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https://www.readbyqxmd.com/read/28100412/virome-of-us-bovine-calf-serum
#1
Mohammadreza Sadeghi, Beatrix Kapusinszky, Danielle M Yugo, Tung Gia Phan, Xutao Deng, Isis Kanevsky, Tanja Opriessnig, Amelia R Woolums, David J Hurley, Xiang-Jin Meng, Eric Delwart
Using viral metagenomics we analyzed four bovine serum pools assembled from 715 calves in the United States. Two parvoviruses, bovine parvovirus 2 (BPV2) and a previously uncharacterized parvovirus designated as bosavirus (BosaV), were detected in 3 and 4 pools respectively and their complete coding sequences generated. Based on NS1 protein identity, bosavirus qualifies as a member of a new species in the copiparvovirus genus. Also detected were low number of reads matching ungulate tetraparvovirus 2, bovine hepacivirus, and several papillomaviruses...
January 15, 2017: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/28100302/fecal-virome-of-healthy-chickens-reveals-a-large-diversity-of-the-eukaryote-viral-community-including-novel-circular-single-stranded-dna-viruses
#2
Diane Lima, Samuel Paulo Cibulski, Fabrine Finkler, Thais Teixeira, Ana Paula Varela, Cristine Cerva, Márcia Loiko, Camila Scheffer, Helton Dos Santos, Fabiana Mayer, Paulo Roehe
This study is focused on the identification of the fecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7,743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with BLASTx revealed that 279 contigs (4%) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes...
January 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28090075/virus-host-interactions-and-their-roles-in-coral-reef-health-and-disease
#3
Rebecca Vega Thurber, Jérôme P Payet, Andrew R Thurber, Adrienne M S Correa
Coral reefs occur in nutrient-poor shallow waters, constitute biodiversity and productivity hotspots, and are threatened by anthropogenic disturbance. This Review provides an introduction to coral reef virology and emphasizes the links between viruses, coral mortality and reef ecosystem decline. We describe the distinctive benthic-associated and water-column- associated viromes that are unique to coral reefs, which have received less attention than viruses in open-ocean systems. We hypothesize that viruses of bacteria and eukaryotes dynamically interact with their hosts in the water column and with scleractinian (stony) corals to influence microbial community dynamics, coral bleaching and disease, and reef biogeochemical cycling...
January 16, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28003936/towards-quantitative-viromics-for-both-double-stranded-and-single-stranded-dna-viruses
#4
Simon Roux, Natalie E Solonenko, Vinh T Dang, Bonnie T Poulos, Sarah M Schwenck, Dawn B Goldsmith, Maureen L Coleman, Mya Breitbart, Matthew B Sullivan
BACKGROUND: Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation)...
2016: PeerJ
https://www.readbyqxmd.com/read/27979823/in-utero-cytomegalovirus-infection-and-development-of-childhood-acute-lymphoblastic-leukemia
#5
Stephen Starko Francis, Amelia D Wallace, George A Wendt, Linlin Li, Fenyong Liu, Lee W Riley, Scott Kogan, Kyle M Walsh, Adam J de Smith, Gary V Dahl, Xiaomei Ma, Eric Delwart, Catherine Metayer, Joseph L Wiemels
It is widely suspected, yet controversial, that infection plays an etiologic role in the development of acute lymphoblastic leukemia (ALL), the most common childhood cancer and a disease with a confirmed prenatal origin in most cases. We investigated infections at diagnosis and then assessed the timing of infection at birth in children with ALL and age, gender, and ethnicity matched controls to identify potential causal initiating infections. Comprehensive untargeted virome and bacterial analyses of pre-treatment bone marrow specimens (n=127 ALL compared to 38 acute myeloid leukemia cases as comparison group) revealed prevalent cytomegalovirus (CMV) infection at diagnosis in childhood ALL, demonstrating active viral transcription in leukemia blasts as well as intact virions in serum...
December 15, 2016: Blood
https://www.readbyqxmd.com/read/27935413/stable-core-virome-despite-variable-microbiome-after-fecal-transfer
#6
Felix Broecker, Giancarlo Russo, Jochen Klumpp, Karin Moelling
We recently described the 4.5-year time course of the enteric bacterial microbiota and virome of a patient cured from recurrent Clostridium difficile infection (rCDI) by fecal microbiota transplantation (FMT). Here, we extended the virome analyses and found the patient's phage population to exhibit highly donor-similar characteristics following FMT, which remained stable for the whole period tested (up to 7 months). Moreover, the detected viral populations of donor and patient exhibited comparable diversity and richness...
December 9, 2016: Gut Microbes
https://www.readbyqxmd.com/read/27907010/viral-metagenomic-analysis-displays-the-co-infection-situation-in-healthy-and-pmws-affected-pigs
#7
Anne-Lie Blomström, Caroline Fossum, Per Wallgren, Mikael Berg
The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs...
2016: PloS One
https://www.readbyqxmd.com/read/27902331/the-plasma-virome-of-febrile-adult-kenyans-shows-frequent-parvovirus-b19-infections-and-a-novel-arbovirus-kadipiro-virus
#8
Carolyne N Ngoi, Juliana Siqueira, Linlin Li, Xutao Deng, Peter Mugo, Susan M Graham, Matt A Price, Eduard J Sanders, Eric Delwart
Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75 %), pegivirus C (GBV-C) (67 %), alpha anellovirus (59 %), gamma anellovirus (55 %), beta anellovirus (41 %), dengue virus genotype 2 (DENV-2) (16 %), human immunodeficiency virus type 1 (6 %), human herpesvirus 6 (6 %), HBV (4 %), rotavirus (4 %), hepatitis B virus (4 %), rhinovirus C (2 %), Merkel cell polyomavirus (MCPyV; 2 %) and Kadipiro virus (2 %)...
December 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27890586/exploring-the-contribution-of-bacteriophages-to-antibiotic-resistance
#9
Itziar Lekunberri, Jèssica Subirats, Carles M Borrego, José Luis Balcázar
Bacteriophages (phages) are the most abundant and diverse biological entities in our planet. They infect susceptible bacterial hosts into which they either multiply or persist. In the latter case, phages can confer new functions to their hosts as a result of gene transfer, thus contributing to their adaptation (short-term) and evolution (long-term). In this regard, the role of phages on the dissemination of antibiotic resistance genes (ARGs) among bacterial hosts in natural environments has not yet been clearly resolved...
January 2017: Environmental Pollution
https://www.readbyqxmd.com/read/27883042/two-novel-viruses-associated-with-the-apis-mellifera-pathogenic-mite-varroa-destructor
#10
Sofia Levin, Noa Sela, Nor Chejanovsky
Varroa destructor infestation of Apis mellifera colonies carries and/or promotes replication of honey bee viruses like the Deformed wing virus, the Varroa destructor virus-1, the Acute bee paralysis virus, the Israeli acute bee paralysis virus and the Kashmir bee virus that have been well described and characterized; but viruses exclusively associated with Varroa were not found. To look for viruses that may associate with- or infect V. destructor we performed deep sequencing (RNA-seq) of RNA extracted from honey bees and mites in Varroa-infested untreated colonies...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27880830/synonymous-co-variation-across-the-e1-e2-gene-junction-of-hepatitis-c-virus-defines-virion-fitness
#11
Brendan A Palmer, Liam J Fanning
Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3'-end of E1 highly conserved and the 5'-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection...
2016: PloS One
https://www.readbyqxmd.com/read/27880757/redefining-the-invertebrate-rna-virosphere
#12
Mang Shi, Xian-Dan Lin, Jun-Hua Tian, Liang-Jun Chen, Xiao Chen, Ci-Xiu Li, Xin-Cheng Qin, Jun Li, Jian-Ping Cao, John-Sebastian Eden, Jan Buchmann, Wen Wang, Jianguo Xu, Edward C Holmes, Yong-Zhen Zhang
Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence...
November 23, 2016: Nature
https://www.readbyqxmd.com/read/27866880/efficacy-of-sterile-fecal-filtrate-transfer-for-treating-patients-with-clostridium-difficile-infection
#13
Stephan J Ott, Georg H Waetzig, Ateequr Rehman, Jacqueline Moltzau-Anderson, Richa Bharti, Juris A Grasis, Liam Cassidy, Andreas Tholey, Helmut Fickenscher, Dirk Seegert, Philip Rosenstiel, Stefan Schreiber
BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is a highly effective therapy for recurrent Clostridium difficile infection (CDI). However, transferring undefined living bacteria entails uncontrollable risks for infectious and metabolic or malignant diseases, particularly in immunocompromised patients. We investigated whether sterile fecal filtrates (containing bacterial debris, proteins, antimicrobial compounds, metabolic products and oligonucleotides/DNA), rather than intact microorganisms, are effective in patients with CDI...
November 17, 2016: Gastroenterology
https://www.readbyqxmd.com/read/27860030/imbalance-of-bacteriome-profiles-within-the-finnish-diabetes-prediction-and-prevention-study-parallel-use-of-16s-profiling-and-virome-sequencing-in-stool-samples-from-children-with-islet-autoimmunity-and-matched-controls
#14
Ondrej Cinek, Lenka Kramna, Jake Lin, Sami Oikarinen, Katerina Kolarova, Jorma Ilonen, Olli Simell, Riitta Veijola, Reija Autio, Heikki Hyöty
BACKGROUND: We set out to explore associations between the stool bacteriome profiles and early-onset islet autoimmunity, taking into account the interactions with the virus component of the microbiome. METHODS: Serial stool samples were longitudinally collected from 18 infants and toddlers with early-onset islet autoimmunity (median age 17.4 months) followed by type 1 diabetes, and 18 tightly matched controls from the Finnish Diabetes Prediction and Prevention (DIPP) cohort...
November 17, 2016: Pediatric Diabetes
https://www.readbyqxmd.com/read/27833560/pharmacometabolomics-informs-viromics-toward-precision-medicine
#15
Angeliki Balasopoulou, George P Patrinos, Theodora Katsila
Nowadays, we are experiencing the big data era with the emerging challenge of single data interpretation. Although the advent of high-throughput technologies as well as chemo- and bio-informatics tools presents pan-omics data as the way forward to precision medicine, personalized health care and tailored-made therapeutics can be only envisaged when interindividual variability in response to/toxicity of xenobiotics can be interpreted and thus, predicted. We know that such variability is the net outcome of genetics (host and microbiota) and environmental factors (diet, lifestyle, polypharmacy, and microbiota) and for this, tremendous efforts have been made to clarify key-molecules from correlation to causality to clinical significance...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/27814394/deep-sequencing-analysis-reveals-the-mycoviral-diversity-of-the-virome-of-an-avirulent-isolate-of-rhizoctonia-solani-ag-2-2-iv
#16
Anika Bartholomäus, Daniel Wibberg, Anika Winkler, Alfred Pühler, Andreas Schlüter, Mark Varrelmann
Rhizoctonia solani represents an important plant pathogenic Basidiomycota species complex and the host of many different mycoviruses, as indicated by frequent detection of dsRNA elements in natural populations of the fungus. To date, eight different mycoviruses have been characterized in Rhizoctonia and some of them have been reported to modulate its virulence. DsRNA extracts of the avirulent R. solani isolate DC17 (AG2-2-IV) displayed a diverse pattern, indicating multiple infections with mycoviruses. Deep sequencing analysis of the dsRNA extract, converted to cDNA, revealed that this isolate harbors at least 17 different mycovirus species...
2016: PloS One
https://www.readbyqxmd.com/read/27769778/a-bioinformatics-approach-reveals-seven-nearly-complete-rna-virus-genomes-in-bivalve-rna-seq-data
#17
Umberto Rosani, Marco Gerdol
Viral metagenomics (viromics) can provide a great contribution in expanding the knowledge of viruses and the relationship with their hosts. Viromic studies on marine organisms are still at a very early stage and only little efforts have been spent in the identification of viruses associated to marine invertebrates to date, leaving the complexity of marine viromes associated to bivalve hosts almost completely unexplored. However, the potential use of viromic approaches in the management of viral diseases affecting aquacultured species has been recently evidenced by the flourishing of studies on the Ostreid herpesvirus type-1, which has been associated with bivalve mortality events...
October 18, 2016: Virus Research
https://www.readbyqxmd.com/read/27761936/epigenetic-treatment-of-persistent-viral-infections
#18
Walter H Moos, Carl A Pinkert, Michael H Irwin, Douglas V Faller, Krishna Kodukula, Ioannis P Glavas, Kosta Steliou
Preclinical Research Approximately 2,500 years ago, Hippocrates used the word herpes as a medical term to describe lesions that appeared to creep or crawl on the skin, advocating heat as a possible treatment. During the last 50 years, pharmaceutical research has made great strides, and therapeutic options have expanded to include small molecule antiviral agents, protease inhibitors, preventive vaccines for a handful of the papillomaviruses, and even cures for hepatitis C virus infections. However, effective treatments for persistent and recurrent viral infections, particularly the highly prevalent herpesviruses, continue to represent a significant unmet medical need, affecting the majority of the world's population...
October 20, 2016: Drug Development Research
https://www.readbyqxmd.com/read/27731934/the-perioperative-lung-transplant-virome-torque-teno-viruses-are-elevated-in-donor-lungs-and-show-divergent-dynamics-in-primary-graft-dysfunction
#19
A A Abbas, J M Diamond, C Chehoud, B Chang, J J Kotzin, J C Young, I Imai, A R Haas, E Cantu, D J Lederer, K Meyer, R K Milewski, K M Olthoff, A Shaked, J D Christie, F D Bushman, R G Collman
Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. Thus far, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 month post-transplant and found that levels of Anellovirus, mainly Torque teno viruses (TTV), were significantly higher than in non-transplant healthy controls...
October 12, 2016: American Journal of Transplantation
https://www.readbyqxmd.com/read/27721694/deep-sequencing-analysis-of-apple-infecting-viruses-in-korea
#20
In-Sook Cho, Davaajargal Igori, Seungmo Lim, Gug-Seoun Choi, John Hammond, Hyoun-Sub Lim, Jae Sun Moon
Deep sequencing has generated 52 contigs derived from five viruses; Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apricot latent virus (ApLV) were identified from eight apple samples showing small leaves and/or growth retardation. Nucleotide (nt) sequence identity of the assembled contigs was from 68% to 99% compared to the reference sequences of the five respective viral genomes. Sequences of ASPV and ASGV were the most abundantly represented by the 52 contigs assembled...
October 2016: Plant Pathology Journal
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