Viral genome assembly and classification
The output sequencing data (.fast5) from MinKNOW software was base-called with Guppy software using the High Accuracy (HAC) model to generate nucleotide sequence data for each fragment (reads) in the fastq format. These base-called data were then processed through the established workflow wf-artic on EPI2ME software to be assembled into consensus sequences. Only reads with average Phred Quality (Q) score above 9 and minimum and maximum length of 250 and 1500 bps were used in the assembly process. The consensus sequences were then classified using the Pangolin tool (4.1.1) and Pangolin data set (v1.14).