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https://www.readbyqxmd.com/read/28649326/viral-gut-metagenomics-of-sympatric-wild-and-domestic-canids-and-monitoring-of-viruses-insights-from-an-endangered-wolf-population
#1
Nádia Conceição-Neto, Raquel Godinho, Francisco Álvares, Claude K Yinda, Ward Deboutte, Mark Zeller, Lies Laenen, Elisabeth Heylen, Sara Roque, Francisco Petrucci-Fonseca, Nuno Santos, Marc Van Ranst, João R Mesquita, Jelle Matthijnssens
Animal host-microbe interactions are a relevant concern for wildlife conservation, particularly regarding generalist pathogens, where domestic host species can play a role in the transmission of infectious agents, such as viruses, to wild animals. Knowledge on viral circulation in wild host species is still scarce and can be improved by the recent advent of modern molecular approaches. We aimed to characterize the fecal virome and identify viruses of potential conservation relevance of diarrheic free-ranging wolves and sympatric domestic dogs from Central Portugal, where a small and threatened wolf population persists in a highly anthropogenically modified landscape...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28643787/single-virus-genomics-reveals-hidden-cosmopolitan-and-abundant-viruses
#2
Francisco Martinez-Hernandez, Oscar Fornas, Monica Lluesma Gomez, Benjamin Bolduc, Maria Jose de la Cruz Peña, Joaquín Martínez Martínez, Josefa Anton, Josep M Gasol, Riccardo Rosselli, Francisco Rodriguez-Valera, Matthew B Sullivan, Silvia G Acinas, Manuel Martinez-Garcia
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28637756/high-resolution-meta-transcriptomics-reveals-the-ecological-dynamics-of-mosquito-associated-rna-viruses-in-western-australia
#3
Mang Shi, Peter Neville, Jay Nicholson, John-Sebastian Eden, Allison Imrie, Edward C Holmes
Mosquitoes harbour a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a meta-transcriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28617757/looking-into-enteric-virome-in-patients-with-ibd-defining-guilty-or-innocence
#4
Susana Lopes, Patricia Andrade, Silvia Conde, Rodrigo Liberal, Cláudia C Dias, Salomão Fernandes, Jorge Pinheiro, Joana S Simões, Fátima Carneiro, Fernando Magro, Guilherme Macedo
BACKGROUND: Although there is some evidence suggesting that certain viruses may be involved in the onset of inflammatory bowel disease (IBD), data regarding viral prevalence and viral load in blood and mucosa of patients with IBD are scarce. The main aim of this study is to evaluate the prevalence and viral load of common Epstein-Barr virus (EBV), cytomegalovirus (CMV), and human herpes virus 6 in blood and mucosa of adult patients with endoscopic active IBD. METHODS: From January to December 2014, ulcerative colitis and Crohn's disease patients with active endoscopic disease were consecutively enrolled...
June 14, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28606917/quantitative-temporal-viromics-of-an-inducible-hiv-1-model-yields-insight-to-global-host-targets-and-phospho-dynamics-associated-with-vpr
#5
John D Lapek, Mary K Lewinski, Jacob M Wozniak, John Guatelli, David J Gonzalez
The mechanisms by which human immunodeficiency virus (HIV) circumvents and coopts cellular machinery to replicate and persist in cells are not fully understood. HIV accessory proteins play key roles in the HIV life cycle by altering host pathways that are often dependent on post-translational modifications (PTMs). Thus, the identification of HIV accessory protein host targets and their PTM status is critical to fully understand how HIV invades, avoids detection and replicates to spread infection. To date, a comprehensive characterization of HIV accessory protein host targets and modulation of their PTM status does not exist...
June 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28595635/the-pepper-virome-natural-co-infection-of-diverse-viruses-and-their-quasispecies
#6
Yeonhwa Jo, Hoseong Choi, Sang-Min Kim, Sun-Lim Kim, Bong Choon Lee, Won Kyong Cho
BACKGROUND: The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host. RESULTS: Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host...
June 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28592325/isolation-and-characterization-of-the-first-phage-infecting-ecologically-important-marine-bacteria-erythrobacter
#7
Longfei Lu, Lanlan Cai, Nianzhi Jiao, Rui Zhang
BACKGROUND: Erythrobacter comprises a widespread and ecologically significant genus of marine bacteria. However, no phage infecting Erythrobacter spp. has been reported to date. This study describes the isolation and characterization of phage vB_EliS-R6L from Erythrobacter. METHODS: Standard virus enrichment and double-layer agar methods were used to isolate and characterize the phage. Morphology was observed by transmission electron microscopy, and a one-step growth curve assay was performed...
June 7, 2017: Virology Journal
https://www.readbyqxmd.com/read/28586923/presence-of-human-hepegivirus-1-in-a-cohort-of-people-who-inject-drugs
#8
Abraham J Kandathil, Florian P Breitwieser, Jaiprasath Sachithanandham, Matthew Robinson, Shruti H Mehta, Winston Timp, Steven L Salzberg, David L Thomas, Ashwin Balagopal
Background: Next-generation metagenomic sequencing (NGMS) has opened new frontiers in microbial discovery but has been clinically characterized in only a few settings. Objective: To explore the plasma virome of persons who inject drugs and to characterize the sensitivity and accuracy of NGMS compared with quantitative clinical standards. Design: Longitudinal and cross-sectional studies. Setting: A clinical trial (ClinicalTrials...
June 6, 2017: Annals of Internal Medicine
https://www.readbyqxmd.com/read/28583442/evolution-of-selective-sequencing-approaches-for-virus-discovery-and-virome-analysis
#9
REVIEW
Arvind Kumar, Satyapramod Murthy, Amit Kapoor
Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once, mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for study of viromes, sample preparation methodologies used different refinements to exclude amplification of non-viral components that can overshadow low-titer viruses...
June 2, 2017: Virus Research
https://www.readbyqxmd.com/read/28570584/characterisation-of-the-canine-faecal-virome-in-healthy-dogs-and-dogs-with-acute-diarrhoea-using-shotgun-metagenomics
#10
Paloma S Moreno, Josef Wagner, Caroline S Mansfield, Matthew Stevens, James R Gilkerson, Carl D Kirkwood
The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented...
2017: PloS One
https://www.readbyqxmd.com/read/28544449/metagenomic-based-impact-study-of-transgenic-grapevine-rootstock-on-its-associated-virome-and-soil-bacteriome
#11
Jean-Michel Hily, Sandrine Demanèche, Nils Poulicard, Mélanie Tannières, Samia Djennane, Monique Beuve, Emmanuelle Vigne, Gérard Demangeat, Véronique Komar, Claude Gertz, Aurélie Marmonier, Caroline Hemmer, Sophie Vigneron, Armelle Marais, Thierry Candresse, Pascal Simonet, Olivier Lemaire
For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment...
May 25, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28539351/bacteriophage-transfer-during-faecal-microbiota-transplantation-in-clostridium-difficile-infection-is-associated-with-treatment-outcome
#12
Tao Zuo, Sunny H Wong, Kelvin Lam, Rashid Lui, Kitty Cheung, Whitney Tang, Jessica Y L Ching, Paul K S Chan, Martin C W Chan, Justin C Y Wu, Francis K L Chan, Jun Yu, Joseph J Y Sung, Siew C Ng
OBJECTIVE: Faecal microbiota transplantation (FMT) is effective for the treatment of recurrent Clostridium difficile infection (CDI). Studies have shown bacterial colonisation after FMT, but data on viral alterations in CDI are scarce. We investigated enteric virome alterations in CDI and the association between viral transfer and clinical outcome in patients with CDI. DESIGN: Ultra-deep metagenomic sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on stool samples from 24 subjects with CDI and 20 healthy controls...
May 24, 2017: Gut
https://www.readbyqxmd.com/read/28533016/drodvir-a-resource-for-exploring-the-virome-diversity-in-rodents
#13
Lihong Chen, Bo Liu, Zhiqiang Wu, Qi Jin, Jian Yang
Emerging zoonotic diseases have received tremendous interests in recent years, as they pose a significant threat to human health, animal welfare, and economic stability. A high proportion of zoonoses originate from wildlife reservoirs. Rodents are the most numerous, widespread, and diverse group of mammals on the earth and are reservoirs for many zoonotic viruses responsible for significant morbidity and mortality. A better understanding of virome diversity in rodents would be of importance for researchers and professionals in the field...
May 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28515299/a-diverse-range-of-novel-rna-viruses-in-geographically-distinct-honey-bee-populations
#14
Emily J Remnant, Mang Shi, Gabriele Buchmann, Tjeerd Blacquière, Edward C Holmes, Madeleine Beekman, Alyson Ashe
Understanding the diversity and consequences of viruses present in honey bees is critical to maintain pollinator health and manage the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as Deformed wing virus. Previous genomic studies have focused on colonies suffering from Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity...
May 17, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28514666/a-temporal-proteomic-map-of-epstein-barr-virus-lytic-replication-in-b-cells
#15
Ina Ersing, Luis Nobre, Liang Wei Wang, Lior Soday, Yijie Ma, Joao A Paulo, Yohei Narita, Camille W Ashbaugh, Chang Jiang, Nicholas E Grayson, Elliott Kieff, Steven P Gygi, Michael P Weekes, Benjamin E Gewurz
Epstein-Barr virus (EBV) replication contributes to multiple human diseases, including infectious mononucleosis, nasopharyngeal carcinoma, B cell lymphomas, and oral hairy leukoplakia. We performed systematic quantitative analyses of temporal changes in host and EBV proteins during lytic replication to gain insights into virus-host interactions, using conditional Burkitt lymphoma models of type I and II EBV infection. We quantified profiles of >8,000 cellular and 69 EBV proteins, including >500 plasma membrane proteins, providing temporal views of the lytic B cell proteome and EBV virome...
May 16, 2017: Cell Reports
https://www.readbyqxmd.com/read/28512096/erratum-for-briese-et-al-virome-capture-sequencing-enables-sensitive-viral-diagnosis-and-comprehensive-virome-analysis
#16
Thomas Briese, Amit Kapoor, Nischay Mishra, Komal Jain, Arvind Kumar, Omar J Jabado, W Ian Lipkin
No abstract text is available yet for this article.
May 16, 2017: MBio
https://www.readbyqxmd.com/read/28506246/vipie-web-pipeline-for-parallel-characterization-of-viral-populations-from-multiple-ngs-samples
#17
Jake Lin, Lenka Kramna, Reija Autio, Heikki Hyöty, Matti Nykter, Ondrej Cinek
BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28501627/detection-of-viromes-of-rna-viruses-using-the-next-generation-sequencing-libraries-prepared-by-three-methods
#18
Yuan Qiu, Ji-Ming Chen, Tong Wang, Guang-Yu Hou, Qing-Ye Zhuang, Run Wu, Kai-Cheng Wang
Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization. In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. The sequencing primers were added through random hybridization and ligation to fragmented viral RNA using a RNA-Seq kit in method 1, through random reverse transcription (RT) and polymerase chain reaction (PCR) in method 2 which was developed in our laboratory, and through hybridization and ligation to fragmented amplicons of random RT-PCR using a single primer in method 3...
May 10, 2017: Virus Research
https://www.readbyqxmd.com/read/28480148/the-use-of-informativity-in-the-development-of-robust-viromics-based-examinations
#19
Siobhan C Watkins, Catherine Putonti
Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin...
2017: PeerJ
https://www.readbyqxmd.com/read/28466442/viral-metagenomics-analysis-of-feces-from-coronary-heart-disease-patients-reveals-the-genetic-diversity-of-the-microviridae
#20
Lianghua Guo, Xiuguo Hua, Wen Zhang, Shixing Yang, Quan Shen, Haibing Hu, Jingjiao Li, Zhijian Liu, Xiaochun Wang, Hua Wang, Chenglin Zhou, Li Cui
Recent studies have declared that members of the ssDNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease (CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls...
April 2017: Virologica Sinica
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