Fig. 1

Genome similarity and phylogenetic analysis of SARS-CoV-2 and related viruses: a SimPlot sliding window analysis of changing patterns of sequence similarity between: the Wuhan SARS-CoV-2 2020 reference genome with the RatTG13 CoV genome (green) and the consensus genomes of the GD Pangolin CoV (red), GX Pangolin CoV (orange), Bat CoVZ (violet) and Bat SL-VoC (gray) groups. Gene limits for genes ORF1ab, S, ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N and ORF10, as well as for the RB domain, are shown at the top of the figure. Different groups of sequences merged in SimPlot analysis are represented by different colors corresponding to species clusters in the whole genome phylogeny shown in panel (b) of the figure; b Whole genome phylogeny of 25 SARS-CoV and SARS-CoV-2-related organisms. Species clusters are indicated on the right. Bootstrap scores are indicated on the internal branches of the tree. Branches with bootstrap score lower than 60% were collapsed. The tree was inferred using the RAxML method with the most suitable for these data, the HKY-gamma evolutionary model, and 100 replicates in bootstrapping