and in a microchip reservoir using a modified version of real-time nucleic acid sequence-based amplification, without the noncyclic phase, and 65°C preheat. A total of 6000 copies/mL of the synthetic sequences were detected within 180 minutes of amplification. Although the sensitivity of research platforms is higher, SMART has the potential to offer comparable sensitivity and speed to commercially available viral load and HIV detection kits. Furthermore, SMART uses an inexpensive, practical, and more accurate isothermal exponential amplification technique. The use of molecular beacons resulted in relatively fast real-time detection (<180 minutes); however, they were also shown to hinder the amplification process when compared with end point detection. Finally, SMART probes were used for modeling of K103N concentrations within an unknown sample. Only 1% of the SMART probes was detected within the wild-type population (6 × 10(8) copies/mL). These results establish the groundwork for point-of-care drug resistance and viral load monitoring in clinical samples, which can revolutionize HIV patient care globally.
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Affiliation(s)
- Kenneth Morabito
- Center for Biomedical Engineering, School of Engineering, Alpert Medical School, Brown University, Providence, RI, USA
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Revell AD, Wang D, Wood R, Morrow C, Tempelman H, Hamers RL, Alvarez-Uria G, Streinu-Cercel A, Ene L, Wensing AMJ, DeWolf F, Nelson M, Montaner JS, Lane HC, Larder BA. Computational models can predict response to HIV therapy without a genotype and may reduce treatment failure in different resource-limited settings. J Antimicrob Chemother 2013; 68:1406-14. [PMID: 23485767 DOI: 10.1093/jac/dkt041] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Genotypic HIV drug-resistance testing is typically 60%-65% predictive of response to combination antiretroviral therapy (ART) and is valuable for guiding treatment changes. Genotyping is unavailable in many resource-limited settings (RLSs). We aimed to develop models that can predict response to ART without a genotype and evaluated their potential as a treatment support tool in RLSs. METHODS Random forest models were trained to predict the probability of response to ART (≤400 copies HIV RNA/mL) using the following data from 14 891 treatment change episodes (TCEs) after virological failure, from well-resourced countries: viral load and CD4 count prior to treatment change, treatment history, drugs in the new regimen, time to follow-up and follow-up viral load. Models were assessed by cross-validation during development, with an independent set of 800 cases from well-resourced countries, plus 231 cases from Southern Africa, 206 from India and 375 from Romania. The area under the receiver operating characteristic curve (AUC) was the main outcome measure. RESULTS The models achieved an AUC of 0.74-0.81 during cross-validation and 0.76-0.77 with the 800 test TCEs. They achieved AUCs of 0.58-0.65 (Southern Africa), 0.63 (India) and 0.70 (Romania). Models were more accurate for data from the well-resourced countries than for cases from Southern Africa and India (P < 0.001), but not Romania. The models identified alternative, available drug regimens predicted to result in virological response for 94% of virological failures in Southern Africa, 99% of those in India and 93% of those in Romania. CONCLUSIONS We developed computational models that predict virological response to ART without a genotype with comparable accuracy to genotyping with rule-based interpretation. These models have the potential to help optimize antiretroviral therapy for patients in RLSs where genotyping is not generally available.
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Affiliation(s)
- A D Revell
- The HIV Resistance Response Database Initiative (RDI), London, UK
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