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Title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels
Authors: Andrey A. Ayginin 
Ekaterina V. Pimkina 
Alina D. Matsvay 
Anna S. Speranskaya 
Marina V. Safonova 
Ekaterina A. Blinova 
Ilya V. Artyushin 
Dedkov, Vladimir G 
German A. Shipulin 
Kamil Khafizov 
Issue Date: Aug-2018
Source: Andrey A. Ayginin, Ekaterina V. Pimkina, Alina D. Matsvay, et al., “The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels,” Advances in Virology, vol. 2018, Article ID 3248285, 10 pages, 2018.
Journal: Advances in Virology 
Abstract: 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
DOI: 10.1155/2018/3248285
Appears in Collections:Cтатьи в журналах/Journal articles

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