Viral metagenomics and sugarcane pathogens

2018 ◽  
pp. 183-200 ◽  
Author(s):  
Philippe Roumagnac ◽  
◽  
Dimitre Mollov ◽  
Jean-Heinrich Daugrois ◽  
Denis Filloux ◽  
...  
Keyword(s):  
Viral Metagenomics

scholarly journals Viral metagenomics

2007 ◽  
Vol 17 (2) ◽  
pp. 115-131 ◽  
Author(s):  
Eric L. Delwart
Keyword(s):  
Viral Metagenomics

Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities

2018 ◽  
pp. 77-95 ◽  
Author(s):  
Sarah François ◽  
Denis Filloux ◽  
Emmanuel Fernandez ◽  
Mylène Ogliastro ◽  
Philippe Roumagnac
Keyword(s):  
High Resolution ◽  
Viral Metagenomics ◽  
Viral Communities

scholarly journals Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jian Zeng ◽  
Yan Wang ◽  
Ju Zhang ◽  
Shixing Yang ◽  
Wen Zhang
Keyword(s):  
Gc Content ◽  
Cloacal Swab ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Viral Metagenomics ◽  
Toxin Gene ◽  
Microbial Genomes ◽  
The Family ◽  
Zonula Occludens Toxin ◽  
Reference Strains

AbstractMembers of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.

scholarly journals A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil

Virology ◽  
2021 ◽  
Vol 552 ◽  
pp. 1-9
Author(s):  
Samuel Cibulski ◽  
Diane Alves de Lima ◽  
Helton Fernandes dos Santos ◽  
Thais Fumaco Teixeira ◽  
Caroline Tochetto ◽  
...  
Keyword(s):  
Viral Metagenomics

scholarly journals Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1432
Author(s):  
Xavier Fernandez-Cassi ◽  
Sandra Martínez-Puchol ◽  
Marcelle Silva-Sales ◽  
Thais Cornejo ◽  
Rosa Bartolome ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Gastroenteritis ◽  
Clinical Analysis ◽  
Viral Metagenomics ◽  
Next Generation ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Viral Pathogen ◽  
Infectious Gastroenteritis ◽  
Generation Sequencing

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.

scholarly journals An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1057 ◽  
Author(s):  
Ian Hewson ◽  
Mitchell R. Johnson ◽  
Ian R. Tibbetts
Keyword(s):  
Viral Genome ◽  
Sea Cucumber ◽  
Rna Viruses ◽  
Viral Metagenomics ◽  
Single Specimen ◽  
Wasting Disease ◽  
Double Stranded Rna ◽  
Marine Habitats ◽  
Positive Sense ◽  
Normal Specimen

Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.

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