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https://www.readbyqxmd.com/read/29334978/plasma-virome-of-cattle-from-forest-region-revealed-diverse-small-circular-ssdna-viral-genomes
#1
Hao Wang, Shouxin Li, Asif Mahmood, Shixing Yang, Xiaochun Wang, Quan Shen, Tongling Shan, Xutao Deng, Jingjiao Li, Xiuguo Hua, Li Cui, Eric Delwart, Wen Zhang
BACKGROUND: Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers. METHODS: Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China. RESULTS: The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses...
January 15, 2018: Virology Journal
https://www.readbyqxmd.com/read/29329230/metagenomic-virome-analysis-of-culex-mosquitoes-from-kenya-and-china
#2
Evans Atoni, Yujuan Wang, Samuel Karungu, Cecilia Waruhiu, Ali Zohaib, Vincent Obanda, Bernard Agwanda, Morris Mutua, Han Xia, Zhiming Yuan
Many blood-feeding arthropods are known vectors of viruses that are a source of unprecedented global health concern. Mosquitoes are an integral part of these arthropod vectors. Advancements in next-generation sequencing and bioinformatics has expanded our knowledge on the richness of viruses harbored by arthropods. In the present study, we applied a metagenomic approach to determine the intercontinental virome diversity of Culex quinquefasciatus and Culex tritaeniorhynchus in Kwale, Kenya and provinces of Hubei and Yunnan in China...
January 12, 2018: Viruses
https://www.readbyqxmd.com/read/29322922/analysis-of-viral-diversity-for-vaccine-target-discovery
#3
Asif M Khan, Yongli Hu, Olivo Miotto, Natascha M Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J Thomas August
BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29311639/exploring-viral-diversity-in-a-unique-south-african-soil-habitat
#4
Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don Cowan
The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29306554/the-neglected-soil-virome-potential-role-and-impact
#5
REVIEW
Akbar Adjie Pratama, Jan Dirk van Elsas
Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings...
January 3, 2018: Trends in Microbiology
https://www.readbyqxmd.com/read/29291225/application-of-viromics-a-new-approach-to-the-understanding-of-viral-infections-in-humans
#6
REVIEW
Mageshbabu Ramamurthy, Sathish Sankar, Rajesh Kannangai, Balaji Nandagopal, Gopalan Sridharan
This review is focused at exploring the strengths of modern technology driven data compiled in the areas of virus gene sequencing, virus protein structures and their implication to viral diagnosis and therapy. The information for virome analysis (viromics) is generated by the study of viral genomes (entire nucleotide sequence) and viral genes (coding for protein). Presently, the study of viral infectious diseases in terms of etiopathogenesis and development of newer therapeutics is undergoing rapid changes...
December 2017: Virusdisease
https://www.readbyqxmd.com/read/29291212/variation-in-virome-diversity-in-wild-populations-of-penaeus-monodon-fabricius-1798-with-emphasis-on-pathogenic-viruses
#7
Fredmoore L Orosco, Arturo O Lluisma
Marine animals typically harbor a community of viruses, a number of which are known to cause diseases. In shrimp aquaculture, viral pathogens are the principal causes of major economic losses. However, the composition of the viral load of shrimps in wild population is poorly known. In this study, we explored the viral diversity in the microbiome of wild Penaeus monodon collected from six sites in the Philippines, with a view to detecting pathogenic forms. We employed a metagenomic approach via particle-associated nucleic acid isolation, sequence-independent single primer amplification, and pyrosequencing...
September 2017: Virusdisease
https://www.readbyqxmd.com/read/29280016/virome-analysis-of-lily-plants-reveals-a-new-potyvirus
#8
Yongqiang Li, Anning Jia, Yan Qiao, Jun Xiang, Yongjiang Zhang, Wenhe Wang
Lily plants exhibiting virus-like symptoms of leaf yellowing, twisting and brownish necrotic spots were collected, and next-generation sequencing of small RNAs was conducted to identify the associated viruses. Cucumber mosaic virus, lily symptomless virus and a hitherto unrecorded potyvirus, tentatively named "lily yellow mosaic virus" (LYMV), were detected. The genomic RNA of LYMV was 9811 nt in length, encoding a large polyprotein of 3,124 amino acids with a predicted Mr of 353.3 kDa. BLAST analysis showed that LYMV shared a high degree of amino acid sequence identity with Thunberg fritillary mosaic virus (55%), bean yellow mosaic virus (52%), clover yellow vein virus (51%), leek yellow stripe virus (51%), and lily mottle virus (52%), and these viruses clustered together in a phylogenetic tree...
December 26, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29206186/genomic-characterisation-of-vinegar-hill-virus-an-australian-nairovirus-isolated-in-1983-from-argas-robertsi-ticks-collected-from-cattle-egrets
#9
Penelope J Gauci, Jane McAllister, Ian R Mitchell, Daisy Cybinski, Toby St George, Aneta J Gubala
This report describes the near complete genomic sequence and subsequent analysis of Vinegar Hill virus (VINHV; tentative member of the genus Orthonairovirus, family Nairoviridae, order Bunyavirales). VINHV is the second nairovirus reported to be isolated on mainland Australia and the first to be sequenced and analysed. Our genetic analysis shows that VINHV belongs to the Dera Ghazi Khan genogroup, a group of viruses previously isolated in other parts of the world including Asia, South Africa, and the USA. We discuss possible routes of entry for nairoviruses into Australia and the need to understand the virome of Australian ticks in the context of new and emerging disease...
December 5, 2017: Viruses
https://www.readbyqxmd.com/read/29203935/viral-enteritis-in-calves
#10
REVIEW
Diego E Gomez, J Scott Weese
A complex community of bacteria, viruses, fungi, protists, and other microorganisms inhabit the gastrointestinal tract of calves and play important roles in gut health and disease. The viral component of the microbiome (the virome) is receiving increasing attention for its role in neonatal calf diarrhea (NCD). Rotavirus and coronavirus have for a long time been associated with NCD and commercial vaccines have been produced against these agents. Recently, several other viruses which may play a role in diarrhea have been discovered in calf fecal samples, mostly by sequence-based methods...
December 2017: Canadian Veterinary Journal. la Revue Vétérinaire Canadienne
https://www.readbyqxmd.com/read/29185594/simple-protocol-for-population-sanger-sequencing-for-zika-virus-genomic-regions
#11
Gabriela Bastos Cabral, João Leandro de Paula Ferreira, Renato Pereira de Souza, Mariana Sequetin Cunha, Adriana Luchs, Cristina Adelaide Figueiredo, Luís Fernando de Macedo Brígido
BACKGROUND: A number of Zika virus (ZIKV) sequences were obtained using Next-generation sequencing (NGS), a methodology widely applied in genetic diversity studies and virome discovery. However Sanger method is still a robust, affordable, rapid and specific tool to obtain valuable sequences. OBJECTIVE: The aim of this study was to develop a simple and robust Sanger sequencing protocol targeting ZIKV relevant genetic regions, as envelope protein and nonstructural protein 5 (NS5)...
November 27, 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29179741/dietary-energy-drives-the-dynamic-response-of-bovine-rumen-viral-communities
#12
Christopher L Anderson, Matthew B Sullivan, Samodha C Fernando
BACKGROUND: Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen...
November 28, 2017: Microbiome
https://www.readbyqxmd.com/read/29175107/viruses-of-archaea-structural-functional-environmental-and-evolutionary-genomics
#13
REVIEW
Mart Krupovic, Virginija Cvirkaite-Krupovic, Jaime Iranzo, David Prangishvili, Eugene V Koonin
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics...
November 22, 2017: Virus Research
https://www.readbyqxmd.com/read/29155033/the-gut-virome-of-the-protochordate-model-organism-ciona-intestinalis-subtype-a
#14
Brittany A Leigh, Anni Djurhuus, Mya Breitbart, Larry J Dishaw
The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members...
November 15, 2017: Virus Research
https://www.readbyqxmd.com/read/29154906/increase-in-taxonomic-assignment-efficiency-of-viral-reads-in-metagenomic-studies
#15
S François, D Filloux, M Frayssinet, P Roumagnac, D P Martin, M Ogliastro, R Froissart
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms...
November 14, 2017: Virus Research
https://www.readbyqxmd.com/read/29140453/faecal-transplantation-for-ibd-management-pitfalls-and-promises
#16
M N Quraishi, T Critchlow, N Bhala, N Sharma, T Iqbal
Background: Faecal microbiota transplantation (FMT) as a potential treatment for inflammatory bowel disease (IBD) is an area of active current research, having been stimulated by the remarkable efficacy of FMT in treatment of Clostridium difficile-associated colitis. Sources of data: This review is based on data from numerous case series on FMT in IBD since 1989 and results of four RCTs in ulcerative colitis (UC); three fully published. Areas of agreement: Early signals of short to medium-term efficacy of FMT for UC are promising...
November 13, 2017: British Medical Bulletin
https://www.readbyqxmd.com/read/29138044/new-insight-into-the-rna-aquatic-virosphere-via-viromics
#17
REVIEW
Alexander Culley
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research...
November 11, 2017: Virus Research
https://www.readbyqxmd.com/read/29133882/discovery-of-an-expansive-bacteriophage-family-that-includes-the-most-abundant-viruses-from-the-human-gut
#18
Natalya Yutin, Kira S Makarova, Ayal B Gussow, Mart Krupovic, Anca Segall, Robert A Edwards, Eugene V Koonin
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery (1-3) . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome (4) . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study...
November 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29118750/an-rna-virome-associated-to-the-golden-orb-weaver-spider-nephila-clavipes
#19
Humberto J Debat
The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated to N...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29117243/virome-analysis-of-two-sympatric-bat-species-desmodus-rotundus-and-molossus-molossus-in-french-guiana
#20
Arielle Salmier, Sourakhata Tirera, Benoit de Thoisy, Alain Franc, Edith Darcissac, Damien Donato, Christiane Bouchier, Vincent Lacoste, Anne Lavergne
Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats...
2017: PloS One
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