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Winans S, Yu HJ, de Los Santos K, Wang GZ, KewalRamani VN, Goff SP. A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats. Nat Commun 2022; 13:1474. [PMID: 35304442 PMCID: PMC8933506 DOI: 10.1038/s41467-022-29097-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/24/2022] [Indexed: 11/25/2022] Open
Abstract
Retroviruses utilize the viral integrase (IN) protein to integrate a DNA copy of their genome into host chromosomal DNA. HIV-1 integration sites are highly biased towards actively transcribed genes, likely mediated by binding of the IN protein to specific host factors, particularly LEDGF, located at these gene regions. We here report a substantial redirection of integration site distribution induced by a single point mutation in HIV-1 IN. Viruses carrying the K258R IN mutation exhibit a high frequency of integrations into centromeric alpha satellite repeat sequences, as assessed by deep sequencing, a more than 10-fold increase over wild-type. Quantitative PCR and in situ immunofluorescence assays confirm this bias of the K258R mutant virus for integration into centromeric DNA. Immunoprecipitation studies identify host factors binding to IN that may account for the observed bias for integration into centromeres. Centromeric integration events are known to be enriched in the latent reservoir of infected memory T cells, as well as in elite controllers who limit viral replication without intervention. The K258R point mutation in HIV-1 IN is also present in databases of latent proviruses found in patients, and may reflect an unappreciated aspect of the establishment of viral latency. HIV-1 integration sites are biased towards actively transcribed genes, likely mediated by binding of the viral integrase (IN) protein to host factors. Here, Winans et al. show that the K258R point mutation in IN eredirects viral DNA integration to the centromeres of host chromosomes, which may affect HIV latency.
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Affiliation(s)
- Shelby Winans
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, USA
| | - Kenia de Los Santos
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Gary Z Wang
- Department of Pathology, Columbia University Medical Center, New York, NY, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA. .,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA. .,Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
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Antiretroviral (ARV) Drug Resistance and HIV-1 Subtypes among Injecting Drug Users in the Coastal Region of Kenya. Adv Virol 2022; 2022:3217749. [PMID: 35186083 PMCID: PMC8853818 DOI: 10.1155/2022/3217749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 11/21/2022] Open
Abstract
HIV-1 genetic diversity results into the development of widespread drug-resistant mutations (DRMs) for the first-line retroviral therapy. Nevertheless, few studies have investigated the relationship between DRMs and HIV-1 subtypes among HIV-positive injecting drug users (IDUs). This study therefore determined the association between HIV-1 genotypes and DRMs among the 200 IDUs. Stanford HIV Drug Resistance Database was used to interpret DRMs. The five HIV-1 genotypes circulating among the IDUs were A1 (25 (53.2%)), A2 (2 (4.3%)), B (2 (4.3%)), C (9 (19.1%)), and D (9 (19.1%)). The proportions of DRMs were A1 (12 (52.2%)), A2 (1 (4.3%)), B (0 (0.0%)), C (5 (21.7%)), and D (5 (21.7%)). Due to the large proportion of drug resistance across all HIV-1 subtypes, surveillance and behavioral studies need to be explored as IDUs may be spreading the drug resistance to the general population. In addition, further characterization of DRMs including all the relevant clinical parameters among the larger population of IDUs is critical for effective drug resistance surveillance.
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Cytokines and Chemokines Involved in Hepatitis B Surface Antigen Loss in Human Immunodeficiency Virus/Hepatitis B Virus Coinfected Patients. J Clin Med 2021; 10:jcm10040833. [PMID: 33670625 PMCID: PMC7922731 DOI: 10.3390/jcm10040833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 11/16/2022] Open
Abstract
It has been reported that hepatic flare (HF), attributable to the development of immune reconstitution inflammatory syndrome (IRIS) in human immunodeficiency virus (HIV)/hepatitis B virus (HBV) coinfected patients, occurs frequently after the start of anti-retroviral therapy (ART). We have observed several cases of hepatitis B surface antigen (HBsAg) loss after IRIS. However, the factors leading to HBsAg clearance remain unknown. We measured CD4+ and CD8+ T cells, cytokines and chemokines in 16 patients coinfected HIV-1 and HBV with IRIS, and analyzed the factors leading to HBsAg clearance after IRIS. There was no significant difference in the CD4+ and CD8+ T cell counts between the HBsAg clearance and non-clearance groups, while the serum concentrations of almost all cytokines and chemokines in the HBsAg clearance group were higher than in the HBsAg non-clearance group at any time of observation. In particular, IP-10 at the ALT peak, GM-CSF and IL-12 one month after the ALT peak and TNF-α and GM-CSF after the ALT concentrations fell to within normal limits, were significantly higher in the HBsAg clearance group. It seems that HBsAg loss after IRIS requires continued immune responses against HBV, involving Th1 cytokines.
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Shiino T, Hachiya A, Hattori J, Sugiura W, Yoshimura K. Nation-Wide Viral Sequence Analysis of HIV-1 Subtype B Epidemic in 2003–2012 Revealed a Contribution of Men Who Have Sex With Men to the Transmission Cluster Formation and Growth in Japan. FRONTIERS IN REPRODUCTIVE HEALTH 2020; 2:531212. [PMID: 36304701 PMCID: PMC9580810 DOI: 10.3389/frph.2020.531212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
Background: To better understand the epidemiology of human immunodeficiency virus type 1 (HIV-1) subtype B transmission in Japan, phylodynamic analysis of viral pol sequences was conducted on individuals newly diagnosed as HIV-1 seropositive. Methodology: A total of 5,018 patients newly diagnosed with HIV-1 infection and registered in the Japanese Drug Resistance HIV Surveillance Network from 2003 to 2012 were enrolled in the analysis. Using the protease-reverse transcriptase nucleotide sequences, their subtypes were determined, and phylogenetic relationships among subtype B sequences were inferred using three different methods: distance-matrix, maximum likelihood, and Bayesian Markov chain Monte Carlo. Domestically spread transmission clusters (dTCs) were identified based on the following criteria: >95% in interior branch test, >95% in Bayesian posterior probability and <10% in depth-first searches for sub-tree partitions. The association between dTC affiliation and individuals' demographics was analyzed using univariate and multivariate analyses. Results: Among the cases enrolled in the analysis, 4,398 (87.6%) were classified as subtype B. Many of them were Japanese men who had sex with men (MSM), and 3,708 (84.3%) belonged to any of 312 dTCs. Among these dTCs, 243 (77.9%) were small clusters with <10 individuals, and the largest cluster consisted of 256 individuals. Most dTCs had median time of the most recent common ancestor between 1995 and 2005, suggesting that subtype B infection was spread among MSMs in the second half of the 1990s. Interestingly, many dTCs occurred within geographical regions. Comparing with singleton cases, TCs included more MSM, young person, and individuals with high CD4+ T-cell count at the first consultation. Furthermore, dTC size was significantly correlated with gender, age, transmission risks, recent diagnosis and relative population size of the region mainly distributed. Conclusions: Our study clarified that major key population of HIV-1 subtype B epidemic in Japan is local MSM groups. The study suggests that HIV-1 subtype B spread via episodic introductions into the local MSM groups, some of the viruses spread to multiple regions. Many cases in dTC were diagnosed during the early phase of infection, suggesting their awareness to HIV risks.
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Affiliation(s)
- Teiichiro Shiino
- Surveillance and Information Division, Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Teiichiro Shiino
| | - Atsuko Hachiya
- Division of Biological Information Analysis, Department of Clinical Research Management, Crinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Junko Hattori
- Division of Biological Information Analysis, Department of Clinical Research Management, Crinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Wataru Sugiura
- Division of Biological Information Analysis, Department of Clinical Research Management, Crinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhisa Yoshimura
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Research Institute Director, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
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5
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Digban TO, Iweriebor BC, Obi LC, Nwodo U, Okoh AI. Molecular Genetics and the Incidence of Transmitted Drug Resistance Among Pre-Treatment HIV-1 Infected Patients in the Eastern Cape, South Africa. Curr HIV Res 2020; 17:335-342. [PMID: 31584370 DOI: 10.2174/1570162x17666191004093433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Transmitted drug resistance (TDR) remains a significant threat to Human immunodeficiency virus (HIV) infected patients that are not exposed to antiretroviral treatment. Although, combined antiretroviral therapy (cART) has reduced deaths among infected individuals, emergence of drug resistance is gradually on rise. OBJECTIVE To determine the drug resistance mutations and subtypes of HIV-1 among pre-treatment patients in the Eastern Cape of South Africa. METHODS Viral RNA was extracted from blood samples of 70 pre-treatment HIV-1 patients while partial pol gene fragment amplification was achieved with specific primers by RT-PCR followed by nested PCR and positive amplicons were sequenced utilizing ABI Prism 316 genetic sequencer. Drug resistance mutations (DRMs) analysis was performed by submitting the generated sequences to Stanford HIV drug resistance database. RESULTS Viral DNA was successful for 66 (94.3%) samples of which 52 edited sequences were obtained from the protease and 44 reverse transcriptase sequences were also fully edited. Four major protease inhibitor (PI) related mutations (I54V, V82A/L, L76V and L90M) were observed in seven patients while several other minor and accessory PIs were also identified. A total of 11(25.0%) patients had NRTIs related mutations while NNRTIs were observed among 14(31.8%) patients. K103N/S, V106M and M184V were the most common mutations identified among the viral sequences. Phylogenetic analysis of the partial pol gene indicated all sequences clustered with subtype C. CONCLUSION This study indicates that HIV-1 subtype C still predominates and responsible for driving the epidemic in the Eastern Cape of South Africa with slow rise in the occurrence of transmitted drug resistance.
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Affiliation(s)
- Tennison Onoriode Digban
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Benson Chucks Iweriebor
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Larry Chikwelu Obi
- Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Uchechuwku Nwodo
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Anthony Ifeanyi Okoh
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
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Platt L, French CE, McGowan CR, Sabin K, Gower E, Trickey A, McDonald B, Ong J, Stone J, Easterbrook P, Vickerman P. Prevalence and burden of HBV co-infection among people living with HIV: A global systematic review and meta-analysis. J Viral Hepat 2020; 27:294-315. [PMID: 31603999 PMCID: PMC7383613 DOI: 10.1111/jvh.13217] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022]
Abstract
Globally, in 2017 35 million people were living with HIV (PLHIV) and 257 million had chronic HBV infection (HBsAg positive). The extent of HIV-HBsAg co-infection is unknown. We undertook a systematic review to estimate the global burden of HBsAg co-infection in PLHIV. We searched MEDLINE, Embase and other databases for published studies (2002-2018) measuring prevalence of HBsAg among PLHIV. The review was registered with PROSPERO (#CRD42019123388). Populations were categorized by HIV-exposure category. The global burden of co-infection was estimated by applying regional co-infection prevalence estimates to UNAIDS estimates of PLHIV. We conducted a meta-analysis to estimate the odds of HBsAg among PLHIV compared to HIV-negative individuals. We identified 506 estimates (475 studies) of HIV-HBsAg co-infection prevalence from 80/195 (41.0%) countries. Globally, the prevalence of HIV-HBsAg co-infection is 7.6% (IQR 5.6%-12.1%) in PLHIV, or 2.7 million HIV-HBsAg co-infections (IQR 2.0-4.2). The greatest burden (69% of cases; 1.9 million) is in sub-Saharan Africa. Globally, there was little difference in prevalence of HIV-HBsAg co-infection by population group (approximately 6%-7%), but it was slightly higher among people who inject drugs (11.8% IQR 6.0%-16.9%). Odds of HBsAg infection were 1.4 times higher among PLHIV compared to HIV-negative individuals. There is therefore, a high global burden of HIV-HBsAg co-infection, especially in sub-Saharan Africa. Key prevention strategies include infant HBV vaccination, including a timely birth-dose. Findings also highlight the importance of targeting PLHIV, especially high-risk groups for testing, catch-up HBV vaccination and other preventative interventions. The global scale-up of antiretroviral therapy (ART) for PLHIV using a tenofovir-based ART regimen provides an opportunity to simultaneously treat those with HBV co-infection, and in pregnant women to also reduce mother-to-child transmission of HBV alongside HIV.
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Affiliation(s)
- Lucy Platt
- Faculty of Public Health & PolicyLondon School of Hygiene & Tropical MedicineLondonUK
| | - Clare E. French
- NIHR Health Protection Research Unit in Evaluation of InterventionsPopulation Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Catherine R. McGowan
- Faculty of Public Health & PolicyLondon School of Hygiene & Tropical MedicineLondonUK
- Humanitarian Public Health Technical UnitSave the Children UKLondonUK
| | | | - Erin Gower
- Centre for Disease Control and PreventionAtlantaUSA
| | - Adam Trickey
- NIHR Health Protection Research Unit in Evaluation of InterventionsPopulation Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Bethan McDonald
- Oxford School of Public HealthNuffield Department of Population HealthUniversity of OxfordOxfordUK
- Oxford University Hospitals NHS Foundation TrustJohn Radcliffe HospitalOxfordUK
- Department of Clinical ResearchLondon School of Hygiene and Tropical MedicineLondonUK
| | - Jason Ong
- Department of Clinical ResearchLondon School of Hygiene and Tropical MedicineLondonUK
| | - Jack Stone
- NIHR Health Protection Research Unit in Evaluation of InterventionsPopulation Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | | | - Peter Vickerman
- NIHR Health Protection Research Unit in Evaluation of InterventionsPopulation Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
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7
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Full-Genome Analysis of Hepatitis C Virus in Japanese and Non-Japanese Patients Coinfected With HIV-1 in Tokyo. J Acquir Immune Defic Syndr 2019; 80:350-357. [PMID: 30550489 DOI: 10.1097/qai.0000000000001919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Acute hepatitis C virus (HCV) infection is increasing among HIV-1-infected individuals in Tokyo. Appropriate clinical management is needed. SETTING To delineate the epidemiological status of HCV transmission, we analyzed stocked plasma samples of HCV/HIV-1-coinfected patients seen at the largest referral center for HIV care in Tokyo. METHODS HCV full-genome sequences were amplified and determined using next-generation sequencing. HCV genotyping and phylogenetic and phylodynamic analyses of thus obtained sequences were performed and combined with the analysis of HIV-1 reverse transcriptase sequences. RESULTS HCV phylogenetic analysis identified 3 dense clusters containing cases of men who have sex with men (MSM) and injection drug users (IDUs). Most of the confirmed acute infection cases were included within these clusters, indicating that the clustered viruses are currently being actively transmitted among HIV-1-infected MSM and IDU. Phylodynamic analysis indicated population expansion of one of these clusters from 2006 to 2008, during which the largest number of HIV-1-infected MSM was diagnosed in Tokyo. HIV-1 reverse transcriptase sequences of HCV-coinfected patients included in the same clusters did not converge together and did not form clusters, but rather diverged in the area of subtype B in the phylogenetic tree, indicating that they acquired HCV infection from individuals different from those from whom they had acquired HIV-1 infection. It is considered that these MSM changed their sexual partners and that IDU changed their drug use groups. CONCLUSIONS The results warrant careful monitoring of high-risk groups including MSM and IDU and early introduction of HCV treatment to prevent HCV epidemic.
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8
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Yuan D, Du Z, Zhou J, Ye L, Su L, Yang H, Yuan F, Li Y, Liu H, Zhai W, Liang S, Yang S. HIV-1 subtype diversity, drug resistance, and genetic transmission networks in men who have sex with men with virologic failure in antiretroviral therapy in Sichuan, China, 2011 to 2017. Medicine (Baltimore) 2019; 98:e17585. [PMID: 31651864 PMCID: PMC6824707 DOI: 10.1097/md.0000000000017585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study sought to examine the human immunodeficiency virus type 1 (HIV-1) genetic diversity on drug resistance among men who have sex with men (MSM) with virologic failure in antiretroviral therapy (ART), and investigate linking-associated factors for genetic transmission networks.Seven hundred and thirty-four HIV-positive MSM with virologic failure in ART were recruited into our study from 2011 to 2017. HIV-1 pol gene sequences were used for phylogenetic and genotypic drug resistance analyses. The drug resistance mutations were determined using the Stanford University HIV Drug Resistance Database. The genetic transmission networks were analyzed for CRF01_AE and CRF07_BC sequences by the genetic distance-based method.Of 734 subjects, 372 (50.68%) showed drug resistance, in which CRF01_AE and CRF07_BC were the predominating subtypes. Drug resistance more frequently occurred in non-nucleoside reverse transcriptase inhibitors (NNRTIs) treatment (48.64%), and followed by nucleoside reverse transcriptase inhibitors (NRTIs) (36.51%) and PIs (4.03%). The most common drug resistance-associated mutations in protease inhibitors (PIs), NRTIs and NNRTIs were K20I/R, M184V/I and K103N/KN, respectively. For 283CRF01_AE sequences, 64 (22.61%) fell into clusters at a genetic distance of 0.011, resulting in 17 clusters ranging in size from 2 to 16 individuals. For 230 CRF07_BC sequences, 66 (28.69%) were connected to at least one other sequence with 0.005 genetic distances, resulting in 8 clusters ranging in size from 2 to 52 individuals. Individuals who showed drug resistance to ART were less likely to fall into clusters than those who did not. The genetic linkage was robust by the exclusion of sites associated with drug resistance.CRF01_AE and CRF07_BC were the main strains among MSM with virologic failure in ART, and the drug resistance more frequently occurred in NNRTIs, followed by NRTIs and PIs. Genetic transmission networks revealed a complexity of transmission pattern, suggesting early-diagnosis and in-time intervention among MSM.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Zonglun Du
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China,
| | - Junmin Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Ling Su
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Hong Yang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Fengshun Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Honglu Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Wenwen Zhai
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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9
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Hayashida T, Hachiya A, Ode H, Nishijima T, Tsuchiya K, Sugiura W, Takiguchi M, Oka S, Gatanaga H. Rilpivirine resistance mutation E138K in HIV-1 reverse transcriptase predisposed by prevalent polymorphic mutations. J Antimicrob Chemother 2016; 71:2760-6. [PMID: 27330069 DOI: 10.1093/jac/dkw224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/11/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Rilpivirine is listed as a recommended or alternative key drug in the current ART guidelines. E138K in HIV-1 reverse transcriptase (RT) is a primary mutation in resistance to rilpivirine, although in vitro experiments showed it confers only <3-fold resistance. An unidentified mechanism could amplify resistance to rilpivirine conferred by E138K. OBJECTIVES The objective of this study was to reveal the mechanism amplifying rilpivirine resistance conferred by E138K. PATIENTS AND METHODS HIV-1 RT sequences were compared in patients who failed rilpivirine-containing ART virologically. The effects of mutations commonly identified with E138K on rilpivirine susceptibility were analysed by using recombinant HIV-1 variants. RESULTS Rilpivirine-containing ART was introduced in 162 HIV-1-infected patients at the outpatient clinic of the AIDS Clinical Center (National Center for Global Health and Medicine, Tokyo, Japan) between May 2012 and June 2015. Virological treatment failure occurred in six of these patients. E138K emerged in three patients while other rilpivirine resistance mutations emerged in the other three patients. I135T/L were identified in only three patients with E138K and existed before the introduction of rilpivirine-containing ART. Analysis of recombinant HIV-1 variants indicated that E138K conferred low-level rilpivirine resistance and that coexistence of I135T/L with E138K amplified the resistance. CONCLUSIONS I135T/L, escape mutations from HLA-B*51/52-restricted cytotoxic T lymphocytes, which are prevalent in Japan, may predispose HIV-1 to harbour E138K upon failure of rilpivirine-containing ART. The mutation patterns of drug resistance may vary due to baseline polymorphic mutations.
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Affiliation(s)
- Tsunefusa Hayashida
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Takeshi Nishijima
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Wataru Sugiura
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | | | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan Center for AIDS Research, Kumamoto University, Kumamoto, Japan
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10
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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] [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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Ode H, Matsuda M, Matsuoka K, Hachiya A, Hattori J, Kito Y, Yokomaku Y, Iwatani Y, Sugiura W. Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq. Front Microbiol 2015; 6:1258. [PMID: 26617593 PMCID: PMC4641896 DOI: 10.3389/fmicb.2015.01258] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/29/2015] [Indexed: 12/29/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) exhibits high between-host genetic diversity and within-host heterogeneity, recognized as quasispecies. Because HIV-1 quasispecies fluctuate in terms of multiple factors, such as antiretroviral exposure and host immunity, analyzing the HIV-1 genome is critical for selecting effective antiretroviral therapy and understanding within-host viral coevolution mechanisms. Here, to obtain HIV-1 genome sequence information that includes minority variants, we sought to develop a method for evaluating quasispecies throughout the HIV-1 near-full-length genome using the Illumina MiSeq benchtop deep sequencer. To ensure the reliability of minority mutation detection, we applied an analysis method of sequence read mapping onto a consensus sequence derived from de novo assembly followed by iterative mapping and subsequent unique error correction. Deep sequencing analyses of aHIV-1 clone showed that the analysis method reduced erroneous base prevalence below 1% in each sequence position and discarded only < 1% of all collected nucleotides, maximizing the usage of the collected genome sequences. Further, we designed primer sets to amplify the HIV-1 near-full-length genome from clinical plasma samples. Deep sequencing of 92 samples in combination with the primer sets and our analysis method provided sufficient coverage to identify >1%-frequency sequences throughout the genome. When we evaluated sequences of pol genes from 18 treatment-naïve patients' samples, the deep sequencing results were in agreement with Sanger sequencing and identified numerous additional minority mutations. The results suggest that our deep sequencing method would be suitable for identifying within-host viral population dynamics throughout the genome.
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Affiliation(s)
- Hirotaka Ode
- 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
| | - Kazuhiro Matsuoka
- 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
| | - Junko Hattori
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yumiko Kito
- 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
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Graduate School of Medicine, Nagoya University Nagoya, Japan
| | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Graduate School of Medicine, Nagoya University Nagoya, Japan
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Ng E, Salihovic S, Lind PM, Mahajan A, Syvänen AC, Axelsson T, Ingelsson E, Lindgren CM, van Bavel B, Morris AP, Lind L. Genome-wide association study of plasma levels of polychlorinated biphenyls disclose an association with the CYP2B6 gene in a population-based sample. ENVIRONMENTAL RESEARCH 2015; 140:95-101. [PMID: 25839716 PMCID: PMC4509719 DOI: 10.1016/j.envres.2015.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Polychlorinated biphenyls (PCBs) are a group of man-made environmental pollutants which accumulate in humans with adverse health effects. To date, very little effort has been devoted to the study of the metabolism of PCBs on a genome-wide level. OBJECTIVES Here, we conducted a genome-wide association study (GWAS) to identify genomic regions involved in the metabolism of PCBs. METHODS Plasma levels of 16 PCBs ascertained in a cohort of elderly individuals from Sweden (n=1016) were measured using gas chromatography-high resolution mass spectrophotometry (GC-HRMS). DNA samples were genotyped on the Infinium Omni Express bead microarray, and imputed up to reference panels from the 1000 Genomes Project. Association testing was performed in a linear regression framework under an additive model. RESULTS Plasma levels of PCB-99 demonstrated genome-wide significant association with single nucleotide polymorphisms (SNPs) mapping to chromosome 19q13.2. The SNP with the strongest association was rs8109848 (p=3.7×10(-13)), mapping to an intronic region of CYP2B6. Moreover, when all PCBs were conditioned on PCB-99, further signals were revealed for PCBs -74, -105 and -118, mapping to the same genomic region. The lead SNPs were rs8109848 (p=3.8×10(-12)) for PCB-118, rs4802104 (p=1.4×10(-9)) for PCB-74 and rs4803413 (p=2.5×10(-9)) for PCB-105, all of which map to CYP2B6. CONCLUSIONS In our study, we found plasma levels of four lower-chlorinated PCBs to be significantly associated with the genetic region mapping to the CYP2B6 locus. These findings show that CYP2B6 is of importance for the metabolism of PCBs in humans, and may help to identify individuals who may be susceptible to PCB toxicity.
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Affiliation(s)
- Esther Ng
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
| | - Samira Salihovic
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P Monica Lind
- Department of Medical Sciences, Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anne-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tomas Axelsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Bert van Bavel
- MTM Research Centre, Örebro University, 701 82 Örebro, Sweden
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden.
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The prevalence and determinants of drug-resistance-associated mutations in the HIV-1-infected MSM population of Henan Province in China. Arch Virol 2015; 160:2051-61. [PMID: 26077516 DOI: 10.1007/s00705-015-2481-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/31/2015] [Indexed: 02/01/2023]
Abstract
To estimate the prevalence of human immunodeficiency virus (HIV) drug resistance (DR) in a population of men who have sex with men (MSM) from Henan Province of China and to identify the DR-associated HIV-1 mutations in these MSM. The HIV-positive status of the MSM subjects in this study was confirmed using ELISA and Western blotting. The MSM subjects were classified into non-treatment group (n = 106) and treatment group (n = 313). CD4(+) T-lymphocyte counts were obtained by flow cytometry, and viral load was measured by branched DNA (bDNA) signal amplification assay. HIV-1 genotypic resistance tests were performed by sequence analysis of the HIV-1 protease and reverse transcriptase genes. In the non-treatment group, 15 patients (14.2 %) displayed DR to non-nucleoside reverse transcriptase inhibitor (NNRTI). In the treatment group, the failure rate of viral suppression was 38.33 % and the DR rate was 33.2 %, which was higher than the rate observed in the non-treatment group (P < 0.05). The incidence of mutations corresponding to NNRTI resistance was significantly higher than the incidence of mutations corresponding to nucleoside reverse transcriptase inhibitor (NRTI) resistance (32.9 % vs. 26.5 %) in the cohort. After antiretroviral therapy (ART), the frequencies of K103N, G190A, Y181C, and V106A mutations were highly elevated. Logistic regression analysis results showed that duration of treatment, poor treatment compliance, drug abuse and homosexual orientation are the major risk factors for DR in this MSM population (all P < 0.05). Our results showed that DR-associated mutations in the HIV-1-infected MSM population increased significantly after ART. Furthermore, duration of treatment, poor treatment compliance, drug abuse and homosexual orientation were identified as the risk factors for DR in the MSM population from Henan Province in China.
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Yoshida S, Hattori J, Matsuda M, Okada K, Kazuyama Y, Hashimoto O, Ibe S, Fujisawa SI, Chiba H, Tatsumi M, Kato S, Sugiura W. Japanese external quality assessment program to standardize HIV-1 drug-resistance testing (JEQS2010 program) using in vitro transcribed RNA as reference material. AIDS Res Hum Retroviruses 2015; 31:318-25. [PMID: 25469535 DOI: 10.1089/aid.2014.0059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To design appropriate antiretroviral therapy regimens and avoid the emergence of human immunodeficiency virus (HIV)-1 variants with reduced susceptibility to antiretroviral drugs, genotypic drug-resistance testing (HIV genotyping) is strongly recommended. To monitor the quality of HIV genotyping in Japan, we performed an external quality assessment (EQA), named the Japanese external quality assessment program, to standardize HIV genotyping (JEQS). To accurately evaluate the quality of HIV genotyping, we employed as reference material (RM) a well-characterized sample, in vitro transcribed RNA (trRNA) that includes the HIV gag-pol sequence, and created a JEQS2010 panel consisting of three single variant and three mixed trRNA samples. All 11 participating laboratories showed high concordance rates (>96%) for the single variant samples. Eight laboratories also showed good rates of detecting minor variants, but three laboratories failed to detect the variants comprising one-half of the sample. These three laboratories used a common primer that had four internal mismatches to the minor trRNA clone. This program showed the usefulness of trRNA as RM, the high quality of HIV genotyping, and extensive interlaboratory variation in the ability to detect minor variants. These results suggest that improving the quality of HIV genotyping in Japan requires regularly implementing the EQA program and improving the HIV genotyping protocol in each laboratory.
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Affiliation(s)
- Shigeru Yoshida
- Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Junko Hattori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Kiyomi Okada
- Kitasato Otsuka Biomedical Assay Laboratories Co., Ltd., Kanagawa, Japan
| | - Yukumasa Kazuyama
- Kitasato Otsuka Biomedical Assay Laboratories Co., Ltd., Kanagawa, Japan
| | - Osamu Hashimoto
- Mitsubishi Chemical Medience Corporation Central Laboratory, Tokyo, Japan
| | - Shiro Ibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Shin-ichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Hitoshi Chiba
- Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | | | - Shingo Kato
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Sugiura
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
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Development and customization of a color-coded microbeads-based assay for drug resistance in HIV-1 reverse transcriptase. PLoS One 2014; 9:e109823. [PMID: 25314293 PMCID: PMC4196989 DOI: 10.1371/journal.pone.0109823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/10/2014] [Indexed: 11/23/2022] Open
Abstract
Background Drug resistance (DR) of HIV-1 can be examined genotypically or phenotypically. Although sequencing is the gold standard of the genotypic resistance testing (GRT), high-throughput GRT targeted to the codons responsible for DR may be more appropriate for epidemiological studies and public health research. Methods We used a Japanese database to design and synthesize sequence-specific oligonucleotide probes (SSOP) for the detection of wild-type sequences and 6 DR mutations in the clade B HIV-1 reverse transcriptase region. We coupled SSOP to microbeads of the Luminex 100 xMAP system and developed a GRT based on the polymerase chain reaction (PCR)-SSOP-Luminex method. Results Sixteen oligoprobes for discriminating DR mutations from wild-type sequences at 6 loci were designed and synthesized, and their sensitivity and specificity were confirmed using isogenic plasmids. The PCR-SSOP-Luminex DR assay was then compared to direct sequencing using 74 plasma specimens from treatment-naïve patients or those on failing treatment. In the majority of specimens, the results of the PCR-SSOP-Luminex DR assay were concordant with sequencing results: 62/74 (83.8%) for M41, 43/74 (58.1%) for K65, 70/74 (94.6%) for K70, 55/73 (75.3%) for K103, 63/73 (86.3%) for M184 and 68/73 (93.2%) for T215. There were a number of specimens without any positive signals, especially for K65. The nucleotide position of A2723G, A2747G and C2750T were frequent polymorphisms for the wild-type amino acids K65, K66 and D67, respectively, and 14 specimens had the D67N mutation encoded by G2748A. We synthesized 14 additional oligoprobes for K65, and the sensitivity for K65 loci improved from 43/74 (58.1%) to 68/74 (91.9%). Conclusions We developed a rapid high-throughput assay for clade B HIV-1 DR mutations, which could be customized by synthesizing oligoprobes suitable for the circulating viruses. The assay could be a useful tool especially for public health research in both resource-rich and resource-limited settings.
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Chabria SB, Gupta S, Kozal MJ. Deep Sequencing of HIV: Clinical and Research Applications. Annu Rev Genomics Hum Genet 2014; 15:295-325. [DOI: 10.1146/annurev-genom-091212-153406] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shiven B. Chabria
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
| | - Shaili Gupta
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
- Section of Infectious Diseases, Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, Connecticut 06516
| | - Michael J. Kozal
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
- Section of Infectious Diseases, Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, Connecticut 06516
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Phylodynamic analysis reveals CRF01_AE dissemination between Japan and neighboring Asian countries and the role of intravenous drug use in transmission. PLoS One 2014; 9:e102633. [PMID: 25025900 PMCID: PMC4099140 DOI: 10.1371/journal.pone.0102633] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 06/21/2014] [Indexed: 11/30/2022] Open
Abstract
Background One major circulating HIV-1 subtype in Southeast Asian countries is CRF01_AE, but little is known about its epidemiology in Japan. We conducted a molecular phylodynamic study of patients newly diagnosed with CRF01_AE from 2003 to 2010. Methods Plasma samples from patients registered in Japanese Drug Resistance HIV-1 Surveillance Network were analyzed for protease-reverse transcriptase sequences; all sequences undergo subtyping and phylogenetic analysis using distance-matrix-based, maximum likelihood and Bayesian coalescent Markov Chain Monte Carlo (MCMC) phylogenetic inferences. Transmission clusters were identified using interior branch test and depth-first searches for sub-tree partitions. Times of most recent common ancestor (tMRCAs) of significant clusters were estimated using Bayesian MCMC analysis. Results Among 3618 patient registered in our network, 243 were infected with CRF01_AE. The majority of individuals with CRF01_AE were Japanese, predominantly male, and reported heterosexual contact as their risk factor. We found 5 large clusters with ≥5 members and 25 small clusters consisting of pairs of individuals with highly related CRF01_AE strains. The earliest cluster showed a tMRCA of 1996, and consisted of individuals with their known risk as heterosexual contacts. The other four large clusters showed later tMRCAs between 2000 and 2002 with members including intravenous drug users (IVDU) and non-Japanese, but not men who have sex with men (MSM). In contrast, small clusters included a high frequency of individuals reporting MSM risk factors. Phylogenetic analysis also showed that some individuals infected with HIV strains spread in East and South-eastern Asian countries. Conclusions Introduction of CRF01_AE viruses into Japan is estimated to have occurred in the 1990s. CFR01_AE spread via heterosexual behavior, then among persons connected with non-Japanese, IVDU, and MSM. Phylogenetic analysis demonstrated that some viral variants are largely restricted to Japan, while others have a broad geographic distribution.
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Clustered epitopes within a new poly-epitopic HIV-1 DNA vaccine shows immunogenicity in BALB/c mice. Mol Biol Rep 2014; 41:5207-14. [PMID: 24842263 DOI: 10.1007/s11033-014-3388-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
Despite a huge number of studies towards vaccine development against human immunodeficiency virus-1, no effective vaccine has been approved yet. Thus, new vaccines should be provided with new formulations. Herein, a new DNA vaccine candidate encoding conserved and immunogenic epitopes from HIV-1 antigens of tat, pol, gag and env is designed and constructed. After bioinformatics analyses to find the best epitopes and their tandem, nucleotide sequence corresponding to the designed multiepitope was synthesized and cloned into pcDNA3.1+ vector. Expression of pcDNA3.1-tat/pol/gag/env plasmid was evaluated in HEK293T cells by RT-PCR and western-blotting. Seven groups of BALB/c mice were intramuscularly immunized three times either with 50, 100, 200 µg of plasmid in 2-week intervals or with similar doses of insert-free plasmid. Two weeks after the last injection, proliferation of T cells and secretion of IL4 and IFN-γ cytokines were evaluated using Brdu and ELISA methods, respectively. Results showed the proper expression of the plasmid in protein and mRNA levels. Moreover, the designed multiepitope plasmid was capable of induction of both proliferation responses as well as IFN-γ and IL-4 cytokine production in a considerable level compared to the control groups. Overall, our primary data warranted further detailed studies on the potency of this vaccine.
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19
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Drescher SM, von Wyl V, Yang WL, Böni J, Yerly S, Shah C, Aubert V, Klimkait T, Taffé P, Furrer H, Battegay M, Ambrosioni J, Cavassini M, Bernasconi E, Vernazza PL, Ledergerber B, Günthard HF, Kouyos RD. Treatment-naive individuals are the major source of transmitted HIV-1 drug resistance in men who have sex with men in the Swiss HIV Cohort Study. Clin Infect Dis 2013; 58:285-94. [PMID: 24145874 DOI: 10.1093/cid/cit694] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) transmitted drug resistance (TDR) can compromise antiretroviral therapy (ART) and thus represents an important public health concern. Typically, sources of TDR remain unknown, but they can be characterized with molecular epidemiologic approaches. We used the highly representative Swiss HIV Cohort Study (SHCS) and linked drug resistance database (SHCS-DRDB) to analyze sources of TDR. METHODS ART-naive men who have sex with men with infection date estimates between 1996 and 2009 were chosen for surveillance of TDR in HIV-1 subtype B (N = 1674), as the SHCS-DRDB contains pre-ART genotypic resistance tests for >69% of this surveillance population. A phylogeny was inferred using pol sequences from surveillance patients and all subtype B sequences from the SHCS-DRDB (6934 additional patients). Potential sources of TDR were identified based on phylogenetic clustering, shared resistance mutations, genetic distance, and estimated infection dates. RESULTS One hundred forty of 1674 (8.4%) surveillance patients carried virus with TDR; 86 of 140 (61.4%) were assigned to clusters. Potential sources of TDR were found for 50 of 86 (58.1%) of these patients. ART-naive patients constitute 56 of 66 (84.8%) potential sources and were significantly overrepresented among sources (odds ratio, 6.43 [95% confidence interval, 3.22-12.82]; P < .001). Particularly large transmission clusters were observed for the L90M mutation, and the spread of L90M continued even after the near cessation of antiretroviral use selecting for that mutation. Three clusters showed evidence of reversion of K103N or T215Y/F. CONCLUSIONS Many individuals harboring viral TDR belonged to transmission clusters with other Swiss patients, indicating substantial domestic transmission of TDR in Switzerland. Most TDR in clusters could be linked to sources, indicating good surveillance of TDR in the SHCS-DRDB. Most TDR sources were ART naive. This, and the presence of long TDR transmission chains, suggests that resistance mutations are frequently transmitted among untreated individuals, highlighting the importance of early diagnosis and treatment.
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Affiliation(s)
- Sara M Drescher
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
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Gatanaga H, Murakoshi H, Hachiya A, Hayashida T, Chikata T, Ode H, Tsuchiya K, Sugiura W, Takiguchi M, Oka S. Naturally Selected Rilpivirine-Resistant HIV-1 Variants by Host Cellular Immunity. Clin Infect Dis 2013; 57:1051-5. [DOI: 10.1093/cid/cit430] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Prevalence and epidemiological traits of HIV infections in populations with high-risk behaviours as revealed by genetic analysis of HBV. Epidemiol Infect 2013; 141:2410-7. [PMID: 23347648 DOI: 10.1017/s0950268812003123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The prevalence and epidemiological traits of human immunodeficiency virus (HIV)/hepatitis B virus (HBV) infections in high-risk populations (HRPs) remained unclarified in Japan. We determined the prevalence of HIV, HBV and Treponema pallidum (TP) and the viral genotypes in HRPs who attended primary sexually transmitted infection (STI) clinics in Osaka province during 2006-2011. Of 7898 specimens, 133 (1·7%) were HIV positive, which was significantly higher than the figures reported by Japanese Red Cross (0·0019%) and public health centres (0·27%) in Japan. The frequency of HIV-1 subtype B was 88·7%, followed by CRF01_AE (2·3%) and C (0·8%), which were almost identical to the national trend. HBV seroprevalence was surprisingly high in the HIV-positive group (63·2%), which was significantly higher than that in the HIV-negative group (25·6%). By contrast, there was no statistical correlation between HIV and TP infection. Interestingly, the distinct HBV genotypes Ae and G were prevalent in the HIV-positive population (60·0% and 20·0%, respectively), although both were rarely detected during nationwide surveillance. The transmission of HIV and HBV appeared to occur largely within a closed community early in life. Of note, about one-quarter of HIV-positive cases would have remained untested if health professionals had not motivated individuals to undergo HIV testing. This is the first evidence-based assessment of HIV positivity and HIV/HBV co-infection in HRPs at primary STIs in Japan and the effect of the involvement of health professionals in the diagnosis of HIV infections in asymptomatic carriers. The genotyping of HBV provided valuable information for understanding HIV epidemical traits.
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Honda M. [Current status and overview of HIV/AIDS infection]. ACTA ACUST UNITED AC 2012. [PMID: 23193646 DOI: 10.3950/jibiinkoka.115.759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shiino T. Phylodynamic analysis of a viral infection network. Front Microbiol 2012; 3:278. [PMID: 22993510 PMCID: PMC3441063 DOI: 10.3389/fmicb.2012.00278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/17/2012] [Indexed: 12/30/2022] Open
Abstract
Viral infections by sexual and droplet transmission routes typically spread through a complex host-to-host contact network. Clarifying the transmission network and epidemiological parameters affecting the variations and dynamics of a specific pathogen is a major issue in the control of infectious diseases. However, conventional methods such as interview and/or classical phylogenetic analysis of viral gene sequences have inherent limitations and often fail to detect infectious clusters and transmission connections. Recent improvements in computational environments now permit the analysis of large datasets. In addition, novel analytical methods have been developed that serve to infer the evolutionary dynamics of virus genetic diversity using sample date information and sequence data. This type of framework, termed "phylodynamics," helps connect some of the missing links on viral transmission networks, which are often hard to detect by conventional methods of epidemiology. With sufficient number of sequences available, one can use this new inference method to estimate theoretical epidemiological parameters such as temporal distributions of the primary infection, fluctuation of the pathogen population size, basic reproductive number, and the mean time span of disease infectiousness. Transmission networks estimated by this framework often have the properties of a scale-free network, which are characteristic of infectious and social communication processes. Network analysis based on phylodynamics has alluded to various suggestions concerning the infection dynamics associated with a given community and/or risk behavior. In this review, I will summarize the current methods available for identifying the transmission network using phylogeny, and present an argument on the possibilities of applying the scale-free properties to these existing frameworks.
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Affiliation(s)
- Teiichiro Shiino
- Infectious Diseases Surveillance Center, National Institute of Infectious Diseases Tokyo, Japan
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Hayashida T, Gatanaga H, Takahashi Y, Negishi F, Kikuchi Y, Oka S. Trends in early and late diagnosis of HIV-1 infections in Tokyoites from 2002 to 2010. Int J Infect Dis 2012; 16:e172-7. [PMID: 22236483 DOI: 10.1016/j.ijid.2011.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 11/05/2011] [Accepted: 11/12/2011] [Indexed: 10/14/2022] Open
Abstract
OBJECTIVE The objective of this study was to delineate the trends in early and late diagnosis of HIV-1 infection in newly diagnosed Tokyoites. METHODS The BED assay was used to identify cases diagnosed at an early stage of infection. BED-positive non-AIDS cases with a CD4 cell count ≥ 200/μl were defined as cases with recent infection. The rates of AIDS and recent infection in 809 newly diagnosed Tokyoites during 2002-2010 were analyzed. RESULTS The AIDS rate was 22.5%. AIDS patients were older (40.4 years) than non-AIDS patients (35.0 years), and a smaller proportion were men who have sex with men (MSM) in AIDS patients (81.7%) than in non-AIDS patients (89.9%). The AIDS rate was persistently lower (≤ 14.3%) in ≤ 29-year-old than in ≥ 30-year-old MSM. The rate of recent infection was 24.4%. Individuals with recent infection (33.0 years old) were younger than the others (37.2 years). The rate of recent infection was lower (≤ 18.5%) in MSM aged ≥ 40 years than in those aged ≤ 39 years during the study period, except for 2007 and 2008. CONCLUSIONS Younger MSM Tokyoites appear to be aware of the risk of their sexual behavior, sufficient to take voluntary HIV testing repeatedly, resulting in early diagnosis. Older MSM did not take HIV testing frequently enough and may be a good target for campaigns promoting testing.
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Affiliation(s)
- Tsunefusa Hayashida
- AIDS Clinical Center, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
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Emerging Viral Resistance: Dealing with Uncertainty in Human Immunodeficiency Virus Chemoprophylaxis. South Med J 2011; 104:81-2. [DOI: 10.1097/smj.0b013e3182023413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Outbreak of infections by hepatitis B virus genotype A and transmission of genetic drug resistance in patients coinfected with HIV-1 in Japan. J Clin Microbiol 2011; 49:1017-24. [PMID: 21248087 DOI: 10.1128/jcm.02149-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The major routes of hepatitis B virus (HBV) infection in Japan has been mother-to-child transmission (MTCT) and blood transfusion. However, HBV cases transmitted through sexual contact are increasing, especially among HIV-1-seropositive patients. To understand the molecular epidemiology of HBV in HBV/HIV-1 coinfection, we analyzed HBV genotypes and HIV-1 subtypes in HBV/HIV-1-coinfected patients at Nagoya Medical Center from 2003 to 2007. Among 394 HIV-1-infected Japanese men having sex with men (MSM) who were newly diagnosed during the study period, 31 (7.9%) tested positive for the hepatitis B virus surface antigen. HBV sequence analyses were successful in 26 cases, with 21 (80.7%) and 5 (19.3%) cases determined as genotypes A and C, respectively. Our finding that HBV genotype A was dominant in HIV-1-seropositive patients alerts clinicians to an alternative outbreak of HBV genotype A in the HIV-1-infected MSM population and a shift in HBV genotype from C to A in Japan. The narrow genetic diversity in genotype A cases suggests that genotype A has been recently introduced into the MSM population and that sexual contacts among MSM were more active than speculated from HIV-1 tree analyses. In addition, we found a lamivudine resistance mutation in one naïve case, suggesting a risk of drug-resistant HBV transmission. As genotype A infection has a higher risk than infection with other genotypes for individuals to become HBV carriers, prevention programs are urgently needed for the target population.
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Sako A, Yasunaga H, Horiguchi H, Hashimoto H, Masaki N, Matsuda S. Acute hepatitis B in Japan: Incidence, clinical practices and health policy. Hepatol Res 2011; 41:39-45. [PMID: 21108704 DOI: 10.1111/j.1872-034x.2010.00745.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AIM The epidemiology of acute hepatitis B is unknown in many countries, and the clinical features of this disease remain unclear. In this study, we used the Diagnosis Procedure Combination (DPC) database to estimate the incidence of acute hepatitis B and investigate the clinical practices for acute hepatitis B in Japan. METHODS The DPC database is a nationwide discharge abstract and administrative claims database, covering 40% of all inpatient admissions to acute care hospitals between 1 July and 31 December each year in Japan. We identified cases with a diagnosis of acute hepatitis B between 2007 and 2008. Patient characteristics, length of stay, in-hospital mortality and total charges were determined. Clinical practice patterns were examined, including drugs used and procedures performed during hospitalization. RESULTS We identified 890 cases with acute hepatitis B among 5.85 million inpatients in the database. The mean age was 40.0 years old and 76% were male. The incidence of acute hepatitis B was estimated to be approximately 2100-2400/year (17-19/1 million people per year). Of 890 cases, 53 (6.0%) developed fulminant hepatitis and 36 (4.0%) died. Nucleos(t)ide analogs were prescribed for 226 cases (25.4%). Only 194 cases (21.8%) were tested for HIV status. CONCLUSION It is essential to monitor the trends of this communicable and preventable disease. The establishment and distribution of appropriate clinical evidence and guidelines are vital to improve the clinical practices for acute hepatitis B.
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Affiliation(s)
- Akahito Sako
- Department of Gastroenterology, National Center for Global Health and Medicine Department of Health Management and Policy, Graduate School of Medicine Department of Health Economics and Epidemiology Research, School of Public Health, University of Tokyo, Tokyo Department of Preventive Medicine and Community Health, University of Occupational and Environmental Health, Fukuoka, Japan
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Hattori J, Shiino T, Gatanaga H, Yoshida S, Watanabe D, Minami R, Sadamasu K, Kondo M, Mori H, Ueda M, Tateyama M, Ueda A, Kato S, Ito T, Oie M, Takata N, Hayashida T, Nagashima M, Matsuda M, Ibe S, Ota Y, Sasaki S, Ishigatsubo Y, Tanabe Y, Koga I, Kojima Y, Yamamoto M, Fujita J, Yokomaku Y, Koike T, Shirasaka T, Oka S, Sugiura W. Trends in transmitted drug-resistant HIV-1 and demographic characteristics of newly diagnosed patients: Nationwide surveillance from 2003 to 2008 in Japan. Antiviral Res 2010; 88:72-9. [DOI: 10.1016/j.antiviral.2010.07.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 07/12/2010] [Accepted: 07/28/2010] [Indexed: 10/19/2022]
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Hoare A, Kerr SJ, Ruxrungtham K, Ananworanich J, Law MG, Cooper DA, Phanuphak P, Wilson DP. Hidden drug resistant HIV to emerge in the era of universal treatment access in Southeast Asia. PLoS One 2010; 5:e10981. [PMID: 20544022 PMCID: PMC2882328 DOI: 10.1371/journal.pone.0010981] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 05/11/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Universal access to first-line antiretroviral therapy (ART) for HIV infection is becoming more of a reality in most low and middle income countries in Asia. However, second-line therapies are relatively scarce. METHODS AND FINDINGS We developed a mathematical model of an HIV epidemic in a Southeast Asian setting and used it to forecast the impact of treatment plans, without second-line options, on the potential degree of acquisition and transmission of drug resistant HIV strains. We show that after 10 years of universal treatment access, up to 20% of treatment-naïve individuals with HIV may have drug-resistant strains but it depends on the relative fitness of viral strains. CONCLUSIONS If viral load testing of people on ART is carried out on a yearly basis and virological failure leads to effective second-line therapy, then transmitted drug resistance could be reduced by 80%. Greater efforts are required for minimizing first-line failure, to detect virological failure earlier, and to procure access to second-line therapies.
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Affiliation(s)
- Alexander Hoare
- National Centre in HIV Epidemiology and Clinical Research, The University of New South Wales, Sydney, Australia
| | - Stephen J. Kerr
- National Centre in HIV Epidemiology and Clinical Research, The University of New South Wales, Sydney, Australia
- The HIV Netherlands Australia Thailand Research Collaboration, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Kiat Ruxrungtham
- The HIV Netherlands Australia Thailand Research Collaboration, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jintanat Ananworanich
- National Centre in HIV Epidemiology and Clinical Research, The University of New South Wales, Sydney, Australia
- The HIV Netherlands Australia Thailand Research Collaboration, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Matthew G. Law
- National Centre in HIV Epidemiology and Clinical Research, The University of New South Wales, Sydney, Australia
| | - David A. Cooper
- National Centre in HIV Epidemiology and Clinical Research, The University of New South Wales, Sydney, Australia
| | - Praphan Phanuphak
- The HIV Netherlands Australia Thailand Research Collaboration, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - David P. Wilson
- National Centre in HIV Epidemiology and Clinical Research, The University of New South Wales, Sydney, Australia
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Impact of human leukocyte antigen-B*51-restricted cytotoxic T-lymphocyte pressure on mutation patterns of nonnucleoside reverse transcriptase inhibitor resistance. AIDS 2010; 24:F15-22. [PMID: 20160632 DOI: 10.1097/qad.0b013e328337b010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The objective of this study is to determine the impact of human leukocyte antigen (HLA)-B*51-restricted cytotoxic T-lymphocyte (CTL) pressure on the development of nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance. DESIGN The prevalence of HIV-1 harboring an escape mutation, I135X, in a major epitope of HLA-B*51-restricted CTL located in reverse transcriptase is increasing worldwide. We analyzed the effects of escape mutations on the emerging mutation patterns of NNRTI resistance. METHODS Monoclonal HIV-1 sequences harboring each of the escape mutations, including I135L (HIV-1I135L), I135V (HIV-1I135V), I135T (HIV-1I135T), and I135R (HIV-1I135R) in reverse transcriptase, and a wild-type monoclonal HIV-1 (HIV-1WT) were cultured in the presence of increasing concentrations of efavirenz. Induced mutations during culture passages of the culture were analyzed. RESULTS E138K emerged during the cultural passages of HIV-1I135V, HIV-1I135T, and HIV-1I135R, but not during the passages of HIV-1WT. The combination of I135T, the most frequent escape mutation, and E138K (HIV-1I135T/E138K) conferred significant resistance to efavirenz, nevirapine, and etravirine. The HIV-1I135L/E138K and HIV-1I135R/E138K were significantly resistant to nevirapine and etravirine, respectively, though each solo of escape mutations and E138K did not confer significant resistance to NNRTI. Computational analysis indicated that I135T and E138K cooperatively extend the gap between the binding site of reverse transcriptase and NNRTI. CONCLUSION HLA-B*51-restricted CTL can induce novel mutation patterns of NNRTI resistance by selecting escape mutations. The spread of CTL escape variants may alter the mutation patterns of drug resistance.
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Sugiura W. [The current status of drug-resistant HIV and its management in Japan]. ACTA ACUST UNITED AC 2009; 98:2788-93. [PMID: 22462131 DOI: 10.2169/naika.98.2788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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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Kim CO, Chin BS, Han SH, Lee HS, Jeong SJ, Choi HK, Choi JY, Song YG, Lee JS, Kim JM. Low prevalence of drug-resistant HIV-1 in patients newly diagnosed with early stage of HIV infection in Korea. TOHOKU J EXP MED 2009; 216:259-65. [PMID: 18987460 DOI: 10.1620/tjem.216.259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There is a concern that the widespread use of antiretroviral drugs to treat HIV infections may result in the increased transmission of a drug-resistant virus. Drug resistance testing before initiating treatment among newly diagnosed HIV patients is helpful in the design of initial regimens. Although HIV infected patients have been increasing in Korea, the transmission rate of drug-resistant HIV is unknown. The aim of this study was to determine the prevalence of antiretroviral drug resistance-associated mutations in patients newly diagnosed as early stage of HIV infection in Korea. We defined patients with early HIV infections as those with confirmed diagnoses who had an indeterminate Western blot. We performed genotypic resistance testing in 66 HIV-1 subjects at an early HIV infection stage who were identified between March 2002 and June 2005. Two of the 66 subjects with early HIV infections showed major mutations associated with resistance. Major mutations by themselves reduce susceptibility to one or more drugs and occur commonly during virological failure. Minor mutations have little or no effect on susceptibility and occur only after other drug-resistance mutations. The resistant mutation of reverse-transcriptase gene was found at E44D, and the major resistant mutation of protease gene was found at M46L. Minor protease resistance mutations were seen in 52 cases. Genetic subtype analysis revealed that all subjects were infected with HIV-1 subtype B. In conclusion, the prevalence of drug-resistant HIV-1 in patients newly diagnosed with HIV in its early infection stage is not high in Korea.
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Affiliation(s)
- Chang Oh Kim
- Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea
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Hachiya A, Shimane K, Sarafianos SG, Kodama EN, Sakagami Y, Negishi F, Koizumi H, Gatanaga H, Matsuoka M, Takiguchi M, Oka S. Clinical relevance of substitutions in the connection subdomain and RNase H domain of HIV-1 reverse transcriptase from a cohort of antiretroviral treatment-naïve patients. Antiviral Res 2009; 82:115-21. [PMID: 19428602 DOI: 10.1016/j.antiviral.2009.02.189] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/27/2009] [Accepted: 02/09/2009] [Indexed: 10/21/2022]
Abstract
Some mutations in the connection subdomain of the polymerase domain and in the RNase H domain of HIV-1 reverse transcriptase (RT) have been shown to contribute to resistance to RT inhibitors. However, the clinical relevance of such mutations is not well understood. To address this point we determined the prevalence of such mutations in a cohort of antiretroviral treatment-naïve patients (n=123) and assessed whether these substitutions are associated with drug resistance in vitro and in vivo. We report here significant differences in the prevalence of substitutions among subtype B, and non-subtype B HIV isolates. Specifically, the E312Q, G333E, G335D, V365I, A371V and A376S substitutions were present in 2-6% of subtype B, whereas the G335D and A371V substitutions were commonly observed in 69% and 75% of non-B HIV-1 isolates. We observed a significant decline in the viral loads of patients that were infected with HIV-1 carrying these substitutions and were subsequently treated with triple drug regimens, even in the case where zidovudine (AZT) was included in such regimens. We show here that, generally, such single substitutions at the connection subdomain or RNase H domain have no influence on drug susceptibility in vitro by themselves. Instead, they generally enhance AZT resistance in the presence of excision-enhancing mutations (EEMs, also known as thymidine analogue-associated mutations, TAMs). However, N348I, A376S and Q509L did confer varying amounts of nevirapine resistance by themselves, even in the absence of EEMs. Our studies indicate that several connection subdomain and RNase H domain substitutions typically act as pre-therapy polymorphisms.
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Affiliation(s)
- Atsuko Hachiya
- AIDS Clinical Center, International Medical Center of Japan, 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] [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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Kousiappa I, van de Vijver DAMC, Demetriades I, Kostrikis LG. Genetic analysis of HIV type 1 strains from newly infected untreated patients in cyprus: high genetic diversity and low prevalence of drug resistance. AIDS Res Hum Retroviruses 2009; 25:23-35. [PMID: 19182918 DOI: 10.1089/aid.2008.0168] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract The molecular epidemiology of HIV-1 infection was first studied in Cyprus in the mid-1990s, but the extent of HIV-1 diversity and the prevalence of drug resistance have remained elusive. In an effort to address this issue, the present study examined HIV-1 strains isolated from 37 newly diagnosed untreated HIV-1 patients, representing 72% of the total number of newly diagnosed and drug-naive patients in the period 2003 to 2006. DNA sequences encoding the gag (p17, p24, p2, p7, p1, and p6), pol (protease and reverse transcriptase), and env (gp160) regions were amplified by RT-PCR from plasma HIV-1 RNA from all patients and sequenced using a newly designed methodology. All amplified products were studied according to established genetic methodologies to determine the genetic subtype and the prevalence of drug-resistance-associated mutations to currently available antiretroviral drugs. Analyses of the obtained viral sequences indicated that subtype A was the most common subtype present and accounted for 38% of the infections followed by subtype B (35%), subtype C (13%), CRF02_AG (8%), and subtypes D and CRF01_AE (3% each). One patient (2.7%) had an M41L/M and another patient (2.7%) an M184V amino acid substitution in the reverse transcriptase (RT) associated with high-level resistance to RT inhibitors. There were no patients with resistant mutations to protease inhibitors (PI). Additionally, one patient (2.7%) had an L44M amino acid substitution within the HR1 region of gp41 conferring resistance to the enfuvirtide (T20) fusion inhibitor. Similar to results of the 1994 molecular epidemiological study, these data demonstrate the extensive heterogeneity of HIV-1 infection in Cyprus and the low prevalence of transmitted resistance to current HIV-1 antiretroviral drugs. Taken together, these findings demonstrate that HIV-1 infection in Cyprus is being replenished by a continuous influx of new strains from many countries, establishing an ever-evolving and polyphyletic infection in the island.
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Affiliation(s)
- Ioanna Kousiappa
- Department of Biological Sciences, University of Cyprus , 1678 Nicosia, Cyprus
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Fukushima K, Ueno Y, Inoue J, Wakui Y, Obara N, Kimura O, Kido O, Nakagome Y, Kakazu E, Matsuda Y, Kogure T, Kondo Y, Nagasaki F, Yamagiwa Y, Ashino Y, Shimosegawa T. A case of HIV co-infected with hepatitis B virus precore/core deletion mutant treated by entecavir. Hepatol Res 2008; 38:842-6. [PMID: 18498361 DOI: 10.1111/j.1872-034x.2008.00332.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report a case of a HIV and hepatitis B virus (HBV)-co-infected patient to whom entecavir (ETV) was administered initially before the notification regarding the potential mutagenesis effect on HIV against the nucleoside analog. Since initial evaluations indicated the advanced stage of chronic hepatitis B and preserved numbers of peripheral CD4+ lymphocytes without the manifestation of immunodeficiency, priority was given to the management of HBV. We started HBV therapy with ETV at a dose of 0.5 mg daily without using any HIV drugs. The viral loads of both HBV and HIV-1 decreased gradually during the 5 months following the initial administration of ETV. HBV was well controlled by the gradual replacement of ETV with highly-active antiretroviral therapy against HIV with a regimen including atazanavir, emtricitabine, and tenofovir. HBV was genotyped as A2 with the quasispecies pool consisting of the -1G precore/core deletion mutant strain.
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Affiliation(s)
- Koji Fukushima
- Department of Internal Medicine, Tohoku University Hospital, Sendai, Japan
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Hayashida T, Gatanaga H, Tanuma J, Oka S. Effects of low HIV type 1 load and antiretroviral treatment on IgG-capture BED-enzyme immunoassay. AIDS Res Hum Retroviruses 2008; 24:495-8. [PMID: 18327979 DOI: 10.1089/aid.2007.0150] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The IgG-capture BED-enzyme immunoassay (BED-CEIA) is used widely at present to detect recent HIV-1 seroconversion. However, antibody levels and antibody kinetics are impacted by HIV-1 load and antiretroviral treatment, which may have a significant effect on the assay results. In this study, we analyzed serial samples from 11 patients with recent infection, including four patients treated by structured treatment interruption (STI), and compared the results with those of 10 untreated and 7 treated patients with chronic infection. The BED-CEIA missidentified one long-term nonprogressor hemophiliac with an extremely low HIV-1 load and five patients with chronic infection who received antiretroviral treatment. We also found that the ODn values increased slowly in patients with recent infection and low HIV-1 loads and that the ODn values fluctuated in parallel with HIV-1 load during STI. Our data indicate that the results of BED-CEIA are influenced by HIV-1 load and antiretroviral treatment. Care should be taken when interpreting the results of BED-CEIA, especially in individuals with low HIV-1 loads. Those on antiretroviral treatment should be excluded from BED-CEIA testing to improve the predictive value of detecting recent infections.
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Affiliation(s)
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, International Medical Center of Japan, Tokyo, Japan
| | - Junko Tanuma
- AIDS Clinical Center, International Medical Center of Japan, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, International Medical Center of Japan, Tokyo, Japan
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Gatanaga H. [Clinical use of anti-HIV agents]. Nihon Yakurigaku Zasshi 2007; 130:152-6. [PMID: 17690498 DOI: 10.1254/fpj.130.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
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