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Mori M, Ode H, Kubota M, Nakata Y, Kasahara T, Shigemi U, Okazaki R, Matsuda M, Matsuoka K, Sugimoto A, Hachiya A, Imahashi M, Yokomaku Y, Iwatani Y. Nanopore Sequencing for Characterization of HIV-1 Recombinant Forms. Microbiol Spectr 2022; 10:e0150722. [PMID: 35894615 PMCID: PMC9431566 DOI: 10.1128/spectrum.01507-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/06/2022] [Indexed: 11/23/2022] Open
Abstract
High genetic diversity, including the emergence of recombinant forms (RFs), is one of the most prominent features of human immunodeficiency virus type 1 (HIV-1). Conventional detection of HIV-1 RFs requires pretreatments, i.e., cloning or single-genome amplification, to distinguish them from dual- or multiple-infection variants. However, these processes are time-consuming and labor-intensive. Here, we constructed a new nanopore sequencing-based platform that enables us to obtain distinctive genetic information for intersubtype RFs and dual-infection HIV-1 variants by using amplicons of HIV-1 near-full-length genomes or two overlapping half-length genome fragments. Repeated benchmark tests of HIV-1 proviral DNA revealed consensus sequence inference with a reduced error rate, allowing us to obtain sufficiently accurate sequence data. In addition, we applied the platform for sequence analyses of 9 clinical samples with suspected HIV-1 RF infection or dual infection according to Sanger sequencing-based genotyping tests for HIV-1 drug resistance. For each RF infection case, replicated analyses involving our nanopore sequencing-based platform consistently produced long consecutive analogous consensus sequences with mosaic genomic structures consisting of two different subtypes. In contrast, we detected multiple heterologous sequences in each dual-infection case. These results demonstrate that our new nanopore sequencing platform is applicable to identify the full-length HIV-1 genome structure of intersubtype RFs as well as dual-infection heterologous HIV-1. Since the genetic diversity of HIV-1 continues to gradually increase, this system will help accelerate full-length genome analysis and molecular epidemiological surveillance for HIV-1. IMPORTANCE HIV-1 is characterized by large genetic differences, including HIV-1 recombinant forms (RFs). Conventional genetic analyses require time-consuming pretreatments, i.e., cloning or single-genome amplification, to distinguish RFs from dual- or multiple-infection cases. In this study, we developed a new analytical system for HIV-1 sequence data obtained by nanopore sequencing. The error rate of this method was reduced to ~0.06%. We applied this system for sequence analyses of 9 clinical samples with suspected HIV-1 RF infection or dual infection, which were extracted from 373 cases of HIV patients based on our retrospective analysis of HIV-1 drug resistance genotyping test results. We found that our new nanopore sequencing platform is applicable to identify the full-length HIV-1 genome structure of intersubtype RFs as well as dual-infection heterologous HIV-1. Our protocol will be useful for epidemiological surveillance to examine HIV-1 transmission as well as for genotypic tests of HIV-1 drug resistance in clinical settings.
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Affiliation(s)
- Mikiko Mori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Kasahara
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Reiko Okazaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsuko Sugimoto
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Takahashi N, Matsuoka S, Thi Minh TT, Ba HP, Naruse TK, Kimura A, Shiino T, Kawana-Tachikawa A, Ishikawa K, Matano T, Nguyen Thi LA. Human leukocyte antigen-associated gag and nef polymorphisms in HIV-1 subtype A/E-infected individuals in Vietnam. Microbes Infect 2018; 21:113-118. [PMID: 30385305 DOI: 10.1016/j.micinf.2018.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
Abstract
Numbers of HLA-associated polymorphisms have been reported on HIV-1 subtypes B and C, but few on other subtypes. Here, we analyzed HLA-associated gag and nef polymorphisms in HIV-1 subtype A/E prevalent in Vietnam. We determined HLA-A, B and C genotypes in 179 HIV-1-infected Vietnamese by next generation sequencing and analyzed proviral genome sequences in 144 of them, showing that 142 of the 144 were subtype A/E. Analysis revealed HLA-associated subtype A/E gag and nef polymorphisms at nineteen residues including those newly determined. Accumulation of these data would contribute to our understanding of HIV-1 subtype A/E and host immune interaction.
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Affiliation(s)
- Naofumi Takahashi
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tam Tran Thi Minh
- Center of BioMedical Research, National Institute of Hygiene and Epidemiology, No.1 Yersin Street, Hanoi, Viet Nam
| | - Hien Pham Ba
- Dong Da General Hospital, No. 192, Nguyen Luong Bang Street, Hanoi, Viet Nam
| | - Taeko K Naruse
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akinori Kimura
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Teiichiro Shiino
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Lan Anh Nguyen Thi
- Center of BioMedical Research, National Institute of Hygiene and Epidemiology, No.1 Yersin Street, Hanoi, Viet Nam.
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Nakashima M, Ode H, Suzuki K, Fujino M, Maejima M, Kimura Y, Masaoka T, Hattori J, Matsuda M, Hachiya A, Yokomaku Y, Suzuki A, Watanabe N, Sugiura W, Iwatani Y. Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance. Front Microbiol 2016; 7:61. [PMID: 26870021 PMCID: PMC4737996 DOI: 10.3389/fmicb.2016.00061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Abstract
Darunavir (DRV) is one of the most powerful protease inhibitors (PIs) for treating human immunodeficiency virus type-1 (HIV-1) infection and presents a high genetic barrier to the generation of resistant viruses. However, DRV-resistant HIV-1 infrequently emerges from viruses exhibiting resistance to other protease inhibitors. To address this resistance, researchers have gathered genetic information on DRV resistance. In contrast, few structural insights into the mechanism underlying DRV resistance are available. To elucidate this mechanism, we determined the crystal structure of the ligand-free state of a protease with high-level DRV resistance and six DRV resistance-associated mutations (including I47V and I50V), which we generated by in vitro selection. This crystal structure showed a unique curling conformation at the flap regions that was not found in the previously reported ligand-free protease structures. Molecular dynamics simulations indicated that the curled flap conformation altered the flap dynamics. These results suggest that the preference for a unique flap conformation influences DRV binding. These results provide new structural insights into elucidating the molecular mechanism of DRV resistance and aid to develop PIs effective against DRV-resistant viruses.
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Affiliation(s)
- Masaaki Nakashima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Hirotaka Ode
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Koji Suzuki
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Masami Maejima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yuki Kimura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Takashi Masaoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Junko Hattori
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Masakazu Matsuda
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuko Hachiya
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yoshiyuki Yokomaku
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuo Suzuki
- Department of Biotechnology, Nagoya University Graduate School of Engineering Nagoya, Japan
| | - Nobuhisa Watanabe
- Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan; Synchrotron Radiation Research Center, Nagoya UniversityNagoya, Japan
| | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of AIDS Research, Nagoya University Graduate School of MedicineNagoya, Japan
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Abstract
UNLABELLED Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30's interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR-p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations. IMPORTANCE Resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations.
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Rossi AH, Rocco CA, Mangano A, Sen L, Aulicino PC. Sequence variability in p6 gag protein and gag/pol coevolution in human immunodeficiency type 1 subtype F genomes. AIDS Res Hum Retroviruses 2013; 29:1056-60. [PMID: 23458243 DOI: 10.1089/aid.2012.0311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Polymorphisms occurring at the p6gag protein of HIV-1 have been previously found to have an impact on viral fitness and antiretroviral (ARV) resistance, mainly on subtype B genomes. We compared p6gag variability in a large group of 165 subtype F gag-pol sequences, with 36 subtype B sequences from the same study source, and identified sites of gag-pol coevolution under ARV selection pressure. Subtype-specific differences in the frequency of point mutations, insertions, and deletions previously associated with ARV resistance were found. Also, in our dataset of subtype F genomes a strong association between mutation P5L in the p1/p6 cleavage region of gag and the nelfinavir (NFV) resistance mutation N88D(PR) was found with no impact on the preference for any of the NFV resistance pathways.
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Affiliation(s)
- Andres H. Rossi
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Juan P. Garran,” CONICET, Buenos Aires, Argentina
| | - Carlos A. Rocco
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Juan P. Garran,” CONICET, Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Juan P. Garran,” CONICET, Buenos Aires, Argentina
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Juan P. Garran,” CONICET, Buenos Aires, Argentina
| | - Paula C. Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Juan P. Garran,” CONICET, Buenos Aires, Argentina
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Fun A, Wensing AMJ, Verheyen J, Nijhuis M. Human Immunodeficiency Virus Gag and protease: partners in resistance. Retrovirology 2012; 9:63. [PMID: 22867298 PMCID: PMC3422997 DOI: 10.1186/1742-4690-9-63] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/17/2012] [Indexed: 12/26/2022] Open
Abstract
Human Immunodeficiency Virus (HIV) maturation plays an essential role in the viral life cycle by enabling the generation of mature infectious virus particles through proteolytic processing of the viral Gag and GagPol precursor proteins. An impaired polyprotein processing results in the production of non-infectious virus particles. Consequently, particle maturation is an excellent drug target as exemplified by inhibitors specifically targeting the viral protease (protease inhibitors; PIs) and the experimental class of maturation inhibitors that target the precursor Gag and GagPol polyproteins. Considering the different target sites of the two drug classes, direct cross-resistance may seem unlikely. However, coevolution of protease and its substrate Gag during PI exposure has been observed both in vivo and in vitro. This review addresses in detail all mutations in Gag that are selected under PI pressure. We evaluate how polymorphisms and mutations in Gag affect PI therapy, an aspect of PI resistance that is currently not included in standard genotypic PI resistance testing. In addition, we consider the consequences of Gag mutations for the development and positioning of future maturation inhibitors.
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Affiliation(s)
- Axel Fun
- Department of Virology, Medical Microbiology, University Medical Center Utrecht, HP G04,614, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
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Chang YCE, Yu X, Zhang Y, Tie Y, Wang YF, Yashchuk S, Ghosh AK, Harrison RW, Weber IT. Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring. J Med Chem 2012; 55:3387-97. [PMID: 22401672 PMCID: PMC3355519 DOI: 10.1021/jm300072d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GRL-02031 (1) is an HIV-1 protease (PR) inhibitor containing a novel P1' (R)-aminomethyl-2-pyrrolidinone group. Crystal structures at resolutions of 1.25-1.55 Å were analyzed for complexes of 1 with the PR containing major drug resistant mutations, PR(I47V), PR(L76V), PR(V82A), and PR(N88D). Mutations of I47V and V82A alter residues in the inhibitor-binding site, while L76V and N88D are distal mutations having no direct contact with the inhibitor. Substitution of a smaller amino acid in PR(I47V) and PR(L76V) and the altered charge of PR(N88D) are associated with significant local structural changes compared to the wild-type PR(WT), while substitution of alanine in PR(V82A) increases the size of the S1' subsite. The P1' pyrrolidinone group of 1 accommodates to these local changes by assuming two different conformations. Overall, the conformation and interactions of 1 with PR mutants resemble those of PR(WT) with similar inhibition constants in good agreement with the antiviral potency on multidrug resistant HIV-1.
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Affiliation(s)
- Yu Chung E. Chang
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - XiaXia Yu
- Department of Computer Science, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Ying Zhang
- Department of Chemistry, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Yunfeng Tie
- Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Yuan Fang Wang
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Sofiya Yashchuk
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Robert W. Harrison
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
,Department of Computer Science, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
,Department of Chemistry, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
,To whom correspondence should be addressed. I.T. Weber, Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30302, USA; Tel: (404) 413-5411; Fax: (404) 413-5301;
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Eberle J, Gürtler L. The evolution of drug resistance interpretation algorithms: ANRS, REGA and extension of resistance analysis to HIV-1 group O and HIV-2. Intervirology 2012; 55:128-33. [PMID: 22286882 DOI: 10.1159/000332009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Antiretroviral drug resistance is mostly linked to a complex interaction of several amino acids with variable importance or a single amino acid. To facilitate the interpretation of observed mutation patterns, hospital university centers have developed several interpretation systems. All the currently available interpretation algorithms evolved, are being continuously updated and have been improved during the last decade. Some discrepancies are still evident that are partially smoothened by link of the individual programs with other systems. After the interpretation of HIV-1 group M subtype B mutations, a refined algorithm for the other group M subtypes was developed followed by the interpretation of HIV-1 group O and HIV-2 mutations. The process of improvement is ongoing, due to the better understanding and interpretation of single and cluster mutations and the availability of new antiretroviral substances. The knowledge gained from the experience of HIV drug resistance testing has been used to establish the interpretation of HBV polymerase mutations and will be extended for the treatment of HCV infected with protease inhibitors.
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Affiliation(s)
- Josef Eberle
- Max von Pettenkofer Institute, Ludwig Maximilian University Munich, Munich, Germany
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[Bioinformatics studies on drug resistance against anti-HIV-1 drugs]. Uirusu 2011; 61:35-47. [PMID: 21972554 DOI: 10.2222/jsv.61.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
More than 20 drugs have been available for anti-HIV-1 treatment in Japan. Combination therapy with these drugs dramatically decreases in morbidity and mortality of AIDS. However, due to high mutation rate of HIV-1, treatment with ineffective drugs toward patients infected with HIV-1 causes accumulation of mutations in the virus, and emergence of drug resistant viruses. Thus, to achieve appropriate application of the drugs toward the respective patients living with HIV-1, methods for predicting the level of drug-resistance using viral sequence information has been developed on the basis of bioinformatics. Furthermore, ultra-deep sequencing by next-generation sequencer whose data analysis is also based on bioinformatics, or in silico structural modeling have been achieved to understand drug resistant mechanisms. In this review, I overview the bioinformatics studies about drug resistance against anti-HIV-1 drugs.
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