Sequence positions in this work refer to GenBank RefSeq sequence NC_045512.2, a genome isolated and sequenced from Wuhan (China), early in the pandemic. Single Nucleotide Polymorphisms (SNPs) and insertions/deletions (INDELs) were assessed in each sample by using snippy variant calling and core genome alignment pipeline v4.6.0 (https://github.com/tseemann/snippy), which uses FreeBayes v1.3.2 [89] variant caller and snpEff v5.0 [90] to annotate and predict the effects of variants on genes and proteins. Genome map and histogram of SNPs were generated after running MAFFT v7.471 alignment using a modified code from Lu et al. 2020 (https://github.com/laduplessis/SARS-CoV-2_Guangdong_genomic_epidemiology/). Moreover, we identified global virus lineages using Nextclade v0.8.1 (https://clades.nextstrain.org/) and Pangolin v2.1.3 (https://github.com/cov-lineages/pangolin [15];).
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