Ip, H.S.; Uhm, S.; Killian, M.L.; Torchetti, M.K. An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology. Microorganisms2023, 11, 529.
Ip, H.S.; Uhm, S.; Killian, M.L.; Torchetti, M.K. An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology. Microorganisms 2023, 11, 529.
Abstract
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 investigated 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 evaluated this platform for routine use in a diagnostic laboratory. In this study we evaluated different primer sets for the whole genome amplification of influenza A virus and evaluated five different library preparation approaches for sequencing on the nanopore platform using the MinION flow-cell. A limited amplification procedure and a rapid procedure were found to be best among the approaches taken.
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
