MinION seq of SARS-CoV-2: Oral and nasopharyngeal swabs
Sequencing of SARS-CoV-2 genomes was performed using the ARTIC SARS-CoV-2 sequencing protocol (https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bp2l6n26rgqe/v3?version_warning=no) on the Oxford Nanopore Technology (UK) MinION device. The ARTIC V3 primer sets were purchased as pools (Integrated DNA Technologies, USA), and the PCR and library preparation were carried out according to the ARTIC V3 sequencing protocol. For suspected Omicron samples, the updated ARTIC V4.1 primer sets were utilised (Integrated DNA Technologies, USA). Sequencing was carried out using an R.9.4.1 flow cell on a MinION device