SARS-CoV-2 Lineage Identification Protocol

Sequencing data was analyzed using DRAGEN COVID Lineage (version 3.5.9; Illumina Inc., USA) and method as described previously [11 (link),12 (link)]. In brief, sequencing reads of human origin were removed using NCBI Human Read Scrubber algorithm. ARTIC primer sequences were removed from the reads, followed by aligning to the reference genome Wuhan-Hu-1 (GenBank accession number MN908947.3) using DRAGEN (Illumina Inc., USA). Samples with less than 90 amplicons detected are filtered. Variant calling and consensus genome assembly with respect to the reference genome were performed using DRAGEN (Illumina Inc., USA) using default parameters. Nucleotide and amino acid positions were numbered according to the reference genome. All genome sequences analyzed in this study were submitted to GISAID under accession numbers EPI_ISI_13822514 to 13822565 and EPI_ISI_14336314 to 14336324. Pangolin lineages of the consensus genomes were assigned using Pangolin COVID-19 Lineage Assigner (version 4.0.2) [13 (link)]. Phylogenetic clades of the consensus genomes were mapped using Nextclade (version 1.11.0) [14 (link)].