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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shigemi U, Yamamura Y, Matsuda M, Okazaki R, Kubota M, Ibe S, Nemoto M, Maejima-Kitagawa M, Sukegawa S, Imahashi M, Kikuchi T, Sugiura W, Iwatani Y, Hachiya A, Yokomaku Y. Evaluation of the Geenius HIV 1/2 confirmatory assay for HIV-2 samples isolated in Japan. J Clin Virol 2022; 152:105189. [DOI: 10.1016/j.jcv.2022.105189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/03/2022] [Accepted: 05/13/2022] [Indexed: 10/18/2022]
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Hachiya A, Kubota M, Shigemi U, Ode H, Yokomaku Y, Kirby KA, Sarafianos SG, Iwatani Y. Specific mutations in the HIV-1 G-tract of the 3'-polypurine tract cause resistance to integrase strand transfer inhibitors. J Antimicrob Chemother 2021; 77:574-577. [PMID: 34894227 PMCID: PMC8865006 DOI: 10.1093/jac/dkab448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In vitro selection experiments identified viruses resistant to integrase strand transfer inhibitors (INSTIs) carrying mutations in the G-tract (six guanosines) of the 3'-polypurine tract (3'-PPT). A clinical study also reported that mutations in the 3'-PPT were observed in a patient receiving dolutegravir monotherapy. However, recombinant viruses with the 3'-PPT mutations that were found in the clinical study were recently shown to be susceptible to INSTIs. OBJECTIVES To identify the specific mutation(s) in the G-tract of the 3'-PPT for acquiring INSTI resistance, we constructed infectious clones bearing single or multiple mutations and systematically characterized the susceptibility of these clones to both first- and second-generation INSTIs. METHODS The infectious clones were tested for their infectivity and susceptibility to INSTIs in a single-cycle assay using TZM-bl cells. RESULTS A single mutation of thymidine (T) at the fifth position (GGG GTG) in the G-tract of the 3'-PPT had no effect on INSTI resistance. A double mutation, cytidine (C) or 'T' at the second position and 'T' at the fifth position (GCG GTG and GTG GTG), increased resistance to INSTIs, with the appearance of a plateau in the maximal percentage inhibition (MPI) of the dose-response curves, consistent with a non-competitive mechanism of inhibition. CONCLUSIONS Mutations at the second and fifth positions in the G-tract of the 3'-PPT may result in complex resistance mechanism(s), rather than simply affecting INSTI binding at the IN active site.
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Affiliation(s)
- Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan,Corresponding author. Present address: Tokyo Medical University, Department of Laboratory Medicine, 6-7-1, Nishishinjuku, Shinjuku-ku, Tokyo 160-0023, Japan and Nitobe Bunka College, Department of Infectious Diseases and Immunology, 3-43-16, Nakano, Nakano-ku, Tokyo 164-0001, Japan. E-mail:
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA,Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA,Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan,Department of AIDS Research, Nagoya University Graduate School of Medicine, Aichi, Japan
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Barabona G, Mahiti M, Masoud S, Mbelele P, Mgunya AS, Minja L, Sunguya B, Shigemi U, Matsuda M, Hachiya A, Iwatani Y, Lyamuya E, Ueno T. Pre-treatment and acquired HIV drug resistance in Dar es Salaam, Tanzania in the era of tenofovir and routine viral load monitoring. J Antimicrob Chemother 2020; 74:3016-3020. [PMID: 31273377 DOI: 10.1093/jac/dkz272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES We investigated the prevalence and patterns of pre-treatment and acquired HIV drug resistance mutations (DRMs) in Tanzania as a 'treat all' strategy, virological monitoring and the progressive increase in usage of tenofovir are being implemented in HIV treatment programmes. METHODS Viral RNA was isolated from plasma of 60 ART-naive and 166 treated-but-viraemic (>400 copies/mL) HIV-1-infected adults attending a care and treatment clinic at Muhimbili National Hospital, Dar es Salaam, Tanzania, between June and October 2017. Viral genes encoding protease and reverse transcriptase were amplified by PCR and directly sequenced. RESULTS Viral genotyping of successfully amplified samples revealed pre-treatment DRMs in 14/47 (29.8%) ART-naive subjects. Of these, 7/47 (14.9%) harboured mutations that confer high-level resistance to at least one drug of the default first-line regimen. In treated-but-viraemic subjects, DRMs were found in 100/111 (90%), where DRMs against NNRTI, NRTI and PI were observed in 95/100 (95%), 92/100 (92%) and 13/100 (13%), respectively. Tenofovir-resistance mutations K65R and K70G/E or ≥3 thymidine analogue resistance mutations including M41L and L210W were found in 18/36 (50%) subjects on a tenofovir-containing regimen at failure. Four patients harboured multiple DRMs, which can confer resistance to all available ART regimens in Tanzania. CONCLUSIONS Taken together, pre-treatment and acquired DRMs were highly prevalent, which represents a major risk for the efficacy of ART programmes in Tanzania. Availability of a newer generation of antiretroviral drugs with a higher genetic barrier to resistance and robust treatment monitoring is warranted for effective and sustainable HIV treatment.
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Affiliation(s)
- Godfrey Barabona
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Macdonald Mahiti
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,St Francis University College of Health and Allied Sciences, Ifakara, Tanzania.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Salim Masoud
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter Mbelele
- Kibong'oto Infectious Diseases Hospital, Moshi, Tanzania
| | | | - Lilian Minja
- Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Bruno Sunguya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan.,Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eligius Lyamuya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Takamasa Ueno
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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Hosaka M, Fujisaki S, Masakane A, Hattori J, Shiino T, Gatanaga H, Shigemi U, Okazaki R, Hachiya A, Matsuda M, Ibe S, Iwatani Y, Yokomaku Y, Sugiura W. HIV-1 CRF01_AE and Subtype B Transmission Networks Crossover: A New AE/B Recombinant Identified in Japan. AIDS Res Hum Retroviruses 2016; 32:412-9. [PMID: 26571151 DOI: 10.1089/aid.2015.0192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The major circulating HIV-1 strains in Japan have been subtype B (B) followed by CRF01_AE (AE) in newly diagnosed HIV/AIDS cases. These two subtypes have distinct epidemiological characteristics; B predominates in men who have sex with men, while AE is observed mostly in heterosexuals engaging in high-risk sex. However, transmission networks of these two high-risk populations appear to be crossing over and diffusing. Here we report the emergence of previously unidentified HIV-1 AE/B recombinants in Japan. We initially identified 13 cases with discordant subtyping results with AE (gag MA)/B (pol PR-RT)/AE (env C2V3) by molecular phylogenetic analysis of 1,070 cases who visited Nagoya Medical Center from 1997 to 2012. Genetic characterization of full-length sequences demonstrated that they shared an identical recombinant structure, and was designated as CRF69_01B by the Los Alamos HIV National Laboratory. By reviewing gag, pol, and env sequences collected in the Japanese Drug Resistance HIV-1 Surveillance Network, we found five other CRF69_01B probable cases from different areas in Japan, suggesting that the strain is transmitted widely throughout the country. The time of the most recent common ancestor analyses estimated that CRF69_01B emerged between 1991 and 1995, soon after AE was introduced from neighboring countries in the mid-1990s. Understanding the current epidemic strains is important for the diagnosis and treatment of HIV/AIDS, as well as for the development of globally effective HIV vaccines.
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Affiliation(s)
- Masumi Hosaka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Seiichiro Fujisaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Aki Masakane
- Department of Clinical Laboratory, Yamaguchi University Hospital, Yamaguchi, Japan
| | - Junko Hattori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Teiichiro Shiino
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, 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
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Shiro Ibe
- 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
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Wataru Sugiura
- 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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6
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Ogawa S, Hachiya A, Hosaka M, Matsuda M, Ode H, Shigemi U, Okazaki R, Sadamasu K, Nagashima M, Toyokawa T, Tateyama M, Tanaka Y, Sugiura W, Yokomaku Y, Iwatani Y. A Novel Drug-Resistant HIV-1 Circulating Recombinant Form CRF76_01B Identified by Near Full-Length Genome Analysis. AIDS Res Hum Retroviruses 2016; 32:284-9. [PMID: 26528581 DOI: 10.1089/aid.2015.0304] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 CRF01_AE and subtype B (B) have dominated and their different circulating recombinant forms (CRFs) have emerged in East and Southeast Asian countries. Here, we report a novel drug-resistant HIV-1 CRF. Five independent recombinant specimens exhibiting discordant subtype results for the gag, pol, and env sequences were isolated. These recombinants had the CRF01_AE (gag p17)/B (pol PR-RT and IN)/CRF01_AE (env C2-V3) pattern similar to CRF69_01B. Sequence analysis of four near full-length HIV-1 genomes revealed a unique phylogenetic cluster distinct from previously reported CRFs. Of the four recombinants, three shared an identical mosaic structure including seven breakpoints in the gag, pol, vif, and env regions, designated CRF76_01B. The one remaining recombinant had additional recombination breakpoints in the vpu region and exhibited another unique recombinant form composed of CRF76_01B and B. These findings provide important insight into the transmission dynamics of HIV-1 in Asia that may be important for its effective prevention.
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Affiliation(s)
- Satoko Ogawa
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
- Department of Virology and Liver Unit, Nagoya City University, Nagoya, Aichi, Japan
| | - Atsuko Hachiya
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
- Department of Clinical Research Management, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Masumi Hosaka
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Masakazu Matsuda
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Hirotaka Ode
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Urara Shigemi
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Reiko Okazaki
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Takao Toyokawa
- Department of Infectious Diseases, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Okinawa, Japan
| | - Masao Tateyama
- Department of Infections, Respiratory and Digestive Medicine Control and Prevention of Infectious Diseases, University of the Ryukyus, Okinawa, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University, Nagoya, Aichi, Japan
| | - Wataru Sugiura
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Yoshiyuki Yokomaku
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Yasumasa Iwatani
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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7
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Hachiya A, Ode H, Matsuda M, Kito Y, Shigemi U, Matsuoka K, Imamura J, Yokomaku Y, Iwatani Y, Sugiura W. Natural polymorphism S119R of HIV-1 integrase enhances primary INSTI resistance. Antiviral Res 2015; 119:84-8. [PMID: 25956162 DOI: 10.1016/j.antiviral.2015.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/25/2015] [Accepted: 04/27/2015] [Indexed: 11/19/2022]
Abstract
Integrase strand transfer inhibitors (INSTIs), which block proviral DNA integration into the host chromosome, are clinically effective against HIV-1 isolates exhibiting resistance to other classes of antiretroviral agents. Although naturally occurring amino acid variation has been less frequently observed in the integrase region, the functional constraints of this variation on primary INSTI resistance-associated mutations are not fully understood. In the present study, we focused on the S119G/R/P/T (S119X) polymorphisms, which are frequently observed in HIV-1 sequences derived from clinical specimens (naïve, n=458, 26%). The frequency of the S119X polymorphism together with Q148H/R (n=8, 63%) or N155H (n=12, 83%) was relatively high compared with that of naïve group. Our in vitro assays revealed that S119G/P/T alone exerted no effect on the susceptibility to INSTIs, whereas S119R enhanced the level of INSTI resistance induced by well-known INSTI resistance-associated mutations (Y143C, Q148H or N155H). Notably, the S119R polymorphism contributed to a significant (5.9-fold) increase in dolutegravir resistance caused by G140S/Q148H. Analysis of two cases of virological failure during raltegravir-based therapy showed that the accumulation and the rapid evolution of primary INSTI resistance-associated mutations coincided with the S119R mutation. These data highlight the role of the S119X polymorphism in INSTI resistance, and this polymorphism might be linked to the potential treatment outcome with INSTI-based therapy.
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Affiliation(s)
- Atsuko Hachiya
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan.
| | - Hirotaka Ode
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Masakazu Matsuda
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yumiko Kito
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Urara Shigemi
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Kazuhiro Matsuoka
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Junji Imamura
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yasumasa Iwatani
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan; Department of AIDS Research, Graduated School of Medicine Nagoya University, Nagoya, Aichi 460-0001, Japan
| | - Wataru Sugiura
- Department of Infectious Disease and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan; Department of AIDS Research, Graduated School of Medicine Nagoya University, Nagoya, Aichi 460-0001, Japan
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Fujisaki S, Ibe S, Hattori J, Shigemi U, Fujisaki S, Shimizu K, Nakamura K, Yokomaku Y, Mamiya N, Utsumi M, Hamaguchi M, Kaneda T. An 11-Year Surveillance of HIV Type 1 Subtypes in Nagoya, Japan. AIDS Res Hum Retroviruses 2009; 25:15-21. [PMID: 19182917 DOI: 10.1089/aid.2008.0056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract To monitor active HIV-1 transmission in Nagoya, Japan, we have been determining the subtypes of HIV-1 infecting therapy-naive individuals who have newly visited the Nagoya Medical Center since 1997. The subtypes were determined by phylogenetic analyses using the base sequences in three regions of the HIV-1 genes including gag p17, pol protease (PR) and reverse transcriptase (RT), and env C2V3. Almost all HIV-1 subtypes from 1997 to 2007 and 93% of all HIV-1 isolates in 2007 were subtype B. HIV-1 subtypes A, C, D, and F have been detected sporadically since 1997, almost all in Africans and South Americans. The first detected circulating recombinant form (CRF ) was CRF01_AE (11-year average annual detection rate, 7.7%). Only two cases of CRF02_AG were detected in 2006. A unique recombinant form (URF ) was first detected in 1998 and the total number of URFs reached 25 by year 2007 (average annual detection rate, 4.7%). Eleven of these 25 were detected from 2000 to 2005 and had subtypes AE/B/AE as determined by base sequencing of the gag p17, pol PR and RT, and env C2V3 genes (average annual detection rate, 3.7%). Unique subtype B has been detected in six cases since 2006. All 17 of these patients were Japanese. Other recombinant HIV-1s have been detected intermittently in eight cases since 1998. During the 11-year surveillance, most HIV-1s in Nagoya, Japan were of subtype B. We expect that subtype B HIV-1 will continue to predominate for the next several years. Active recombination between subtype B and CRF01_AE HIV-1 and its transmission were also shown.
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Affiliation(s)
- Seiichiro Fujisaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Shiro Ibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Junko Hattori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Saeko Fujisaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Kayoko Shimizu
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Kazuyo Nakamura
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Naoto Mamiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Makoto Utsumi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Motohiro Hamaguchi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Tsuguhiro Kaneda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
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Ibe S, Shigemi U, Sawaki K, Fujisaki S, Hattori J, Yokomaku Y, Mamiya N, Hamaguchi M, Kaneda T. Analysis of near full-length genomic sequences of drug-resistant HIV-1 spreading among therapy-naïve individuals in Nagoya, Japan: amino acid mutations associated with viral replication activity. AIDS Res Hum Retroviruses 2008; 24:1121-5. [PMID: 18620491 DOI: 10.1089/aid.2008.0090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed a total of 12 near full-length genomes of drug-resistant HIV-1 spreading among therapy-naïve individuals in Nagoya, Japan. Genomes comprised seven protease inhibitor (PI)-resistant viruses possessing an M46I (n = 6) or L90M mutation (n = 1) and five non-nucleoside reverse transcriptase inhibitor-resistant viruses possessing a K103N mutation. All 12 viruses conserved both an H87Q mutation in the cyclophilin A-binding site of Gag p24 (capsid) and a T23N mutation in the cysteine-rich domain of Tat protein. PI-resistant viruses commonly possessed two cleavage site mutations in the p6(Pol)/protease of Pol polyprotein (F48L in p6(Pol)) and the anchor/core domains of Nef protein (L57V). These amino acid mutations represent candidates for enhancing replication activity of drug-resistant viruses and supporting expansion of such viruses in therapy-naïve individuals.
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Affiliation(s)
- Shiro Ibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Kaori Sawaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Seiichiro Fujisaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Junko Hattori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Naoto Mamiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Motohiro Hamaguchi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Tsuguhiro Kaneda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
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Ibe S, Hattori J, Fujisaki S, Shigemi U, Fujisaki S, Shimizu K, Nakamura K, Kazumi T, Yokomaku Y, Mamiya N, Hamaguchi M, Kaneda T. Trend of drug-resistant HIV type 1 emergence among therapy-naive patients in Nagoya, Japan: an 8-year surveillance from 1999 to 2006. AIDS Res Hum Retroviruses 2008; 24:7-14. [PMID: 18275342 DOI: 10.1089/aid.2007.0129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We studied the emergence of drug-resistant human immunodeficiency virus type 1 (HIV-1) with major amino acid mutations in 402 therapy-naive patients at Nagoya Medical Center, Japan, between 1999 and 2006. The mean prevalence of drug-resistant HIV-1 was 6.7% (range, 2.3-10.0%; n = 27). HIV-1 variants with protease inhibitor (PI)-resistant mutations alone were most frequently found (3.5%, n = 14), followed by those with nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutations alone (1.7%, n = 7). Variants with nucleoside reverse transcriptase inhibitor (NRTI)-resistant mutations alone were sporadically found (1.0%, n = 4). A variant possessing both NRTI- and PI-resistant mutations was detected in one patient (0.2%) and a variant possessing both NNRTI- and PI-resistant mutations was identified in another patient (0.2%). In addition, another 17 variants (4.2%, n = 17) with only 215-revertant mutations (T215C/D/G/L/S) that can easily reconvert to the nucleoside analogue-associated mutation of T215Y/F were found. The 402 viruses were phylogenetically analyzed, revealing three independent clusters comprising PI-resistant variants with the M46I or L90M mutation, NNRTI-resistant variants with the K103N mutation, and 215-revertant variants. The PI-resistant and 215-revertant strains have been spreading since 2000, and the NNRTI-resistant strain has started spreading since 2003. The nature of the epidemic and information for successfully blocking the spread of drug-resistant HIV-1 were clarified in this study.
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Affiliation(s)
- Shiro Ibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Junko Hattori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Seiichiro Fujisaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Saeko Fujisaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Kayoko Shimizu
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Kazuyo Nakamura
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Takejiro Kazumi
- Department of Clinical Research Laboratory, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Naoto Mamiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Motohiro Hamaguchi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
| | - Tsuguhiro Kaneda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center (Tokai Area Central Hospital for AIDS Treatment and Research), Nagoya, Aichi 460-0001, Japan
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Nakamura M, Imaizumi K, Shigemi U, Nakashima Y, Kikuchi Y. Cerebral atherosclerosis in Japanese. Part 5: relationship between cholesterol deposition and glycosaminoglycans. Stroke 1976; 7:594-8. [PMID: 1006735 DOI: 10.1161/01.str.7.6.594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Concentrations of various lipids and glycosaminoglycans (GAG) in the intima of the grossly normal and atherosclerotic cerebral arteries were compared with those of the aorta and coronary arteries. The lowest percentage of esterified cholesterol (EC) in total cholesterol, and of chondroitin sulfate-4/6 (CS-4/6) in total glycosaminoglycans and the highest percentage of heparin sulfate (HS) in total GAG are the characteristic features of the normal intima of normal cerebral arteries when compared with those in the aorta and coronary artery. In the cerebral arterial intimas, but not in the aorta or coronary arteries, there was a significant positive correlation between contents of EC and percentage and total content of CS-4/6. Atherogenesis in cerebral arteries is discussed in comparison to that of the aorta and coronary vessels.
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Imaizumi K, Shigemi U, Nakamura M. Chemical comparison of intimal elastin in the human cerebral and coronary arteries and aorta. A preliminary note. Paroi Arterielle 1975; 2:213-9. [PMID: 1234641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The purpose of our experiments was to clarify the relationship between the susceptibility to atherosclerosis and chemical composition in the human cerebral, coronary arteries and aorta, and the concentration and composition of human arterial intimal elastic tissues were measured. In the cerebral arteries, the concentration of hot alkali-insoluble elastin was higher than that of the coronary arteries and aortas, and gradually decreased with age. Age-related changes of the elastin in the coronary arteries were quite small. The total polar amino acids and crude ash contents of arterial elastins were affected by age and treatment of elastic tissue wheteher or not EDTA-decalcification was applied prior to alkali-extraction. No significant differences in the amino acid composition of elastin was founded between the cerebral, coronary and aortic intimas and no significant changes to elastin, and or collagen, which can explain the slow development of atherosclerosis in the cerebral artery, were founded. Therefore, from these results, the slower development rate of cerebral atherosclerosis, as compared with other arteries, can not be sufficiently concluded.
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Abstract
The
Macaca irus
is a monkey species that is highly susceptible to experimental cholesterol atherosclerosis of the aorta, coronary and cerebral arteries and cutaneous xanthomatosis-like lesions induced by feeding a diet high in cholesterol and/or coconut oil for 14 months.
The monkeys fed an atherogenic diet were divided into two groups: monkeys receiving excess sodium and controls. The excess sodium group showed a significantly higher systolic blood pressure as compared with the control group; however, elevation of blood pressure was mild and was not considered as significant hypertension.
The loading of excess sodium chloride in monkeys fed an atherogenic diet did not enhance severity of atherosclerosis of the aorta, coronary and cerebral arteries.
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Sata T, Shigemi U, Murakami H, Okabayashi T, Nakamura M. Studies on lipids of the coronary artery and aorta. Jpn Circ J 1973; 37:261-7. [PMID: 4740860 DOI: 10.1253/jcj.37.261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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