The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels

Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associatio...

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Bibliographic Details
Published in:Advances in virology 2018-01, Vol.2018 (2018), p.1-10
Main Authors: Khafizov, Kamil, Shipulin, German A., Artyushin, Ilya V., Blinova, Ekaterina A., Safonova, Marina V., Speranskaya, Anna S., Matsvay, Alina D., Pimkina, Ekaterina V., Ayginin, Andrey A., Dedkov, Vladimir G.
Format: Article
Language:English
Subjects:
Bioinformatics
Bird migration
Computer applications
Data processing
Deoxyribonucleic acid
DNA
Genera
Genomes
Identification
Infections
Infectious diseases
Medical research
Methods
Oligonucleotides
Pathogens
Polymerase chain reaction
Primers
rRNA 16S
Severe acute respiratory syndrome
Viral infections
Virology
Viruses
West Nile virus
Zoonoses
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Summary:Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated.
ISSN:1687-8639
1687-8647
DOI:10.1155/2018/3248285