An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-02-01
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| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/2/529 |
| _version_ | 1827756304789143552 |
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| author | Hon S. Ip Sarah Uhm Mary Lea Killian Mia K. Torchetti |
| author_facet | Hon S. Ip Sarah Uhm Mary Lea Killian Mia K. Torchetti |
| author_sort | Hon S. Ip |
| collection | DOAJ |
| description | As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken. |
| first_indexed | 2024-03-11T08:23:17Z |
| format | Article |
| id | doaj.art-949bc92feae341929dda284b612a191b |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T08:23:17Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-949bc92feae341929dda284b612a191b2023-11-16T22:17:09ZengMDPI AGMicroorganisms2076-26072023-02-0111252910.3390/microorganisms11020529An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore TechnologyHon S. Ip0Sarah Uhm1Mary Lea Killian2Mia K. Torchetti3National Wildlife Health Center, U.S. Geological Survey, Department of the Interior, Madison, WI 53711, USADepartment of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USANational Veterinary Services Laboratories, U.S. Department of Agriculture, Ames, IA 50010, USANational Veterinary Services Laboratories, U.S. Department of Agriculture, Ames, IA 50010, USAAs exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken.https://www.mdpi.com/2076-2607/11/2/529avian influenzawhole-genome sequencingnext-generation sequencingnanopore sequencing |
| spellingShingle | Hon S. Ip Sarah Uhm Mary Lea Killian Mia K. Torchetti An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology Microorganisms avian influenza whole-genome sequencing next-generation sequencing nanopore sequencing |
| title | An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology |
| title_full | An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology |
| title_fullStr | An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology |
| title_full_unstemmed | An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology |
| title_short | An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology |
| title_sort | evaluation of avian influenza virus whole genome sequencing approaches using nanopore technology |
| topic | avian influenza whole-genome sequencing next-generation sequencing nanopore sequencing |
| url | https://www.mdpi.com/2076-2607/11/2/529 |
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