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Deuba K, Panta G, Rajbhandari RM, Kunwar R, Pokhrel TN, Pandey LR, Changsom D, Saeng-Aroon S, Thakur SK. Prevalence of viral load suppression and acquired drug resistance among people living with HIV in Nepal: a nationally representative surveillance study. J Glob Antimicrob Resist 2023; 35:122-127. [PMID: 37709138 DOI: 10.1016/j.jgar.2023.09.002] [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: 05/24/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVES This is the first nationally representative study to estimate the prevalence of viral load (VL) suppression and acquired HIV drug resistance (ADR) among people living with HIV (PLHIV) in Nepal. METHODS A cross-sectional study recruited 1418 PLHIV from 20 ART centres in Nepal, using a two-stage cluster design. Participants were eligible if they were HIV-positive individuals on ART for 9-15 months or at least 48 months. Plasma specimens were collected and tested for the quantification of HIV-1 RNA. Specimens with a VL ≥1000 copies/mL were further processed for sequencing of PR and RT genes of HIV-1. The sequences were then analysed to detect mutations causing HIV drug resistance. RESULTS The prevalence of ADR was 3.7% (95% confidence interval [CI]: 1.8-7.6) and 3.0% (95% CI: 1.8-5.2) among PLHIV who received ART for 9-15 months and 48 months or more, respectively. The prevalence of VL suppression was 95.3% (95% CI: 91.7-97.4) among those on ART for 9-15 months, and 96.5% (95% CI: 94.7-97.7) among those on ART for at least 48 months. The prevalence of any detectable acquired resistance to antiretroviral drugs was 80.7% (95% CI: 58.6-92.5) among those on ART for 9-15 months with VL ≥1000 copies/mL and 81.6% (95% CI: 55.4-94.0) among those on ART for at least 48 months with VL ≥1000 copies/mL. CONCLUSION This study suggests that improved accessibility to VL monitoring and timely assessment of drug resistance in routine HIV programs are crucial in Nepal to ensure access to HIV treatment for all in need.
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Affiliation(s)
- Keshab Deuba
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden.
| | - Gopal Panta
- Save the Children International, Kathmandu, Nepal
| | - Rajesh Man Rajbhandari
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado - BIOPOLIS Program in Genomics, Biodiversity, and Land Planning, Campus de Vairão, Universidade do Porto, Vairão, Portugal; SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM & CSIC), Ronda de Toledo s/n, Ciudad Real, Spain
| | | | | | - Lok Raj Pandey
- National Centre for AIDS and STD Control, Ministry of Health and Population, Kathmandu, Nepal
| | - Don Changsom
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Siriphan Saeng-Aroon
- Bureau of Laboratory Quality Standards, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Sanjay Kumar Thakur
- National Centre for AIDS and STD Control, Ministry of Health and Population, Kathmandu, Nepal
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Ekpenyong ME, Adegoke AA, Edoho ME, Inyang UG, Udo IJ, Ekaidem IS, Osang F, Uto NP, Geoffery JI. Collaborative Mining of Whole Genome Sequences for Intelligent HIV-1 Sub-Strain(s) Discovery. Curr HIV Res 2022; 20:163-183. [PMID: 35142269 DOI: 10.2174/1570162x20666220210142209] [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: 08/24/2021] [Revised: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Effective global antiretroviral vaccines and therapeutic strategies depend on the diversity, evolution, and epidemiology of their various strains as well as their transmission and pathogenesis. Most viral disease-causing particles are clustered into a taxonomy of subtypes to suggest pointers toward nucleotide-specific vaccines or therapeutic applications of clinical significance sufficient for sequence-specific diagnosis and homologous viral studies. These are very useful to formulate predictors to induce cross-resistance to some retroviral control drugs being used across study areas. OBJECTIVE This research proposed a collaborative framework of hybridized (Machine Learning and Natural Language Processing) techniques to discover hidden genome patterns and feature predictors, for HIV-1 genome sequences mining. METHOD 630 human HIV-1 genome sequences above 8500 bps were excavated from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov) for 21 countries across different continents, Antarctica exempt. These sequences were transformed and learned using a self-organizing map (SOM). To discriminate emerging/new sub-strain(s), the HIV-1 reference genome was included as part of the input isolates/samples during the training. After training the SOM, component planes defining pattern clusters of the input datasets were generated, for cognitive knowledge mining and subsequent labelling of the datasets. Additional genome features including dinucleotide transmission recurrences, codon recurrences, and mutation recurrences, were finally extracted from the raw genomes to construct output classification targets for supervised learning. RESULTS SOM training explains the inherent pattern diversity of HIV-1 genomes as well as inter- and intra-country transmissions in which mobility might play an active role, as corroborated by literature. Nine sub-strains were discovered after disassembling the SOM correlation hunting matrix space attributed to disparate clusters. Cognitive knowledge mining separated similar pattern clusters bounded by a certain degree of correlation range, discovered by the SOM. A Kruskal-Wallis rank-sum test and Wilcoxon rank-sum test showed statistically significant variations in dinucleotide, codon, and mutation patterns. CONCLUSION Results of the discovered sub-strains and response clusters visualizations corroborate existing literature, with significant haplotype variations. The proposed framework would assist in the development of decision support systems for easy contact tracing, infectious disease surveillance, and studying the progressive evolution of the reference HIV-1 genome.
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Affiliation(s)
- Moses E Ekpenyong
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
- Centre for Research and Development, University of Uyo, Uyo, Nigeria
| | - Anthony A Adegoke
- Department of Microbiology, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Mercy E Edoho
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Udoinyang G Inyang
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Ifiok J Udo
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Itemobong S Ekaidem
- Department of Chemical Pathology, College of Health Sciences, University of Uyo, Uyo, Nigeria
| | - Francis Osang
- Department of Computer Science, Faculty of Science, National Open University, Abuja, Nigeria
| | - Nseobong P Uto
- School of Mathematics and Statistics, University of St Andrews, Scotland, United Kingdom
| | - Joseph I Geoffery
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
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Marty N, Saeng-Aroon S, Heger E, Thielen A, Obermeier M, Pfeifer N, Kaiser R, Klimkait T. Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia. J Clin Virol 2021; 136:104755. [PMID: 33639408 DOI: 10.1016/j.jcv.2021.104755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/24/2020] [Accepted: 02/01/2021] [Indexed: 01/23/2023]
Abstract
OBJECTIVES Geno2pheno[coreceptor] is a widely used tool for the prediction of coreceptor usage (viral tropism) of HIV-1 samples. For HIV-1 CRF01_AE, a significant overcalling of X4-tropism is observed when using the standard settings of Geno2pheno[coreceptor]. The aim of this study was to provide the experimental backing for adaptations to the geno2pheno[coreceptor] algorithm in order to improve coreceptor usage predictions of clinical HIV-1 CRF01_AE isolates STUDY DESIGN: V3-sequences of 20 clinical HIV-1 subtype CRF01_AE samples were sequenced and analyzed by geno2pheno[coreceptor]. In parallel, coreceptor usage was determined for these samples by replicative phenotyping in human cells in the presence of specific X4- or R5-inhibitors. RESULTS The sole introduction of the CRF01_AE V3 region into a full-length otherwise subtype B provirus failed to produce replication-competent viral progeny. A successive genome-replacement strategy revealed that also CRF01_AE derived gag and pol sequences are necessary to generate HIV genomes with sufficient replication competence. Subsequent phenotypic analysis confirmed overcalling of X4-tropism for CRF01_AE viruses using the current version and the standard cut-off at 10% false positive rate (FPR) of geno2pheno[coreceptor]. Lowering the FPR cut-off to 2.5% reduced the X4-overcalling in our sample collection, while still allowing a safe administration of Maraviroc (MCV). CONCLUSION This study demonstrates the successful adjustment of geno2pheno[coreceptor] rules for subtype CRF01_AE. It also supports the unique strength of combining complementing methods, namely phenotyping and genotyping, for validating new bioinformatics tools prior to application in diagnostics.
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Affiliation(s)
- Nina Marty
- Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland.
| | - Siriphan Saeng-Aroon
- Hazardous Pathogen Laboratory, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Eva Heger
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | | | - Nico Pfeifer
- Max Planck Institute for Informatics, Saarland Informatics Campus E1 4, Saarbruecken, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland
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Nakayama EE, Saito A, Sultana T, Jin Z, Nohata K, Shibata M, Hosoi M, Motomura K, Shioda T, Sangkitporn S, Loket R, Saeng-aroon S. Naturally Occurring Mutations in HIV-1 CRF01_AE Capsid Affect Viral Sensitivity to Restriction Factors. AIDS Res Hum Retroviruses 2018; 34:382-392. [PMID: 29325426 PMCID: PMC5899301 DOI: 10.1089/aid.2017.0212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
TRIM5α and MxB are known as restriction factors that inhibit the early step of intracellular HIV-1 replication cycle. Both factors are believed to interact with the incoming virus core to suppress HIV-1 infection. The extreme diversity of HIV-1 is thought to be a consequence of its propensity to mutate to escape immune responses and host restriction factors. We recently determined the capsid sequences for 144 HIV-1 CRF01_AE viruses obtained in Thailand from 2005 to 2011. In this study, we further analyzed the amino acid variations among the capsid sequences of 204 HIV-1 CRF01_AE obtained in Thailand and China, including 84 of the aforementioned 144 viruses, to detect mutations permitting escape from restriction by host factors. We found a characteristic combination of E79D, V83T, and H87Q in sequences from Chinese viruses and subsequently showed that this combination conferred partial resistance to MxB. Interestingly, this combination conferred resistance to human TRIM5α as well. The H87Q mutation alone conferred resistance to MxB in the CRF01_AE background, but not in subtype B virus. In contrast, the H87Q mutation alone conferred resistance to human TRIM5α in both the CFR01_AE and subtype B backgrounds. BLAST analysis revealed the presence of the E79D, V83T, and H87Q combination in CRF01_AE viruses isolated not only in China but also in many other countries. Although the mechanistic details as well as precise role of MxB antiviral activity in infected individuals remain to be clarified, our data suggest an interaction between MxB and the HIV-1 capsid in vivo.
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Affiliation(s)
- Emi E. Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Akatsuki Saito
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tahmina Sultana
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Zhuan Jin
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kyotaro Nohata
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masato Shibata
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Miho Hosoi
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-Emerging Infections (RCC-ERI), Osaka University, Nonthaburi, Thailand
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Somchai Sangkitporn
- National Institute of Health, Department of Medical Science, Ministry of Public Health, Nonthaburi, Thailand
| | - Ruangchai Loket
- National Institute of Health, Department of Medical Science, Ministry of Public Health, Nonthaburi, Thailand
| | - Siriphan Saeng-aroon
- National Institute of Health, Department of Medical Science, Ministry of Public Health, Nonthaburi, Thailand
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Bagaya BS, Tian M, Nickel GC, Vega JF, Li Y, He P, Klein K, Mann JFS, Jiang W, Arts EJ, Gao Y. An in vitro Model to Mimic Selection of Replication-Competent HIV-1 Intersubtype Recombination in Dual or Superinfected Patients. J Mol Biol 2017; 429:2246-2264. [PMID: 28472629 PMCID: PMC6202033 DOI: 10.1016/j.jmb.2017.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 11/23/2022]
Abstract
The low frequency of HIV-1 recombinants within entire viral populations in both individual patients and culture-based infection models impedes investigation of the underlying factors contributing to either the occurrence of recombinants or the survival of recombinants once they are formed. So far, most of the related studies have no consideration of recombinants' functionality. Here, we established a functional recombinant production (FRP) system to produce pure and functional HIV-1 intersubtype Env recombinants and utilized 454 pyrosequencing to investigate the distribution of over 4000 functional and non-functional recombination breakpoints from either the FRP system or dual infection cultures. The results revealed that most of the breakpoints converged in gp41 (62%) and C1 (25.3%) domains of gp120, which has strong correlation with the similarity between the two recombining sequences. Yet, the breakpoints also appeared in C2 (5.2%) and C5 (4.6%) domains not correlated with the recombining sequence similarity. Interestingly, none of the intersubtype gp120 recombinants recombined between C1 and gp41 regions either from the FRP system or from the dual infection culture, and very few from the HIV epidemic were functional. The present study suggests that the selection of functional Env recombinants is one of the reasons for the predominance of C1 and gp41 Env recombinants in the HIV epidemic, and it provides an in vitro model to mimic the selection of replication-competent HIV-1 intersubtype recombination in dual or superinfected patients.
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Affiliation(s)
- Bernard S Bagaya
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, N6A 3K7, Uganda
| | - Meijuan Tian
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Gabrielle C Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - José F Vega
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Yuejin Li
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ping He
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Katja Klein
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Wei Jiang
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Eric J Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Yong Gao
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada.
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