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https://www.readbyqxmd.com/read/27920481/new-real-time-pcr-method-to-identify-single-point-mutations-in-hepatitis-c-virus
#1
Qian Chen, Irene Belmonte, Maria Buti, Leonardo Nieto, Damir Garcia-Cehic, Josep Gregori, Celia Perales, Laura Ordeig, Meritxell Llorens, Maria Eugenia Soria, Rafael Esteban, Juan Ignacio Esteban, Francisco Rodriguez-Frias, Josep Quer
AIM: To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus (HCV). METHODS: In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir...
November 21, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27917342/genomic-studies-of-envelope-gene-sequences-from-mosquito-and-human-samples-from-bangkok-thailand
#2
Pannamthip Pitaksajjakul, Surachet Benjathummarak, Hyun Ngoc Son, Supatra Thongrungkiat, Pongrama Ramasoota
Dengue virus (DENV) is an RNA virus showing a high degree of genetic variation as a consequence of its proofreading inability. This variation plays an important role in virus evolution and pathogenesis. Although levels of within-host genetic variation are similar following equilibrium, variation among different hosts is frequently different. To identify dengue quasispecies present among two hosts, we collected patient samples from six acute DENV cases and two pools of Aedes aegypti mosquitoes and analyzed the genetic variation of regions of the viral envelope gene...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27903277/sequence-diversity-of-dengue-virus-type-2-in-brain-and-thymus-of-infected-interferon-receptor-ko-mice-implications-for-dengue-virulence
#3
Priya Dhole, Emi E Nakayama, Akatsuki Saito, Kriengsak Limkittikul, Supranee Phanthanawiboon, Tatsuo Shioda, Takeshi Kurosu
BACKGROUND: We previously reported that a clinical isolate of dengue virus (DENV) is capable of causing acute-phase systemic infection in mice harboring knockouts of the genes encoding type-I and -II interferon IFN receptors (IFN-α/β/γR KO mice); in contrast, other virulent DENV isolates exhibited slow disease progression in this mice, yielding lethal infection around 20 days post-infection (p.i.). In the present study, we sought to clarify the dynamics of slow disease progression by examining disease progression of a type-2 DENV clinical isolate (DV2P04/08) in mice...
November 30, 2016: Virology Journal
https://www.readbyqxmd.com/read/27902354/humoral-immune-system-targets-clonotypic-antibody-associated-hepatitis-c-virus
#4
Amruta S Naik, Brendan A Palmer, Orla Crossbie, Elizabeth Kenny-Walsh, Liam J Fanning
Hypervariable region 1 (HVR1) is one of the potential neutralisation domains in the E2 glycoprotein of Hepatitis C virus (HCV). Point mutations of the HVR1 can lead to humoral immune escape in HCV infected patients. In this study we segregated the chronically infected viraemic sera from HCV infected patients into populations of antibody free virus (AFV) and antibody associated virus (AAV) and mapped potential epitopes within the E1E2 gene junction of AAV sequences (residues 364-430). Furthermore, we generated pseudotyped HCV particles (HCVpp) derived from AAV sequence to assess their infectivity...
November 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27899444/antigen-dependent-competition-shapes-the-local-repertoire-of-tissue-resident-memory-cd8-t-cells
#5
Andreas Muschaweckh, Veit R Buchholz, Anne Fellenzer, Christian Hessel, Paul-Albert König, Sha Tao, Ronny Tao, Mathias Heikenwälder, Dirk H Busch, Thomas Korn, Wolfgang Kastenmüller, Ingo Drexler, Georg Gasteiger
Tissue-resident memory CD8(+) T cells (TRM) constitute a major component of the immune-surveillance system in nonlymphoid organs. Local, noncognate factors are both necessary and sufficient to support the programming of TRM cell fate in tissue-infiltrating T cells. Recent evidence suggests that TCR signals received in infected nonlymphoid tissues additionally contribute to TRM cell formation. Here, we asked how antigen-dependent pathways influence the generation of skin-resident memory T cells that arise from a polyclonal repertoire of cells induced by infection with an antigenically complex virus and recombinant vaccine vector...
November 29, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27893822/deciphering-multiplicity-of-hiv-1c-infection-transmission-of-closely-related-multiple-viral-lineages
#6
Vlad Novitsky, Sikhulile Moyo, Rui Wang, Simani Gaseitsiwe, M Essex
BACKGROUND: A single viral variant is transmitted in the majority of HIV infections. However, about 20% of heterosexually transmitted HIV infections are caused by multiple viral variants. Detection of transmitted HIV variants is not trivial, as it involves analysis of multiple viral sequences representing intra-host HIV-1 quasispecies. METHODOLOGY: We distinguish two types of multiple virus transmission in HIV infection: (1) HIV transmission from the same source, and (2) transmission from different sources...
2016: PloS One
https://www.readbyqxmd.com/read/27888038/evidence-of-bottleneck-effect-on-hepatitis-c-virus-transmission-between-a-couple-under-interferon-based-therapy
#7
Rafael Alves da Silva, Isabel Maria Vicente Guedes de Carvalho, Renata Prandini Adum de Matos, Lilian Hiromi Tomonari Yamasaki, Cíntia Bittar, Paula Rahal, Ana Carolina Gomes Jardim
Issues on the correlation of viral genetic diversity and treatment response to the hepatitis C infection remain uncertain. The bottleneck effect dictates the characteristics of the viral population that will establish the infection in a new host and is related to how the immune system and treatment will be effective against the virus. Here we evaluated the phylogenetic characteristics of quasispecies population and the treatment response pattern of a HCV infected couple. We also analyzed whether the viral population of these patients indicated that they were exposed to the same source for primer infection...
November 22, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27885563/quasispecies-composition-and-diversity-do-not-reveal-any-predictors-for-chronic-classical-swine-fever-virus-infection
#8
Maria Jenckel, Sandra Blome, Martin Beer, Dirk Höper
Classical swine fever (CSF) can run acute, chronic, and prenatal courses in both domestic pigs and wild boar. Although chronic infections are rare events, their epidemiological impact is very high due to the long-term shedding of virus. So far, little is known about the factors that influence disease course and outcome from either the host or virus's perspective. To elucidate the viral determinants, we analyzed the role of the viral populations for the development of chronic CSF virus (CSFV) infections. Three different animal trials that had led to both chronic and acute infections were chosen for a detailed analysis by deep sequencing...
November 24, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27884765/efficacy-of-clarithromycin-naproxen-oseltamivir-combination-in-the-treatment-of-patients-hospitalized-for-influenza-a-h3n2-infection-an-open-label-randomized-controlled-phase-2b-3-trial
#9
Ivan Fn Hung, Kelvin Kw To, Jasper Fw Chan, Vincent Cc Cheng, Kevin Sh Liu, Anthony Tam, Tuen-Ching Chan, Anna Jinxia Zhang, Patrick Li, Tin-Lun Wong, Ricky Zhang, Michael Ks Cheung, William Leung, Johnson Yn Lau, Manson Fok, Honglin Chen, Kwok-Hung Chan, Kwok-Yung Yuen
BACKGROUND: Influenza causes excessive hospitalizations and deaths. Single agent treatment with oseltamivir in severe influenza might be insufficient. The study assessed the efficacy and safety of oseltamivir-clarithromycin-naproxen combination for treatment of serious influenza. METHODS: From February to April 2015, we conducted a prospective open-label randomized-controlled trial. Adult patients hospitalized for A(H3N2) influenza were randomly assigned to a 2-day combination of clarithromycin 500mg, naproxen 200mg and oseltamivir 75mg twice daily, followed by 3 days of oseltamivir; or oseltamivir 75mg twice daily without placebos for 5 days as control (1:1)...
November 21, 2016: Chest
https://www.readbyqxmd.com/read/27824315/association-study-between-mannose-binding-lectin-haplotypes-and-x-gene-mutation-of-hepatitis-b-virus-from-treatment-na%C3%A3-ve-patients
#10
Chenghao Su, Yong Lin, Qianguo Mao, Daitze Wu, Lina Zhu, Isabel Najera, Fernando Garcia-Alcalde, Jianjun Niu
Mannose binding lectin (MBL) plays important role in the innate immunity of human. Mutations in the MBL2 gene can significantly change the serum level of MBL, and consequently alter the susceptibility and progression of infectious disease. However, the association between the MBL2 profile and the HBV mutation and quasispecies complexity has not yet been reported. Our approach includes the study of the MBL2 gene genotype as well as ultra-deep sequencing of the HBV viruses obtained from the plasma of 50 treatment naïve patients with chronic HBV infection...
November 7, 2016: Aging
https://www.readbyqxmd.com/read/27816216/hepatitis-c-virus-transmission-in-a-skilled-nursing-facility-north-dakota-2013
#11
Dinorah L Calles, Melissa G Collier, Yury Khudyakov, Tonya Mixson-Hayden, Lindsey VanderBusch, Sarah Weninger, Tracy K Miller
BACKGROUND: From March-May 2013, 3 cases of acute hepatitis C virus (HCV) infection were diagnosed among elderly patients residing at the same skilled nursing facility (facility A) and who received health care at hospital X during their likely exposure period. METHODS: We performed HCV testing of at-risk populations; quasispecies analysis was performed to determine relatedness of HCV in persons with current infection. Infection control practice assessments were conducted at facility A and hospital X...
November 2, 2016: American Journal of Infection Control
https://www.readbyqxmd.com/read/27808108/improving-virus-production-through-quasispecies-genomic-selection-and-molecular-breeding
#12
Francisco J Pérez-Rodríguez, Lucía D'Andrea, Montserrat de Castellarnau, Maria Isabel Costafreda, Susana Guix, Enric Ribes, Josep Quer, Josep Gregori, Albert Bosch, Rosa M Pintó
Virus production still is a challenging issue in antigen manufacture, particularly with slow-growing viruses. Deep-sequencing of genomic regions indicative of efficient replication may be used to identify high-fitness minority individuals suppressed by the ensemble of mutants in a virus quasispecies. Molecular breeding of quasispecies containing colonizer individuals, under regimes allowing more than one replicative cycle, is a strategy to select the fittest competitors among the colonizers. A slow-growing cell culture-adapted hepatitis A virus strain was employed as a model for this strategy...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27795410/deep-sequence-identification-and-role-in-virus-replication-of-a-jc-virus-quasispecies-in-patients-with-progressive-multifocal-leukoencephalopathy
#13
Kenta Takahashi, Tsuyoshi Sekizuka, Hitomi Fukumoto, Kazuo Nakamichi, Tadaki Suzuki, Yuko Sato, Hideki Hasegawa, Makoto Kuroda, Harutaka Katano
: JC virus (JCV) is a DNA virus causing progressive multifocal leukoencephalopathy (PML) in immunodeficient patients. In the present study, 22 genetic quasispecies with more than 1.5% variant frequency were detected in JCV genomes from six clinical samples of PML by next-generation sequencing. A mutation from A to C at nt 3495 in JCV Mad1 resulting in a V to G amino acid substitution at aa position 392 of the large T antigen (TAg) was identified in all six cases of PML at 3%-19% variant frequencies...
October 19, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27794054/gp85-genetic-diversity-of-avian-leukosis-virus-subgroup-j-among-different-individual-chickens-from-a-native-flock
#14
Yang Li, Jiayuan Fu, Shuai Cui, Fanfeng Meng, Zhizhong Cui, Jianhua Fan, Shuang Chang, Peng Zhao
To compare the genetic diversity and quasispecies evolution of avian leukosis virus (ALV) among different individuals, 5 chickens, raised in Shandong Provice of China, were randomly selected from a local chicken flock associated with serious tumor cases. Blood samples were collected and inoculated into chicken embryo fibroblast and DF-1 cell lines for virus isolation and identification, respectively, of Marek's disease virus (MDV), reticuloendotheliosis virus (REV), and ALV. Five strains of ALV subgroup J (ALV-J) were identified, and the gp85 gene from each strain was amplified and cloned...
October 28, 2016: Poultry Science
https://www.readbyqxmd.com/read/27791274/hiv-sequence-diversity-during-the-early-phase-of-infection-is-associated-with-hiv-dna-reductions-during-antiretroviral-therapy
#15
Nidan Wang, Yijia Li, Yang Han, Jing Xie, Taisheng Li
BACKGROUND: The association between baseline human immunodeficiency virus (HIV) sequence diversity and HIV DNA decay after the initiation of antiretroviral therapy (ART) remains uncharacterized during the early stages of HIV infection. METHOD: Samples were obtained from a cohort of 17 patients with early HIV infection (<6 months after infection) who initiated ART, and the C2V5 region of the HIV-1 envelope (env) gene was amplified via single genome amplification (SGA) to determine the peripheral plasma HIV quasispecies...
October 28, 2016: Journal of Medical Virology
https://www.readbyqxmd.com/read/27787680/identification-of-a-new-hepatitis-b-virus-recombinant-d2-d3-in-the-city-of-s%C3%A3-o-paulo-brazil
#16
Luiz Claudio Santana, Nathalia Pena Mantovani, Maira Cicero Ferreira, Rafael Arnold, Rodrigo Lopes Sanz Duro, Paulo Roberto Abrão Ferreira, James Richard Hunter, Élcio Leal, Ricardo Sobhie Diaz, Shirley Vasconcelos Komninakis
Two hundred forty million people are chronically infected with hepatitis B virus (HBV) worldwide. The rise of globalization has facilitated the emergence of novel HBV recombinants and genotypes. We evaluated HBV genotypes and recombinants, mutations associated with resistance to antivirals (AVs), progression of hepatic illness, and inefficient hepatitis B vaccination responses in chronically infected individuals in the city of São Paulo, Brazil. Forty-five full-length and 24 partial-length sequences were obtained...
October 27, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27764731/my-cousin-my-enemy-quasispecies-suppression-of-drug-resistance
#17
Karla Kirkegaard, Nicholas J van Buuren, Roberto Mateo
If a freshly minted genome contains a mutation that confers drug resistance, will it be selected in the presence of the drug? Not necessarily. During viral infections, newly synthesized viral genomes occupy the same cells as parent and other progeny genomes. If the antiviral target is chosen so that the drug-resistant progeny's growth is dominantly inhibited by the drug-susceptible members of its intracellular family, its outgrowth can be suppressed. Precedent for 'dominant drug targeting' as a deliberate approach to suppress the outgrowth of inhibitor-resistant viruses has been established for envelope variants of vesicular stomatitis virus and for capsid variants of poliovirus and dengue virus...
October 17, 2016: Current Opinion in Virology
https://www.readbyqxmd.com/read/27725416/sequence-diversity-and-associated-pathogenicity-of-the-hemagglutinin-cleavage-site-of-h5n2-avian-influenza-viruses-isolated-from-chickens-in-taiwan-during-2013-2015
#18
Kuang-Po Li, Poa-Chun Chang, Ming-Chu Cheng, Duen-Huey Tan, Li-Hsuan Chen, Yu-Pin Liu, Yu-Ju Lin, Hsiang-Jung Tsai, Jui-Hung Shien
The sequence at the hemagglutinin (HA) cleavage site (CS) plays a key role in determining the pathogenicity of avian influenza viruses. Three types of HA CS sequences, QREKR/GL, QRKKR/GL and QRRKR/GL, were previously reported in Taiwanese H5N2 viruses that were isolated from chickens from 2003 to 2013. However, no HA CS sequence was reported for viruses isolated after 2013. This article presents the HA CS sequences and pathogenicity of H5N2 viruses that were isolated from chickens in Taiwan during 2013-2015...
October 3, 2016: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/27722049/characteristics-of-cpg-islands-and-their-quasispecies-of-full-length-hepatitis-b-virus-genomes-from-patients-at-different-phases-of-infection
#19
Yuan Xue, Ming-Jie Wang, Su-Yuan Huang, Zhi-Tao Yang, De-Min Yu, Yue Han, Ming-Yu Zhu, Dao Huang, Dong-Hua Zhang, Qi-Ming Gong, Xin-Xin Zhang
BACKGROUND: CpG islands in hepatitis B virus (HBV) genome are potential targets for methylation mediated gene silencing, and may be involved in the pathogenesis of HBV infection. To date, their characteristics in HBV quasispecies (QS) remain largely unknown. The purpose of this study was to investigate the characteristics of CpG islands in HBV QS. METHODS: Forty patients diagnosed as acute hepatitis B (AHB, n = 10), immune-tolerant HBV carriers (IT, n = 9), chronic hepatitis B (CHB, n = 11), or acute on chronic liver failure (ACLF, n = 10), were enrolled in this case-control study...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27714432/abrupt-transitions-to-tumor-extinction-a-phenotypic-quasispecies-model
#20
Josep Sardanyés, Regina Martínez, Carles Simó, Ricard Solé
The dynamics of heterogeneous tumor cell populations competing with healthy cells is an important topic in cancer research with deep implications in biomedicine. Multitude of theoretical and computational models have addressed this issue, especially focusing on the nature of the transitions governing tumor clearance as some relevant model parameters are tuned. In this contribution, we analyze a mathematical model of unstable tumor progression using the quasispecies framework. Our aim is to define a minimal model incorporating the dynamics of competition between healthy cells and a heterogeneous population of cancer cell phenotypes involving changes in replication-related genes (i...
October 6, 2016: Journal of Mathematical Biology
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