An evaluation of avian influenza virus whole-genome sequencing approaches using nanopore technology
February 19, 2023
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.
Citation Information
Publication Year | 2023 |
---|---|
Title | An evaluation of avian influenza virus whole-genome sequencing approaches using nanopore technology |
DOI | 10.3390/microorganisms11020529 |
Authors | Hon S. Ip, Sarah Uhm, Mary Lea Killian, Mia Kim Torchetti |
Publication Type | Article |
Publication Subtype | Journal Article |
Series Title | Microorganisms |
Index ID | 70240833 |
Record Source | USGS Publications Warehouse |
USGS Organization | National Wildlife Health Center |
Related
Raw MinION FASTQ datafiles corresponding to the paper “A comparison of avian influenza virus whole genome sequencing approaches using nanopore technology”
Raw sequencing data as generated by the five different methods used are provided for each of the three samples used in the comparison. The files are in FASTQ format as exported from the Oxford Nanopore’s MK1C using MinION flowcells. Files are labeled according to the method (as described in the paper) and the Sample ID). The MK1C exports data in blocks of 6000 reads per FASTQ file and...
Related
Raw MinION FASTQ datafiles corresponding to the paper “A comparison of avian influenza virus whole genome sequencing approaches using nanopore technology”
Raw sequencing data as generated by the five different methods used are provided for each of the three samples used in the comparison. The files are in FASTQ format as exported from the Oxford Nanopore’s MK1C using MinION flowcells. Files are labeled according to the method (as described in the paper) and the Sample ID). The MK1C exports data in blocks of 6000 reads per FASTQ file and...