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Manisha R Sajnani, D Sudarsanam, Ramesh J Pandit, Tejas Oza, Ankit T Hinsu, Subhash J Jakhesara, Siddhardha Solosanc, Chaitanya G Joshi, Vaibhav D Bhatt
The incidence and severity of respiratory diseases in commercial broiler chicken flocks have increased recently in India because of intensification of the broiler industry. Viral population are predominant in respiratory tract infections and they pose continuous economic burden to poultry industry by causing severe economic losses through decreased productivity [1], [2]. To understand viral metagenome of poultry associated with respiratory infections, we performed DNA virome sequencing and data analysis of broilers from 8 districts of Gujarat State in India...
February 2018: Data in Brief
Fiona Newberry, Shen-Yuan Hsieh, Tom Wileman, Simon R Carding
Myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) (ME/CFS) is a disabling and debilitating disease of unknown aetiology. It is a heterogeneous disease characterized by various inflammatory, immune, viral, neurological and endocrine symptoms. Several microbiome studies have described alterations in the bacterial component of the microbiome (dysbiosis) consistent with a possible role in disease development. However, in focusing on the bacterial components of the microbiome, these studies have neglected the viral constituent known as the virome...
March 15, 2018: Clinical Science (1979-)
Xue-Lian Luo, Shan Lu, Dong Jin, Jing Yang, Shu-Sheng Wu, Jianguo Xu
Wildlife has been considered the main source of novel viruses causing emerging infectious diseases. Marmota himalayana is endemic to the Qinghai-Tibetan Plateau, China. Here, based on a high-throughput method using Illumina RNA sequencing, we studied the RNA virome of M. himalayana and discovered multiple novel viruses, especially picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae. A total of 63% of the viral contigs corresponded to PBVs, comprising 274 segment 1 and 56 segment 2 sequences...
March 7, 2018: Emerging Microbes & Infections
Maria José de la Cruz Peña, Francisco Martinez-Hernandez, Inmaculada Garcia-Heredia, Mónica Lluesma Gomez, Òscar Fornas, Manuel Martinez-Garcia
Single-cell genomics has unveiled the metabolic potential of dominant microbes inhabiting different environments, including the human body. The lack of genomic information for predominant microbes of the human body, such as bacteriophages, hinders our ability to answer fundamental questions about our viral communities. Here, we applied single-virus genomics (SVGs) to natural human salivary samples in combination with viral metagenomics to gain some insights into the viral community structure of the oral cavity...
March 6, 2018: Viruses
Jan D Brüwer, Christian R Voolstra
Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia ( sensu Exaiptasia pallida ), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium ...
2018: PeerJ
Han Xia, Yujuan Wang, Chenyan Shi, Evans Atoni, Lu Zhao, Zhiming Yuan
Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this study, a total of 2222 mosquitoes were collected from the same geographic location, and RNAs were sequenced using the Illumina Miseq platform. After querying to the Refseq database, a total of 3,435,781, 2,223,509, 5,727,523, and 6,387,867 paired-end reads were classified under viral sequences from An...
March 2, 2018: Virologica Sinica
Artemis Rumbou, Thierry Candresse, Armelle Marais, Sebastien Theil, Juliane Langer, Risto Jalkanen, Carmen Büttner
In declining birches (Betula sp.) from different European stands affected by the "birch leaf-roll disease" (BLRD) a novel virus is identified by means of RNA-Seq virome analysis. The virus represents a new member in the genus Badnavirus, family Caulimoviridae, tentatively named Birch leaf roll-associated virus (BLRaV) and it is the first badnavirus found to infect birch. Complete genome sequences (7,862-7,864 nucleotides) of three viral isolates of Finnish and German origin have been determined. The virus sequences show a typical badnavirus organization with three major open reading frames (ORFs) and a fourth potential ORF overlapping with the end of ORF3...
2018: PloS One
Arnfinn Lodden Økland, Are Nylund, Ali May, Adalberto Costessi, Walter Pirovano
Discovery of viral genomes in fish has historically been based on viral enrichment, random priming, cloning, and Sanger sequencing. However, the development of next-generation sequencing has enabled the possibility to sequence the entire virome of a tissue sample. This has led to an enormous increase in discovery of new viruses. In this chapter, we describe a simple and rapid method for viral discovery in fish. The method is based on Illumina sequencing of total RNA from diseased tissue or cell culture and in silico removal of host RNA...
2018: Methods in Molecular Biology
Luca Nerva, Giovanna C Varese, Massimo Turina
Here we describe the protocols to characterize the virome associated to fungi isolated from marine organisms assessed on the seagrass Posidonia oceanica and on the marine animal Holothuria poli. We provide detailed protocols for fungal isolation, fungal growth, and total RNA extraction. Ribosomal RNA depletion, cDNA library synthesis and normalization, and sequencing runs on different platforms are part of the protocols that are generally outsourced and therefore are not described in this chapter. We describe, instead, how raw reads are assembled into contigs and how to search for putative viral sequences...
2018: Methods in Molecular Biology
Ion Gutiérrez-Aguirre, Denis Kutnjak, Nejc Rački, Matevž Rupar, Maja Ravnikar
Viruses exist in aquatic media and many of them use this media as transmission route. Next-generation sequencing (NGS) technologies have opened new doors in virus research, allowing also to reveal a hidden diversity of viral species in aquatic environments. Not surprisingly, many of the newly discovered viruses are found in environmental fresh and marine waters. One of the problems in virome research can be the low amount of viral nucleic acids present in the sample in contrast to the background ones (host, eukaryotic, prokaryotic, environmental)...
2018: Methods in Molecular Biology
Dennis Carroll, Peter Daszak, Nathan D Wolfe, George F Gao, Carlos M Morel, Subhash Morzaria, Ariel Pablos-Méndez, Oyewale Tomori, Jonna A K Mazet
No abstract text is available yet for this article.
February 23, 2018: Science
Chunhua Wang, Shuaifeng Zhou, Wanhua Xue, Liang Shen, Wei Huang, Yi Zhang, Xuguang Li, Junzhi Wang, Hong Zhang, Xuejun Ma
The management of hand-foot-and-mouth disease(HFMD) epidemic is difficult due to the frequent emergence of non-EV71 and non-CVA16 enteroviruses and some cases testing negative for HFMD-associated causative agents. To clarify the virus spectrum of mild and severe HFMD, a comprehensive virome analysis of 238 samples was performed using next-generation sequencing (NGS). The data revealed total thirteen mammalian- and plant- virus families and diverse viral populations including enteroviruses, common respiratory viruses, diarrhea-related viruses, plant viruses and anelloviruses...
February 19, 2018: Virology
Steven M Valles, Sanford D Porter, Luis A Calcaterra
Metagenomics and next generation sequencing were employed to discover new virus natural enemies of the fire ant, Solenopsis invicta Buren in its native range (i.e., Formosa, Argentina) with the ultimate goal of testing and releasing new viral pathogens into U.S. S. invicta populations to provide natural, sustainable control of this ant. RNA was purified from worker ants from 182 S. invicta colonies, which was pooled into 4 groups according to location. A library was created from each group and sequenced using Illumina Miseq technology...
2018: PloS One
Jose A Romero-Espinoza, Yazmin Moreno-Valencia, Rodrigo H Coronel-Tellez, Manuel Castillejos-Lopez, Andres Hernandez, Aaron Dominguez, Angel Miliar-Garcia, Arturo Barbachano-Guerrero, Rogelio Perez-Padilla, Alejandro Alejandre-Garcia, Joel A Vazquez-Perez
BACKGROUND: Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively...
2018: PloS One
Geert Cremers, Lavinia Gambelli, Theo van Alen, Laura van Niftrik, Huub J M Op den Camp
With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which may cause an unavoidable bias. Here, we describe a case study in which the virome of a bioreactor is sequenced using Ion Torrent technology...
2018: PeerJ
Mary E Anderson, Dorottya Nagy-Szakal, Komal Jain, Christina C Patrone, Mark G Frattini, W Ian Lipkin, Larisa J Geskin
No abstract text is available yet for this article.
February 7, 2018: Journal of Investigative Dermatology
Colin Sharp, Tanya Golubchik, William F Gregory, Anna L McNaughton, Nicholas Gow, Mathyruban Selvaratnam, Alina Mirea, Dona Foster, Monique Andersson, Paul Klenerman, Katie Jeffery, Philippa C Matthews
OBJECTIVES: There is increasing interest in the use of metagenomic (next generation sequencing, NGS) approaches for diagnosis of infection. We undertook a pilot study to screen samples submitted to a diagnostic microbiology laboratory in a UK teaching hospital using Illumina HiSeq. In the short-term, this small dataset provides insights into the virome of human respiratory and cerebrospinal fluid (CSF) samples. In the longer term, assimilating metagenomic data sets of this nature can inform optimization of laboratory and bioinformatic methods, and develop foundations for the interpretation of results in a clinical context...
February 9, 2018: BMC Research Notes
Silvia Turco, Victor Golyaev, Jonathan Seguin, Céline Gilli, Laurent Farinelli, Thomas Boller, Oliveir Schumpp, Mikhail Pooggin
In plants, RNA silencing-based antiviral defense generates viral small RNAs (sRNAs) faithfully representing the viral genomes. We employed sRNA sequencing and bioinformatics (sRNA-omics) to characterize antiviral defense and to reconstruct the full genomic sequences and their variants in the evolving viral quasispecies in cultivated solanaceous plants carrying mixed infections. In naturally-infected Solanum tuberosum (potato), one case study revealed a virome comprising Potato virus Y (genus Potyvirus) and Potato virus X (genus Potexvirus), which was reconstructed by de novo assembling separate genome-size sRNA contigs...
February 9, 2018: Molecular Plant-microbe Interactions: MPMI
Barry I Freedman, Amy L Kistler, Peter Skewes-Cox, Don Ganem, Mitzie Spainhour, Jolyn Turner, Jasmin Divers, Carl D Langefeld, Mariana Murea, Pamela J Hicks, Ashok K Hemal, James A Snipes, Lihong Zhao, Johanna R Abend, Douglas S Lyles, Lijun Ma, Karl L Skorecki
Background: Viral infections can trigger chronic kidney disease (CKD) and the urine virome may inform risk. The Natural History of APOL1-Associated Nephropathy Study (NHAANS) reported that urine JC polyomavirus (JCPyV) associated with a lower risk of APOL1-associated nephropathy in African Americans. Herein, association was assessed between urine JCPyV with CKD in African Americans independent from the APOL1 genotype. Methods: Quantitative polymerase chain reaction was performed for urinary detection of JCPyV and BK polyoma virus (BKPyV) in 200 newly recruited nondiabetic African Americans...
February 6, 2018: Nephrology, Dialysis, Transplantation
Vicente Pérez-Brocal, Andrés Moya
We have analysed oral wash samples from 72 healthy young adults in Valencia (Spain) for a metagenomic analysis through the construction of shotgun libraries and high-throughput-sequencing. The oral viral communities have been taxonomically characterised as well as and the gene content from the latter. The majority of viruses are found in few individuals, with single occurrences being the most widespread ones, whereas universally distributed viruses, while present, are relatively rare, with bacteriophages from families Siphoviridae and Myoviridae, and Streptococcus phages, as well as the eukaryotic viral family Herpesviridae amongst the most widespread viruses...
2018: PloS One
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