Fig. 3
From: Development of a portable avian influenza virus characterisation system: bringing the inside-out
Portable AIV characterisation system. (1) Swabs were collected from mallard ducks in several locations around New Zealand between 2023 and 2024. (2) RNA was extracted using QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany) on the Bento Lab Pro (Bento Bioworks Ltd, London, UK) centrifuge component. The Influenza A RT-qPCR assay can be performed on the MIC PCR instrument (BioMolecular Systems, New South Wales, Australia) prior to whole-genome amplification of the virus. (3) Whole-genome amplification by multi-segment AIV-specific RT-PCR was performed on the Bento Lab Pro thermal cycler component. (4) Quantification of purified amplicons was measured using Qubit 4.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). There is an option to run the purified amplicons on a precast electrophoresis gel to determine the size of the amplicons prior to sequencing (not shown). (5) Amplified cDNA products were prepared for sequencing using the Oxford Nanopore Technologies Rapid Barcoding kit V14 (Oxford Nanopore Technologies, London, UK) and sequenced using R10.4.1 MinION flow cells (Oxford Nanopore Technologies, London, UK). (6) AIV subtypes for each sample were identified using the automated subtyping pipeline that we developed, Flui. In blue boxes, are the approximate time needed for each step. Created in BioRender. Wilson, A. (2025) https://BioRender.com/7erudlf.
