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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| Format: | Article |
| Language: | English |
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Wiley
2018-01-01
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| Series: | Advances in Virology |
| Online Access: | http://dx.doi.org/10.1155/2018/3248285 |
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| author | Andrey A. Ayginin Ekaterina V. Pimkina Alina D. Matsvay Anna S. Speranskaya Marina V. Safonova Ekaterina A. Blinova Ilya V. Artyushin Vladimir G. Dedkov German A. Shipulin Kamil Khafizov |
| author_facet | Andrey A. Ayginin Ekaterina V. Pimkina Alina D. Matsvay Anna S. Speranskaya Marina V. Safonova Ekaterina A. Blinova Ilya V. Artyushin Vladimir G. Dedkov German A. Shipulin Kamil Khafizov |
| author_sort | Andrey A. Ayginin |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-3363cc522a944a3d853ee1c58ac1da5a |
| institution | Kabale University |
| issn | 1687-8639 1687-8647 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advances in Virology |
| spelling | doaj-art-3363cc522a944a3d853ee1c58ac1da5a2025-02-03T05:48:01ZengWileyAdvances in Virology1687-86391687-86472018-01-01201810.1155/2018/32482853248285The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer PanelsAndrey A. Ayginin0Ekaterina V. Pimkina1Alina D. Matsvay2Anna S. Speranskaya3Marina V. Safonova4Ekaterina A. Blinova5Ilya V. Artyushin6Vladimir G. Dedkov7German A. Shipulin8Kamil Khafizov9Central Research Institute of Epidemiology, Moscow 111123, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaLomonosov Moscow State University, Moscow 119991, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaCentral Research Institute of Epidemiology, Moscow 111123, RussiaAdvances 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.http://dx.doi.org/10.1155/2018/3248285 |
| spellingShingle | Andrey A. Ayginin Ekaterina V. Pimkina Alina D. Matsvay Anna S. Speranskaya Marina V. Safonova Ekaterina A. Blinova Ilya V. Artyushin Vladimir G. Dedkov German A. Shipulin Kamil Khafizov The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels Advances in Virology |
| title | The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels |
| title_full | The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels |
| title_fullStr | The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels |
| title_full_unstemmed | The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels |
| title_short | The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels |
| title_sort | study of viral rna diversity in bird samples using de novo designed multiplex genus specific primer panels |
| url | http://dx.doi.org/10.1155/2018/3248285 |
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