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https://www.readbyqxmd.com/read/28646219/efficient-and-unbiased-metagenomic-recovery-of-rna-virus-genomes-from-human-plasma-samples
#1
Carmen F Manso, David F Bibby, Jean L Mbisa
RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses - HIV, HCV and HEV...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28644134/the-conundrum-of-the-epstein-barr-virus-associated-gastric-carcinoma-in-the-americas
#2
REVIEW
Gonzalo Carrasco-Avino, Ismael Riquelme, Oslando Padilla, Miguel Villaseca, Francisco R Aguayo, Alejandro H Corvalan
Epstein-Barr virus-associated gastric carcinoma shows a higher prevalence in the Americas than Asia. We summarize all studies of Epstein Barr virus-associated gastric carcinoma in the Americas, focusing on host characteristics, environmental associations and phylogeographic diversity of Epstein-Barr virus strains. In the Americas, the prevalence of Epstein Barr virus-associated gastric carcinoma is 11.4%, more frequent in males and portray predominantly diffuse-type histology. EBERs, EBNAs, BARTs and LMP are the highest expressed genes; their variations in healthy individuals may explain the phylogeographic diversity of Epstein-Barr virus across the region...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643180/first-complete-genome-sequences-of-genogroup-v-genotype-3-porcine-sapoviruses-common-5-terminal-genomic-feature-of-sapoviruses
#3
Tomoichiro Oka, Yen Hai Doan, Takashi Shimoike, Kei Haga, Takenori Takizawa
Sapoviruses (SaVs) are enteric viruses and have been detected in various mammals. They are divided into multiple genogroups and genotypes based on the entire major capsid protein (VP1) encoding region sequences. In this study, we determined the first complete genome sequences of two genogroup V, genotype 3 (GV.3) SaV strains detected from swine fecal samples, in combination with Illumina MiSeq sequencing of the libraries prepared from viral RNA and PCR products. The lengths of the viral genome (7494 nucleotides [nt] excluding polyA tail) and short 5'-untranslated region (14 nt) as well as two predicted open reading frames are similar to those of other SaVs...
June 22, 2017: Virus Genes
https://www.readbyqxmd.com/read/28641998/construction-of-a-hepatitis-b-virus-neutralizing-chimeric-monoclonal-antibody-recognizing-escape-mutants-of-the-viral-surface-antigen-hbsag
#4
Forough Golsaz-Shirazi, Mohammad Mehdi Amiri, Samira Farid, Motahareh Bahadori, Felix Bohne, Sebastian Altstetter, Lisa Wolff, Tohid Kazemi, Jalal Khoshnoodi, Mohammad Hojjat-Farsangi, Michael Chudy, Mahmood Jeddi-Tehrani, Ulrike Protzer, Fazel Shokri
Hepatitis B virus (HBV) infection is a global burden on the health-care system and is considered as the tenth leading cause of death in the world. Over 248 million patients are currently suffering from chronic HBV infection worldwide and annual mortality rate of this infection is 686000. The "a" determinant is a hydrophilic region present in all antigenic subtypes of hepatitis B surface antigen (HBsAg), and antibodies against this region can neutralize the virus and are protective against all subtypes. We have recently generated a murine anti-HBs monoclonal antibody (4G4), which can neutralize HBV infection in HepaRG cells and recognize most of the escape mutant forms of HBsAg...
June 19, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28641865/influence-of-baseline-meld-score-in-the-efficacy-of-treatment-of-hepatitis-c-with-simeprevir-and-sofosbuvir
#5
José María Moreno-Planas, Juan Ramón Larrubia-Marfil, Juan José Sánchez-Ruano, Julia Morillas-Ariño, Roberto Patón-Arenas, Rosa María Sáiz-Chumillas, Emilia Tébar-Romero, Alfredo Lucendo-Villarín, Pilar Gancedo-Bringas, Mario Solera-Muñoz, María Del Mar Vicente-Gutiérrez, Elisa Martínez-Alfaro
INTRODUCTION: There are few published studies on predictors of response to treatment with sofosbuvir and simeprevir in HCV patients. OBJECTIVE: The objective of the study was to analyse possible predictors of response to simeprevir (SMV) and sofosbuvir (SOF) in patients infected with hepatitis C genotypes 1 or 4. PATIENTS AND METHODS: Prospective observational cohort study in 12 hospitals. The primary efficacy endpoint was SVR rate 12 weeks after end of treatment (SVR12)...
June 19, 2017: Enfermedades Infecciosas y Microbiología Clínica
https://www.readbyqxmd.com/read/28640813/identification-of-a-sj%C3%A3-gren-s-syndrome-susceptibility-locus-at-oas1-that-influences-isoform-switching-protein-expression-and-responsiveness-to-type-i-interferons
#6
He Li, Tove Ragna Reksten, John A Ice, Jennifer A Kelly, Indra Adrianto, Astrid Rasmussen, Shaofeng Wang, Bo He, Kiely M Grundahl, Stuart B Glenn, Corinne Miceli-Richard, Simon Bowman, Sue Lester, Per Eriksson, Maija-Leena Eloranta, Johan G Brun, Lasse G Gøransson, Erna Harboe, Joel M Guthridge, Kenneth M Kaufman, Marika Kvarnström, Deborah S Cunninghame Graham, Ketan Patel, Adam J Adler, A Darise Farris, Michael T Brennan, James Chodosh, Rajaram Gopalakrishnan, Michael H Weisman, Swamy Venuturupalli, Daniel J Wallace, Kimberly S Hefner, Glen D Houston, Andrew J W Huang, Pamela J Hughes, David M Lewis, Lida Radfar, Evan S Vista, Contessa E Edgar, Michael D Rohrer, Donald U Stone, Timothy J Vyse, John B Harley, Patrick M Gaffney, Judith A James, Sean Turner, Ilias Alevizos, Juan-Manuel Anaya, Nelson L Rhodus, Barbara M Segal, Courtney G Montgomery, R Hal Scofield, Susan Kovats, Xavier Mariette, Lars Rönnblom, Torsten Witte, Maureen Rischmueller, Marie Wahren-Herlenius, Roald Omdal, Roland Jonsson, Wan-Fai Ng, Gunnel Nordmark, Christopher J Lessard, Kathy L Sivils
Sjögren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study...
June 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28640739/hepatitis-b-virus-core-antigen-mutations-predict-post-operative-prognosis-of-patients-with-primary-hepatocellular-carcinoma
#7
Jian'an Jia, Huiming Li, Hui Wang, Shipeng Chen, Mengmeng Wang, Huijuan Feng, Yuzhen Gao, Yunjiu Wang, Meng Fang, Chunfang Gao
The aim of this study was to explore the relationship between hepatitis B virus (HBV) core antigen (HBc) mutations and the post-operative prognosis of HBV-related hepatocellular carcinoma (HCC). In total, 98 patients suffering from HBV-related HCC and treated with surgery were enrolled, with a 48 month follow-up. The preCore/Core region of the HBV genome from tumour tissue (TT) and paired adjacent non-tumour tissue (ANTT) of these patients was sequenced, and a phylogenetic tree was reconstructed. The correlations between the viral features and evolutionary divergence of preCore/Core amino acid sequences from 67 paired TTs and ANTTs were analysed...
June 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28639212/surveillance-of-noroviruses-in-rio-de-janeiro-brazil-occurrence-of-new-giv-genotype-in-clinical-and-wastewater-samples
#8
Julia Monassa Fioretti, Tulio Machado Fumian, Mônica Simões Rocha, Ingrid de Arruda Lucena Dos Santos, Filipe Aníbal Carvalho-Costa, Matheus Ribeiro de Assis, Janaina de Souza Rodrigues, José Paulo Gagliardi Leite, Marize Pereira Miagostovich
Genogroup (G) IV norovirus (NoV) has been described in the literature as infectious agents in humans, although there are few reports regarding the frequency and spread of this virus, resulting in insufficient epidemiological data. The aim of this study was to investigate the occurrence of GIV norovirus in the State of Rio de Janeiro, Brazil in order to evaluate frequency, concentration, and genetic diversity using clinical and environmental approaches. For this purpose, 316 stool samples were collected from acute gastroenteritis cases reported over a period of three years...
June 21, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/28638221/prevalence-of-ifnl3-rs4803217-single-nucleotide-polymorphism-and-clinical-course-of-chronic-hepatitis-c
#9
Bogna Świątek-Kościelna, Ewelina Kałużna, Ewa Strauss, Jerzy Nowak, Iwona Bereszyńska, Ewelina Gowin, Jacek Wysocki, Jolanta Rembowska, Dominika Barcińska, Iwona Mozer-Lisewska, Danuta Januszkiewicz-Lewandowska
AIM: To evaluate the association of IFNL3 (IL28B) SNP rs4803217 with severity of disease and treatment outcome in chronic hepatitis C (CHC). METHODS: The study enrolled 196 CHC Polish patients (82 women and 114 men in age 20-64) infected with hepatitis C virus (HCV) genotype 1. They were treatment naïve and qualified to pegylated interferon alpha (PEG-IFN-α) and ribavirin (RBV) therapy. The analyzed baseline parameters included: degree of inflammation, stage of fibrosis, viral load as well as alanine aminotransferase (ALT), asparagine aminotransferase (AST) and total bilirubin (TBIL)...
June 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28637755/seasonal-h3n2-and-2009-pandemic-h1n1-influenza-a-viruses-reassort-efficiently-but-produce-attenuated-progeny
#10
Kara L Phipps, Nicolle Marshall, Hui Tao, Shamika Danzy, Nina Onuoha, John Steel, Anice C Lowen
Reassortment of gene segments between co-infecting influenza A viruses (IAV) facilitates viral diversification and has significant epidemiological impact on seasonal and pandemic influenza. Since 1977, human IAVs of H1N1 and H3N2 subtypes have co-circulated with relatively few documented cases of reassortment. We evaluated the potential for viruses of the 2009 pandemic H1N1 (pH1N1) and seasonal H3N2 lineages to reassort under experimental conditions. Results of heterologous co-infections with pH1N1 and H3N2 viruses were compared to those obtained following co-infection with homologous, genetically tagged, pH1N1 viruses as a control...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637462/outbreak-tracking-of-aleutian-mink-disease-virus-amdv-using-partial-ns1-gene-sequencing
#11
P Ryt-Hansen, C K Hjulsager, E E Hagberg, M Chriél, T Struve, A G Pedersen, L E Larsen
BACKGROUND: Aleutian Mink Disease (AMD) is an infectious disease of mink (Neovison vison) and globally a major cause of economic losses in mink farming. The disease is caused by Aleutian Mink Disease Virus (AMDV) that belongs to the genus Amdoparvovirus within the Parvoviridae family. Several strains have been described with varying virulence and the severity of infection also depends on the host's genotype and immune status. Clinical signs include respiratory distress in kits and unthriftiness and low quality of the pelts...
June 21, 2017: Virology Journal
https://www.readbyqxmd.com/read/28636636/sensiscreen%C3%A2-kras-exon-2-sensitive-simplex-and-multiplex-real-time-pcr-based-assays-for-detection-of-kras-exon-2-mutations
#12
Alice Riva, Michael BØrgesen, Mariann Guldmann-Christensen, Majbritt Hauge Kyneb, Kirsten Voogd, Christina Andersen, Samantha Epistolio, Elisabetta Merlo, Tine Yding Wolff, Stephen Hamilton-Dutoit, Jan Lorenzen, Ulf Bech Christensen, Milo Frattini
Activating mutations in codon 12 and codon 13 of the KRAS (Kirsten rat sarcoma viral oncogene homolog) gene are implicated in the development of several human cancer types and influence their clinical evaluation, treatment and prognosis. Numerous different methods for KRAS genotyping are currently available displaying a wide range of sensitivities, time to answer and requirements for laboratory equipment and user skills. Here we present SensiScreen® KRAS exon 2 simplex and multiplex CE IVD assays, that use a novel real-time PCR-based method for KRAS mutation detection based on PentaBase's proprietary DNA analogue technology and designed to work on standard real-time PCR instruments...
2017: PloS One
https://www.readbyqxmd.com/read/28634687/noninvasive-serum-models-to-predict-significant-liver-related-events-in-chronic-hepatitis-c
#13
Ragesh Babu Thandassery, Saad Al Kaabi, Madiha E Soofi, Benjamin Tharian, Rajvir Singh
AIM: We aim to compare 20 noninvasive fibrosis scores (NIFS), derived from routine blood tests, for predicting significant liver-related adverse events (SLRE) in patients with chronic hepatitis C (CHC) after anti-viral treatment (AVT) with the goal to identify independent predictors for these outcomes. METHODS: From 1605 patients who received AVT (pegylated interferon and ribavirin) from January 2002 to June 2014, 20 NIFS were calculated from routine blood tests prior to AVT...
June 20, 2017: Hepatology International
https://www.readbyqxmd.com/read/28633097/results-of-the-first-international-hiv-1-coreceptor-proficiency-panel-test
#14
Eva Heger, Rolf Kaiser, Elena Knops, Maria Neumann-Fraune, Eugen Schuelter, Alejandro Pironti, Thomas Lengauer, Hauke Walter, Saleta Sierra
BACKGROUND: Quality Assurance (QA) programs are essential to evaluate performance in diagnostics laboratories. OBJECTIVES: We present the results from the first QA for HIV-1 genotypic tropism testing, organized and coordinated by the Institute of Virology at the University of Cologne. STUDY DESIGN: 12 cell culture-derived viral strains of different HIV-1 clades from the NIH AIDS Reagent Program were sent to the participants to be processed with their standard diagnostic methods Fasta files containing the V3 region sequence were centrally analyzed at the Institute of Virology, Cologne...
June 10, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28631602/nationwide-overview-of-the-distribution-of-hepatitis-b-virus-genotypes-in-brazil-a-1000-sample-multicentre-study
#15
Elisabeth Lampe, Francisco C A Mello, Marcia P do Espírito-Santo, Cintia M C Oliveira, Dennis A Bertolini, Neiva S L Gonçales, Regina C Moreira, Carlos A S Fernandes, Haydée C L Nascimento, Rejane M T Grotto, Maria Inês M C Pardini, On Behalf Of The Brazilian Hepatitis B Research Group
The influence of hepatitis B virus (HBV) genotypes in the natural history of the disease and its response to antiviral treatment have been addressed in many studies. In Brazil, studies on HBV genotype circulation have been restricted to specific population groups and states. Here, we have conducted a nationwide multicentre study with an unprecedented sample size representing all Brazilian regions in an effort to better understand the viral variants of HBV circulating among chronic carriers. Seven HBV genotypes were found circulating in Brazil...
June 20, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28631053/characterization-of-an-orf-virus-isolate-from-an-outbreak-in-heilongjiang-province-china
#16
Yongzhong Yu, Qiang Tan, Wenbo Zhao, Xue Zhang, Jinzhu Ma, Zhijun Wu, Zhanbo Zhu, Yudong Cui
Contagious ecthyma, caused by orf virus (ORFV), is an epitheliotrophic contagious disease with zoonotic implications that mainly affects sheep, goats, wild ruminants, and humans. Recently, a novel ORFV strain, OV/HLJ/04, was successfully isolated from the skin and mucosal lesions of a goat with severe clinical sore mouth symptoms in Heilongjiang province of China. The OV/HLJ/04 isolate was characterized by electron microscopy, serological tests, and experimental reproduction of disease. The purified virions exhibited a typical ovoid shape when observed by electron microscopy...
June 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28629383/epitope-mapping-and-characterization-of-a-novel-nsp10-specific-monoclonal-antibody-that-differentiates-genotype-2-prrsv-from-genotype-1-prrsv
#17
Zhibang Zhang, Xuexia Wen, Jianguo Dong, Xinna Ge, Lei Zhou, Hanchun Yang, Xin Guo
BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV), the causative agent of PRRS, has two distinct and highly diverse genotypes (genotype 1 and genotype 2) in the field. Accurate diagnosis and differentiation of the two genotypes of PRRSV are critical to the effective prevention and control of PRRS. The non-structural protein 10 (Nsp10) plays a vital role in viral replication and is one of the most conserved proteins of PRRSV, thus constituting a good candidate for PRRSV diagnosis...
June 19, 2017: Virology Journal
https://www.readbyqxmd.com/read/28627822/development-of-a-one-step-reverse-transcription-loop-mediated-isothermal-amplification-system-for-a-highly-sensitive-detection-of-rabbit-hepatitis-e-virus
#18
Jing Wang, Hua Zhang, Shengyuan Yan, Yichao Wang, Xin Lu, Hongwei Fu
BACKGROUND: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in areas with poor sanitation. Rabbit is one of important animal reservoirs of the virus. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) system is a novel nucleic acid amplification assay, for which the specificity and sensitivity are much higher than that of conventional PCR. However, previously reported RT-LAMP system cannot detect rabbit HEV, which was identified recently and seems to be another potential source of human HEV infection...
May 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28622345/the-infection-staging-and-profile-of-genotypic-distribution-and-drug-resistance-mutation-among-the-human-immunodeficiency-virus-1-infected-blood-donors-from-five-chinese-blood-centers-2012-2014
#19
Peibin Zeng, Yu Liu, Miao He, Jingxing Wang, Sheila Keating, Wei Mao, Mei Huang, Hongli Ma, Weilan He, Xinhong Bi, Dan Liao, Michael Busch, Paul Ness, Jing Liu, Hua Shan
The increasing complexity and diversity of the human immunodeficiency virus-1 (HIV-1) infections challenge the disease control and anti-retrovirus treatment in China. The infection stages and molecular characteristics of HIV-1 from infected Chinese blood donors were examined to shed light on the HIV genotype distribution and the status of drug resistance mutations (DRMs) in the changing HIV epidemic in China. Western blot (WB) confirmed HIV-1 positive plasma samples were collected from blood donors at five Chinese blood centers from April 16, 2012, through June 30, 2014...
2017: PloS One
https://www.readbyqxmd.com/read/28621670/analyses-of-a-whole-genome-inter-clade-recombination-map-of-hepatitis-delta-virus-suggest-a-host-polymerase-driven-and-viral-rna-structure-promoted-template-switching-mechanism-for-viral-rna-recombination
#20
Mei Chao, Tzu-Chi Wang, Chia-Chi Lin, Robert Yung-Liang Wang, Wen-Bin Lin, Shang-En Lee, Ying-Yu Cheng, Chau-Ting Yeh, Shan-Bei Iang
The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV...
June 1, 2017: Oncotarget
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