Fig. 1

Genetic comparison of S gene of SARS-CoV-2 and other coronaviruses. a Phylogenetic tree depicting the relationship between S gene of 76 coronavirus (CoVs) isolates from different hosts and 148 SARS-CoV-2 isolates. CoVs were classified by genus (α, β, γ and δCoVs) and each cluster is shown in a different color. The A7 cluster in red, grouped the SARS-CoV-2 and other related CoVs, each one is marked with a colored circle. The number presented in the nodes indicates posterior probabilities, and the scale bar represents the average number of nucleotide substitutions. All nodes in the A7 cluster had posterior probabilities of 1.0. b Haplotype network of S gene, the colored circles represent each CoV according to the A7 cluster in the tree. The PcoV_GX_P5L, P5E, P1E, P4L and P2V were named as Pangolin groups. Small black circles represent hypothetical or unsampled haplotypes. The small black circles, marked with a (?), indicate the hypothetical ancestors of SARS-CoV-2_Wuhan_Hu-1, RaTG13, RaTG13, MP789 and RmYN02. The numbers indicate the number of mutations that separate each haplotype. c Patterns of nucleotide sequence identity in the S gene for SARS-CoV-2_Wuhan_Hu-1, RaTG13, MP789, RmYN02 and Pangolin group. Similarity was calculated within sliding window of 300 bp moving with steps of 30 bp