Amplicon sequencing of SARS-CoV-2: nasal wash DI hamster 4 4dpi
The cDNA was used to amplify a fragment of 356bp along the spike region of interest (positions 23,468 to 23,821) using the Artic primer pair nCoV-2019_78 V3 (https://artic.network/ncov-2019). The purified amplicons were barcoded with the Native Barcode expansion kit (Oxford Nanopore, EXP-NBD196) and PCR-free libraries were prepared using the ligation sequencing (Oxford Nanopore, SQK-LSK109). A total of 20 fmol of the multiplexed library was sequenced on a Flongle flowcell (Oxford Nanopore, FLO-FLG001) in a single 8-hour run. Sequencing data acquisition was done with the ONT software MinKNOW v4.3.7.