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Villandré L, Labbe A, Brenner B, Roger M, Stephens DA. DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference. BMC Bioinformatics 2018; 19:324. [PMID: 30217139 PMCID: PMC6137936 DOI: 10.1186/s12859-018-2347-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 08/29/2018] [Indexed: 12/24/2022] Open
Abstract
Background Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they often produce conflicting measures of confidence in clusters. The current study proposes a new Bayesian phylogenetic clustering algorithm, which we refer to as DM-PhyClus (Dirichlet-Multinomial Phylogenetic Clustering), that identifies sets of sequences resulting from quick transmission chains, thus yielding easily-interpretable clusters, without using any ad hoc distance or confidence requirement. Results Simulations reveal that DM-PhyClus can outperform conventional clustering methods, as well as the Gap procedure, a pure distance-based algorithm, in terms of mean cluster recovery. We apply DM-PhyClus to a sample of real HIV-1 sequences, producing a set of clusters whose inference is in line with the conclusions of a previous thorough analysis. Conclusions DM-PhyClus, by eliminating the need for cutpoints and producing sensible inference for cluster configurations, can facilitate transmission cluster detection. Future efforts to reduce incidence of infectious diseases, like HIV-1, will need reliable estimates of transmission clusters. It follows that algorithms like DM-PhyClus could serve to better inform public health strategies. Electronic supplementary material The online version of this article (10.1186/s12859-018-2347-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luc Villandré
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, 1020 avenue des Pins Ouest, Montreal, H3A 1A2, QC, Canada.
| | - Aurélie Labbe
- Department of Decision Science, HEC Montréal, 3000, chemin de la Côte-Sainte-Catherine, Montreal, H3T 2A7, QC, Canada
| | - Bluma Brenner
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 chemin de la Côte-Sainte-Catherine, Montreal, H3T 1E2, QC, Canada
| | - Michel Roger
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue Saint-Denis, Pavillon R, Montreal, H2X 0A9, QC, Canada.,Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 boul. Edouard-Montpetit, Montreal, H3T 1J4, QC, Canada
| | - David A Stephens
- Department of Mathematics and Statistics, McGill University, 805 rue Sherbrooke Ouest, Montreal, H3A 0B9, QC, Canada
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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] [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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Lo YR, Kato M, Phanuphak N, Fujita M, Duc DB, Sopheap S, Pendse R, Yu D, Wu Z, Chariyalertsak S. Challenges and potential barriers to the uptake of antiretroviral-based prevention in Asia and the Pacific region. Sex Health 2014; 11:126-36. [DOI: 10.1071/sh13094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 03/11/2014] [Indexed: 01/06/2023]
Abstract
Evidence has emerged over the past few years on the effectiveness of antiretroviral-based prevention technologies to prevent (i) HIV transmission while decreasing morbidity and mortality in HIV-infected persons, and (ii) HIV acquisition in HIV-uninfected individuals through pre-exposure prophylaxis (PrEP). Only few of the planned studies on treatment as prevention (TasP) are conducted in Asia. TasP might be more feasible and effective in concentrated rather than in generalised epidemics, as resources for HIV testing and antiretroviral treatment could focus on confined and much smaller populations than in the generalised epidemics observed in sub-Saharan Africa. Several countries such as Cambodia, China, Thailand and Vietnam, are now paving the way to success. Similar challenges arise for both TasP and PrEP. However, the operational issues for PrEP are amplified by the need for frequent retesting and ensuring adherence. This paper describes challenges for the implementation of antiretroviral-based prevention and makes the case that TasP and PrEP implementation research in Asia is much needed to provide insights into the feasibility of these interventions in populations where firm evidence of ‘real world’ effectiveness is still lacking.
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Kanizsai S, Ghidán A, Ujhelyi E, Bánhegyi D, Nagy K. Monitoring of drug resistance in therapy-naïve HIV infected patients and detection of African HIV subtypes in Hungary. Acta Microbiol Immunol Hung 2010; 57:55-68. [PMID: 20350879 DOI: 10.1556/amicr.57.2010.1.5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutations in the HIV-1 pol gene associated with resistance to antiretroviral drugs in therapy-naïve Hungarian individuals transmitted as primary infection by their foreign sexual partners originated from African, Asian and other European countries had been analyzed. Drug resistance genotyping of HIV RT and PR genes were performed where mutations of 72 codons - among them 64 specific resistance codons representing 6 nucleoside reverse transcriptase inhibitor (NRTIs), 2 non-nucleoside reverse transcriptase inhibitor (NNRTIs) and 6 proteinase inhibitor (PRIs) drugs - had been analyzed by Truegene HIV-1 Genotyping kit and OpenGene Sequencing System. Viral variants harboring resistance mutations in the po l gene were detected in 14% of the subjects. The highest rate of resistance to a single class of inhibitors was detected towards PR inhibitors (12%), followed by NRTI (8%) and NNRTI (5%). On the contrary, 25% of viruses transmitted by homosexual activity contained mutations led to resistance to NNRT. Viruses from 11 percent of cases were resistant to 2 classes of inhibitors, and 7 percent to three classes of inhibitors. Based upon sequence data non-B subtypes and CRFs were detected in more than 71% of cases. HIV-1 C (10.7%), HIV-F1 (7.2%) and HIV-1 G (3.6%) were detected as the more frequent subtypes. Among the HIV-1 recombinant viruses CRF02_AG variants were found more frequently (28.5%) followed by CRF06_cpx (17.8%) indicating penetration of non-B subtypes and recombinant African variants into Hungary, which raises serious clinical and public health consequences.
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Affiliation(s)
- Szilvia Kanizsai
- Semmelweis University Institute of Medical Microbiology Budapest Hungary
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Chin BS, Choi JY, Han Y, Kuang J, Li Y, Han SH, Choi H, Chae YT, Jin SJ, Baek JH, Lim YS, Kim CO, Song YG, Yong D, Li T, Kim JM. Comparison of genotypic resistance mutations in treatment-naive HIV type 1-infected patients in Korea and China. AIDS Res Hum Retroviruses 2010; 26:217-21. [PMID: 20156103 DOI: 10.1089/aid.2009.0157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Seventy-six treatment-naive human immunodeficiency virus (HIV)-1-infected patients were recruited from Korea and China to evaluate transmitted drug resistance (TDR). Although no major TDR was observed within the study population, some resistance-associated mutations in the reverse transcriptase region were observed (V118I 9.2%, V179D 7.9%). The frequencies of resistance-associated mutations in NNRTI (V179D) and PI minor mutations were higher in Korean patients compared with Chinese patients (13.6% vs. 0%, 45.5% vs. 12.5%, p < 0.05). Although unique clustering was observed in phylogenetic analyses according to geographic sources, cautious monitoring is recommended due to increasing TDR reports in this area where the population shares close geographic and cultural aspects.
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Affiliation(s)
- Bum Sik Chin
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Jun Yong Choi
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Yang Han
- Department of Internal Medicine, Peking Union Medical College, Beijing, China
| | - Jiqiu Kuang
- Department of Internal Medicine, Peking Union Medical College, Beijing, China
| | - Yanling Li
- Department of Internal Medicine, Peking Union Medical College, Beijing, China
| | - Sang Hoon Han
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Heekyoung Choi
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Yun Tae Chae
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Sung Joon Jin
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Ji-Hyeon Baek
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Young-Soun Lim
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Oh Kim
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Young Goo Song
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - TaiSheng Li
- Department of Internal Medicine, Peking Union Medical College, Beijing, China
| | - June Myung Kim
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
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Chan PA, Kantor R. Transmitted drug resistance in nonsubtype B HIV-1 infection. ACTA ACUST UNITED AC 2009; 3:447-465. [PMID: 20161523 DOI: 10.2217/hiv.09.30] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 nonsubtype B variants account for the majority of HIV infections worldwide. Drug resistance in individuals who have never undergone antiretroviral therapy can lead to early failure and limited treatment options and, therefore, is an important concern. Evaluation of reported transmitted drug resistance (TDR) is challenging owing to varying definitions and study designs, and is further complicated by HIV-1 subtype diversity. In this article, we discuss the importance of various mutation lists for TDR definition, summarize TDR in nonsubtype B HIV-1 and highlight TDR reporting and interpreting challenges in the context of HIV-1 diversity. When examined carefully, TDR in HIV-1 non-B protease and reverse transcriptase is still relatively low in most regions. Whether it will increase with time and therapy access, as observed in subtype-B-predominant regions, remains to be determined.
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Magiorkinis E, Detsika M, Hatzakis A, Paraskevis D. Monitoring HIV drug resistance in treatment-naive individuals: molecular indicators, epidemiology and clinical implications. ACTA ACUST UNITED AC 2009. [DOI: 10.2217/hiv.09.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transmitted drug resistance (TDR) has been documented to occur soon after the introduction of HAART. The purpose of this review is to summarize the current knowledge regarding the epidemiology, the clinical implications and the trends in the research field of TDR. Until now, there have been different approaches for monitoring TDR, however, the surveillance drug resistance-associated mutations list seems fairly advantageous for TDR surveillance compared with other methods. The prevalence of TDR is approximately 10% in Europe and North America among recently or newly infected individuals sampled over the last few years. TDR was found to be higher among patients infected in Europe and North America compared with those in geographic areas with a high prevalence of HIV-1, reflecting the differences in the access to HAART in the two populations. Resistant viruses show different reversal rates to wild-type depending on the fitness cost of particular mutations. TDR in treatment-naive individuals is of major importance in HIV clinical practice and for this reason British–European and USA guideline panels recommend drug-resistance testing prior to treatment.
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Affiliation(s)
- Emmanouil Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, University of Athens, M. Asias 75, 11527, Greece
| | - Maria Detsika
- National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, University of Athens, M. Asias 75, 11527, Greece
| | - Angelos Hatzakis
- National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, University of Athens, M. Asias 75, 11527, Greece
| | - Dimitrios Paraskevis
- National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, University of Athens, M. Asias 75, 11527, Greece
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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] [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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Juhász E, Ghidán A, Kemény B, Nagy K. Emergence of antiretroviral drug resistance in therapy-naive HIV infected patients in Hungary. Acta Microbiol Immunol Hung 2008; 55:383-94. [PMID: 19130746 DOI: 10.1556/amicr.55.2008.4.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutations in the HIV-1 genes associated with resistance to antiretroviral drugs were detected also in primary HIV infected individuals who did not receive antiretroviral treatment. Drug resistance genotyping of HIV pol gene was done by in situ DNA hybridization using a Line Probe Assay and by direct sequencing. Viral variants harbouring resistance mutations such as: M41, T69R, K70R, M184V, T215Y in the pol gene were detected in 14% of the subjects. HIV mutants resistant to NRT inhibitors were found in 10 and 20% of patients infected before and after the year 2000, respectively. Multiple drug resistant viruses (2-3 drug classes) were present in 3.5% of the mainly recently infected patients. In protease gene only minor resistant mutations were found such as L101 and A71V. These findings indicate the evolution of drug resistance showing a correlation with the time of introduction of combination therapy in our country, where more than 70% of HIV infections were by homo/bisexual transmission. This confirms the transmission of drug-resistant HIV shown by genotype testing during primary infection in therapy-naive patients and initiates serious clinical and public health consequences.
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Affiliation(s)
- Emese Juhász
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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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] [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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Lall M, Gupta RM, Sen S, Kapila K, Tripathy SP, Paranjape RS. Profile of primary resistance in HIV-1-infected treatment-naive individuals from Western India. AIDS Res Hum Retroviruses 2008; 24:987-90. [PMID: 18593351 DOI: 10.1089/aid.2008.0079] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The majority of the HIV drug resistance (HIVDR) testing studies have focused on subtype B virus. The predominance of subtype C in the Indian subcontinent along with greater access to antiretroviral therapy (ART) necessitates studies on HIVDR genotyping. We determined the prevalence of mutations associated with protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI), and nonnucleoside reverse transcriptase inhibitors (NNRTI) from plasma of 40 antiretroviral drug-naive study participants in Indian HIV-1 pol gene sequences. Of these, 36 sequences belonged to subtype C, two to subtype A1, and two were subtype A1C recombinants. The heterosexual route was the most common route of transmission. Drug resistance-associated mutations were observed in 10% (4/40) of the study participants. The resistance mutation observed in the protease gene was V82A, whereas in the RT gene, M41L, D67N, M184V, and A98G were documented. This is the first study reporting major protease mutations by genotyping in ART-naive individuals from western India.
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Affiliation(s)
- Mahima Lall
- Department of Microbiology, Armed Forces Medical College, Pune, India
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