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HIV sequence

Noboru Hirashima, Hiroaki Iwase, Masaaki Shimada, Nobumitsu Ryuge, Junji Imamura, Hiroki Ikeda, Yasuhito Tanaka, Nobuyuki Matsumoto, Chiaki Okuse, Fumio Itoh, Yoshiyuki Yokomaku, Tsunamasa Watanabe
Co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) often accelerates the course of HCV-associated liver disease. Daclatasvir (DCV) plus asunaprevir (ASV) have been shown to be highly effective for HCV-infected patients with genotype 1b. Three patients co-infected with HIV/HCV genotype 1b were enrolled in this study. Prior to initiation of HCV treatment, the variants associated with L31 and Y93 in the non-structural protein 5A (NS5A) region of the HCV genome were confirmed to be absent using a direct sequencing method...
October 20, 2016: Clinical Journal of Gastroenterology
Sutas Suttiprapa, Gabriel Rinaldi, Isheng J Tsai, Victoria H Mann, Larisa Dubrovsky, Hong-Bin Yan, Nancy Holroyd, Thomas Huckvale, Caroline Durrant, Anna V Protasio, Tatiana Pushkarsky, Sergey Iordanskiy, Matthew Berriman, Michael I Bukrinsky, Paul J Brindley
Schistosomiasis is the most important helminthic disease of humanity in terms of morbidity and mortality. Facile manipulation of schistosomes using lentiviruses would enable advances in functional genomics in these and related neglected tropical diseases pathogens including tapeworms, and including their non-dividing cells. Such approaches have hitherto been unavailable. Blood stream forms of the human blood fluke, Schistosoma mansoni, the causative agent of the hepatointestinal schistosomiasis, were infected with the human HIV-1 isolate NL4-3 pseudotyped with vesicular stomatitis virus glycoprotein...
October 2016: PLoS Pathogens
Wenjun Zhang, Junfang Chen, Xiao Hong Pan, Jiafeng Zhang, Zhihong Guo, Yan Luo, Jiezhe Yang, Yan Xia, Lin He, Yun Xu, Ke Xu, Xiaobei Ding
OBJECTIVE: To investigate the HIV-1 molecular epidemiology among young people (18 to 25 years old) in Hangzhou. METHODS: Plasma samples from 262 newly diagnosed HIV-1 infected patients were collected between 2009 and 2013 from Hangzhou of Zhejiang province. HIV-1 nucleotide sequences of pol gene regions were amplified using a nested PCR method and sequenced. Phylogenetic and recombination analyses were used to determine the HIV-1 genotypes. RESULTS: Based on all sequences generated, the subtype/circulating recombinant forms (CRF) distribution was as follows: CRF01_AE (68...
October 20, 2016: AIDS Research and Human Retroviruses
Yihong Hu, Zhenzhou Wan, Yan-Heng Zhou, Davey M Smith, Yong-Tang Zheng, Chiyu Zhang
The on-going generation of HIV-1 inter-subtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. Here, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URFs sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3.5.1...
October 20, 2016: AIDS Research and Human Retroviruses
Elizabeth Wolf, Joshua Herbeck, Stephen Van Rompaey, Mari M Kitahata, Katherine K Thomas, Gregory Pepper, Lisa Frenkel
HIV-1 incidence among youth, especially men who have sex with men (MSM), is increasing in the US. We aimed to better understand the patterns of adolescent HIV-1 acquisition, in order to help guide future prevention interventions. We conducted a study combining epidemiologic and HIV-1 pol sequence data from a retrospective cohort of HIV-infected adults and adolescents in Seattle, WA between 2000 and 2013. Adolescents were defined as 13-24 years of age at the time of first HIV-1 care. Maximum-likelihood phylogenetic trees were reconstructed to identify putative viral transmission clusters of two or more individuals, followed by multivariable regression tests of associations between clustering and demographic and clinical parameters...
October 20, 2016: AIDS Research and Human Retroviruses
K V Shur, M V Zaychikova, N E Mikheecheva, K M Klimina, O B Bekker, S N Zhdanova, O B Ogarkov, V N Danilenko
We report a draft genome sequence of Mycobacterium tuberculosis strain B9741 belonging to Beijing B0/W lineage isolated from a HIV patient from Siberia, Russia. This clinical isolate showed MDR phenotype and resistance to isoniazid, rifampin, streptomycin and pyrazinamide. We analyzed SNPs associated with virulence and resistance. The draft genome sequence and annotation have been deposited at GenBank under the accession NZ_LVJJ00000000.
December 2016: Genomics Data
Rosemary Fama, Edith V Sullivan, Stephanie A Sassoon, Adolf Pfefferbaum, Natalie M Zahr
BACKGROUND: Executive functioning and episodic memory impairment occur in HIV infection (HIV) and chronic alcoholism (ALC). Comorbidity of these conditions (HIV + ALC) is prevalent and heightens risk of vulnerability to separate and compounded deficits. Age and disease-related variables can also serve as mediators of cognitive impairment and should be considered, given the extended longevity of HIV-infected individuals in this era of improved pharmacological therapy. METHODS: HIV, ALC, HIV + ALC, and normal controls (NC) were administered traditional and computerized tests of executive function and episodic memory...
October 19, 2016: Alcoholism, Clinical and Experimental Research
Sa Liu, Yulong Chen, Shiping Xie, Qianlei Xu, Jianshe Chen, Changhai Wang, Zhao Wang, Suna Ma, Xingwei Wu, Ning Zhang
OBJECTIVES: Traditional Chinese Medicine (TCM) applied in the clinic as a complementary and alternative therapy has helped improve immunity and reduce side effects and symptomatic treatment in patients with HIV/AIDS. However, the mechanisms of TCM syndromes are not clear. Transcriptomics enables the study of such TCM syndromes. DESIGN: This study compared the messenger RNA (mRNA) expressions of healthy persons and patients with HIV/AIDS who had two common TCM syndromes, qi-yin deficiency and dampness-heat retention, to find the difference in HIV/AIDS with TCM syndromes...
October 19, 2016: Journal of Alternative and Complementary Medicine: Research on Paradigm, Practice, and Policy
Julie Yamaguchi, Catherine A Brennan, Elodie Alessandri, Jean-Christophe Plantier, Gavin Cloherty, Michael G Berg
HIV-2 exhibits a natural history of infection distinct from HIV-1. Primarily found in West Africa and in only 10-20% of HIV infections in this region, patients with HIV-2 typically exhibit a slower progression to AIDS, lower viral loads, and decreased rates of transmission. Here we used next-generation sequencing (NGS) to determine the sequence and phylogenetic classification of 9 HIV-2 genomes. We identified a patient with a series of mutations in an invariant cytotoxic lymphocyte (CTL)-restricted gag epitope required for retroviral structure and replication, and implicated in long-term non-progression to AIDS...
October 19, 2016: AIDS Research and Human Retroviruses
T Hertz, M G Logan, M Rolland, C A Magaret, C Rademeyer, A Fiore-Gartland, P T Edlefsen, A DeCamp, H Ahmed, N Ngandu, B B Larsen, N Frahm, J Marais, R Thebus, D Geraghty, J Hural, L Corey, J Kublin, G Gray, M J McElrath, J I Mullins, P B Gilbert, C Williamson
INTRODUCTION: The Merck Adenovirus-5 Gag/Pol/Nef HIV-1 subtype-B vaccine evaluated in predominately subtype B epidemic regions (Step Study), while not preventing infection, exerted vaccine-induced immune pressure on HIV-1 breakthrough infections. Here we investigated if the same vaccine exerted immune pressure when tested in the Phambili Phase 2b study in a subtype C epidemic. MATERIALS AND METHODS: A sieve analysis, which compares breakthrough viruses from placebo and vaccine arms, was performed on 277 near full-length genomes generated from 23 vaccine and 20 placebo recipients...
October 15, 2016: Vaccine
Zhonglan Wu, Lijia Cui, Weiming Zhao, Dongzhi Yang, Hui Chen, Ruiqing Wang, Xuemin Wang, Linqi Zhang, Tianhua He
BACKGROUND: Current prevalence and genotype distribution of hepatitis C virus (HCV) infection remain unknown in Ningxia, northwest China. METHODS: From June to December 2013, 13,022 individuals were screened in Ningxia HIV/AIDS Sentinel Surveillance System, with their demographic features collected and serum samples tested for HCV antibody. Sero-positive drug users were further subjected to sequencing of NS5B and Core regions of HCV. RESULTS: The anti-HCV prevalence was 0...
October 18, 2016: Virology Journal
Denis R Chopera, Roman Ntale, Nonkululeko Ndabambi, Nigel Garrett, Clive M Gray, David Matten, Quarraisha Abdool Karim, Salim Abdool Karim, Carolyn Williamson
OBJECTIVE: HIV-1 escape from cytotoxic T-lymphocytes (CTL) results in the accumulation of HLA-associated mutations in the viral genome. To understand the contribution of early escape to disease progression, this study investigated the evolution and pathogenic implications of CTL escape in a cohort followed from infection for five years. METHODS: Viral loads and CD4+ counts were monitored in 78 subtype C infected individuals from onset of infection until CD4+ decline to <350 cells/μl or five years post-infection...
October 14, 2016: AIDS
Martin Hoenigl, Josué Pérez-Santiago, Masato Nakazawa, Michelli Faria de Oliveira, Yonglong Zhang, Malcolm A Finkelman, Scott Letendre, Davey Smith, Sara Gianella
BACKGROUND: The extent of gut microbial translocation, which plays roles in HIV disease progression and non-AIDS comorbidities, appears to vary with the composition of the gut microbiome, particularly the presence of Lactobacillales, which reduce mucosal injury. While low proportions of Lactobacillales in the distal gut microbiome are a very promising indicator of microbial translocation, measurement is expensive and complicated and not feasible for clinical routine. (1→3)-β-d-Glucan (BDG) is a component of most fungal cell walls and might be a surrogate marker for Lactobacillales proportion in the gut and a useful indicator of HIV-associated gut injury...
2016: Frontiers in Immunology
Jian Huang, Lei Zhao, Ping Yang, Zhen Chen, Ni Tang, Xiong Z Ruan, Yaxi Chen
Hepatitis B virus (HBV) is a hepatocyte-specific DNA virus whose gene expression and replication are closely associated with hepatic metabolic processes. Thus, a potential anti-viral strategy is to target the host metabolic factors necessary for HBV gene expression and replication. Recent studies revealed that fatty acid translocase CD36 is involved in the replication, assembly, storage, and secretion of certain viruses, such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV). However, the relationship between CD36 and the HBV life cycle remains unclear...
2016: PloS One
Bingjie Shi, Juan Li, Xuanling Shi, Wenxu Jia, Yi Wen, Xiongbing Hu, Fengfeng Zhuang, Jianzhong Xi, Linqi Zhang
Transcription activator-like effector nuclease (TALEN) represents a valuable tool for genomic engineering due to its single-nucleotide precision, high nuclease activity and low cytotoxicity. We report here systematic design and characterization of twenty eight novel TALENs targeting multiple regions of CCR5 gene (CCR5-TALEN) which encodes the co-receptor critical for entry of human immunodeficiency virus type I (HIV-1). By systemic characterization of these CCR5-TALENs, we have identified one (CCR5-TALEN-515) with higher nuclease activity, specificity and lower cytotoxicity compared to zinc-finger nuclease (CCR5-ZFN) currently undergoing clinical trials...
October 3, 2016: Journal of Acquired Immune Deficiency Syndromes: JAIDS
Charles Béguelin, Darius Moradpour, Roland Sahli, Franziska Suter-Riniker, Alexander Lüthi, Matthias Cavassini, Huldrych F Günthard, Manuel Battegay, Enos Bernasconi, Patrick Schmid, Alexandra Calmy, Dominique Braun, Hansjakob Furrer, Andri Rauch, Gilles Wandeler
BACKGROUND AND AIMS: Hepatitis delta virus (HDV) infection accelerates the progression of hepatitis B virus (HBV)-related liver disease. We assessed the epidemiological characteristics of HDV infection in the nationwide Swiss HIV Cohort Study and evaluated its impact on clinical outcomes. METHODS: All HIV-infected patients with a positive HBsAg test were considered and tested for anti-HDV antibodies. HDV amplification and sequencing were performed in anti-HDV-positive patients...
October 13, 2016: Journal of Hepatology
Emma Cunningham, Yuen-Ting Chan, Adamma Aghaizu, David F Bibby, Gary Murphy, Jennifer Tosswill, Ross J Harris, Richard Myers, Nigel Field, Valerie Delpech, Patricia A Cane, O Noel Gill, Jean L Mbisa
OBJECTIVES: To determine the prevalence of inferred low-frequency HIV-1 transmitted drug resistance (TDR) in MSM in the UK and its predicted effect on first-line therapy. METHODS: The HIV-1 pol gene was amplified from 442 newly diagnosed MSM identified as likely recently infected by serological avidity testing in 2011-13. The PCR products were sequenced by next-generation sequencing with a mutation frequency threshold of >2% and TDR mutations defined according to the 2009 WHO surveillance drug resistance mutations list...
October 14, 2016: Journal of Antimicrobial Chemotherapy
Santiago Avila-Ríos, Claudia García-Morales, Margarita Matías-Florentino, Daniela Tapia-Trejo, Bismarck F Hernández-Álvarez, Sumaya E Moreira-López, Carlos J Quant-Durán, Guillermo Porras-Cortés, Gustavo Reyes-Terán
BACKGROUND: Increasing HIV pre-treatment drug resistance (PDR) levels have been observed in regions with increasing antiretroviral treatment (ART) coverage. However, data is lacking for several low/middle-income countries. We present the first PDR survey in Nicaragua since ART introduction in the country in 2003. METHODS: HIV-infected, ART-naïve Nicaraguan individuals were enrolled at Roberto Calderón Hospital, the largest national HIV referral center, from 2011 to 2015...
2016: PloS One
Xintao Hu, Antonio Valentin, Frances Dayton, Viraj Kulkarni, Candido Alicea, Margherita Rosati, Bhabadeb Chowdhury, Rajeev Gautam, Kate E Broderick, Niranjan Y Sardesai, Malcolm A Martin, James I Mullins, George N Pavlakis, Barbara K Felber
HIV sequence diversity and the propensity of eliciting immunodominant responses targeting variable regions of the HIV proteome are hurdles in the development of an effective AIDS vaccine. An HIV-derived conserved element (CE) p24(gag) plasmid DNA (pDNA) vaccine is able to redirect immunodominant responses to otherwise subdominant and often more vulnerable viral targets. By homology to the HIV immunogen, seven CE were identified in SIV p27(Gag) Analysis of 31 rhesus macaques vaccinated with full-length SIV gag pDNA showed inefficient induction (58% response rate) of cellular responses targeting these CE...
October 12, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
M L Mzingwane, C T Tiemessen, K L Richter, S H Mayaphi, G Hunt, S M Bowyer
BACKGROUND: Although the use of highly active antiretroviral therapy in HIV positive individuals has proved to be effective in suppressing the virus to below detection limits of commonly used assays, virological failure associated with drug resistance is still a major challenge in some settings. The prevalence and effect of pre-treatment resistance associated variants on virological outcomes may also be underestimated because of reliance on conventional population sequencing data which excludes minority species...
October 12, 2016: Virology Journal
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