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https://www.readbyqxmd.com/read/28515299/a-diverse-range-of-novel-rna-viruses-in-geographically-distinct-honey-bee-populations
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28466051/comparative-study-of-viromes-from-freshwater-samples-of-the-ile-balkhash-region-of-kazakhstan-captured-through-metagenomic-analysis
#8
Madina Saparbaevna Alexyuk, Aizhan Sabirzhanovna Turmagambetova, Pavel Gennadievich Alexyuk, Andrey Pavlinovich Bogoyavlenskiy, Vladimir Eleazarovich Berezin
Viruses are the most abundant biological entities on Earth and can be found in a variety of environments. A high prevalence of viruses in marine and freshwater systems was initially reported by Spencer in 1955, but the ecological significance of viruses is insufficiently known even until the present day. Viruses are known to play a key role in the biology of freshwater bacteria: controlling the bacterial abundance, composition of species, and acting as intermediaries in the transfer of genes between bacterial populations...
March 2017: Virusdisease
https://www.readbyqxmd.com/read/28448616/abundance-profiling-of-specific-gene-groups-using-precomputed-gut-metagenomes-yields-novel-biological-hypotheses
#9
Konstantin Yarygin, Alexander Tyakht, Andrey Larin, Elena Kostryukova, Sergei Kolchenko, Vilgelm Bitner, Dmitry Alexeev
The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions...
2017: PloS One
https://www.readbyqxmd.com/read/28421059/phages-in-the-human-body
#10
REVIEW
Ferran Navarro, Maite Muniesa
Bacteriophages, viruses that infect bacteria, have re-emerged as powerful regulators of bacterial populations in natural ecosystems. Phages invade the human body, just as they do other natural environments, to such an extent that they are the most numerous group in the human virome. This was only revealed in recent metagenomic studies, despite the fact that the presence of phages in the human body was reported decades ago. The influence of the presence of phages in humans has yet to be evaluated; but as in marine environments, a clear role in the regulation of bacterial populations could be envisaged, that might have an impact on human health...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28383679/ezmap-a-simple-pipeline-for-reproducible-analysis-of-the-human-virome
#11
Patrick Czeczko, Steven C Greenway, A P Jason de Koning
Summary: In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully-automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome...
April 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28377764/carbohydrate-staple-food-modulates-gut-microbiota-of-mongolians-in-china
#12
Jing Li, Qiangchuan Hou, Jiachao Zhang, Haiyan Xu, Zhihong Sun, Bilige Menghe, Heping Zhang
Gut microbiota is a determining factor in human physiological functions and health. It is commonly accepted that diet has a major influence on the gut microbial community, however, the effects of diet is not fully understood. The typical Mongolian diet is characterized by high and frequent consumption of fermented dairy products and red meat, and low level of carbohydrates. In this study, the gut microbiota profile of 26 Mongolians whom consumed wheat, rice and oat as the sole carbohydrate staple food for a week each consecutively was determined...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28366188/corrigendum-the-plasma-virome-of-febrile-adult-kenyans-shows-frequent-parvovirus-b19-infections-and-a-novel-arbovirus-kadipiro-virus
#13
Carolyne N Ngoi, Juliana Siqueira, Linlin Li, Xutao Deng, Peter Mugo, Susan M Graham, Matt A Price, Eduard J Sanders, Eric Delwart
No abstract text is available yet for this article.
March 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28331089/diversity-distribution-and-evolution-of-tomato-viruses-in-china-uncovered-by-small-rna-sequencing
#14
Chenxi Xu, Xuepeng Sun, Angela Taylor, Chen Jiao, Yimin Xu, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Guanghui Pan, Quanxi Wang, Zhangjun Fei, Quanhua Wang
Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with coldspots and hotspots. Most samples were co-infected by multiple viruses and the majority of identified viruses are positive-sense single-stranded RNA viruses...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28328962/the-blood-dna-virome-in-8-000-humans
#15
Ahmed Moustafa, Chao Xie, Ewen Kirkness, William Biggs, Emily Wong, Yaron Turpaz, Kenneth Bloom, Eric Delwart, Karen E Nelson, J Craig Venter, Amalio Telenti
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches...
March 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28327667/genetic-and-functional-diversity-of-ubiquitous-dna-viruses-in-selected-chinese-agricultural-soils
#16
Li-Li Han, Dan-Ting Yu, Li-Mei Zhang, Ju-Pei Shen, Ji-Zheng He
Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28304358/a-pelagic-microbiome-viruses-to-protists-from-a-small-cup-of-seawater
#17
Flavia Flaviani, Declan C Schroeder, Cecilia Balestreri, Joanna L Schroeder, Karen Moore, Konrad Paszkiewicz, Maya C Pfaff, Edward P Rybicki
The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment...
March 17, 2017: Viruses
https://www.readbyqxmd.com/read/28270584/viruses-in-the-oceanic-basement
#18
Olivia D Nigro, Sean P Jungbluth, Huei-Ting Lin, Chih-Chiang Hsieh, Jaclyn A Miranda, Christopher R Schvarcz, Michael S Rappé, Grieg F Steward
Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge...
March 7, 2017: MBio
https://www.readbyqxmd.com/read/28261669/environmental-viral-genomes-shed-new-light-on-virus-host-interactions-in-the-ocean
#19
Yosuke Nishimura, Hiroyasu Watai, Takashi Honda, Tomoko Mihara, Kimiho Omae, Simon Roux, Romain Blanc-Mathieu, Keigo Yamamoto, Pascal Hingamp, Yoshihiko Sako, Matthew B Sullivan, Susumu Goto, Hiroyuki Ogata, Takashi Yoshida
Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral "dark matter." However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs)...
March 2017: MSphere
https://www.readbyqxmd.com/read/28261185/metagenomic-sequencing-for-surveillance-of-food-and-waterborne-viral-diseases
#20
David F Nieuwenhuijse, Marion P G Koopmans
A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E...
2017: Frontiers in Microbiology
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