design: Double-stranded cDNA using the NEBNext ARTIC SARS-CoV-2 RT-PCR Module V1. Library preparation using Nextera DNA Library Prep kit with 1 ng of double-stranded cDNA product then sequenced using the MiSeq System (Illumina). Paired-end Illumina reads were assembled using a custom reference guided alignment script (https://github.com/APHA-VGBR/WGS_Pipelines/blob/7f73c31629f483994b8aa366e157028abf69f824/RefGuidedAlignment_Public.sh) using SARS-CoV-2/human/China/WIV04/2020 (GenBank Accession No: MN996528) as the reference sequence.