scholarly journals Evolution of selective-sequencing approaches for virus discovery and virome analysis

2017 ◽  
Vol 239 ◽  
pp. 172-179 ◽  
Author(s):  
Arvind Kumar ◽  
Satyapramod Murthy ◽  
Amit Kapoor
2013 ◽  
Vol 19 (5) ◽  
pp. 743-747 ◽  
Author(s):  
Jordan Levinson ◽  
Tiffany L. Bogich ◽  
Kevin J. Olival ◽  
Jonathan H. Epstein ◽  
Christine K. Johnson ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Claudia Kohl ◽  
Annika Brinkmann ◽  
Aleksandar Radonić ◽  
Piotr Wojtek Dabrowski ◽  
Kristin Mühldorfer ◽  
...  

AbstractBats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.


2013 ◽  
Vol 16 (4) ◽  
pp. 507-513 ◽  
Author(s):  
Sandra Junglen ◽  
Christian Drosten

2018 ◽  
Vol 64 (10) ◽  
pp. 761-773 ◽  
Author(s):  
Joost T.P. Verhoeven ◽  
Marta Canuti ◽  
Hannah J. Munro ◽  
Suzanne C. Dufour ◽  
Andrew S. Lang

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (less than US$5 per sample), and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing, and microbiome profiling. ViDiT–CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal–cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT–CACTUS demonstrated its validity in a wide range of microbiology applications, and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Harrison S. Edwards ◽  
Raga Krishnakumar ◽  
Anupama Sinha ◽  
Sara W. Bird ◽  
Kamlesh D. Patel ◽  
...  

An amendment to this paper has been published and can be accessed via a link at the top of the paper.


2015 ◽  
Vol 89 (13) ◽  
pp. 6532-6535 ◽  
Author(s):  
Marilyn J. Roossinck

Viruses are being redefined as more than just pathogens. They are also critical symbiotic partners in the health of their hosts. In some cases, viruses have fused with their hosts in symbiogenetic relationships. Mutualistic interactions are found in plant, insect, and mammalian viruses, as well as with eukaryotic and prokaryotic microbes, and some interactions involve multiple players of the holobiont. With increased virus discovery, more mutualistic interactions are being described and more will undoubtedly be discovered.


Viruses ◽  
2011 ◽  
Vol 3 (10) ◽  
pp. 1849-1869 ◽  
Author(s):  
Sijun Liu ◽  
Diveena Vijayendran ◽  
Bryony C. Bonning

2014 ◽  
Vol 61 (4) ◽  
pp. 293-299 ◽  
Author(s):  
T. Rosseel ◽  
B. Pardon ◽  
K. De Clercq ◽  
O. Ozhelvaci ◽  
S. Van Borm

2015 ◽  
Vol 105 (6) ◽  
pp. 716-727 ◽  
Author(s):  
Marilyn J. Roossinck ◽  
Darren P. Martin ◽  
Philippe Roumagnac

In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems—aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.


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