a, Similarity plot of the full-length genomes and S gene sequences of pangolin-CoV against sequences of SARS-CoV-2 strain WIV02, as well as RaTG13, ZC45 and ZXC21. Although pangolin-CoV has a high sequence identity to SARS-CoV-2 and RaTG13 in most regions of the S gene, it is more similar to ZXC21 and ZC45 at the 5′ end. SARS-rCoV, SARS-related coronavirus. Parameters for the similarity plots are: window, 500 bp; step, 50 bp; gap strip, on; Kimura (2 parameter); T/t 2.0. b, Because of the presence of genetic recombination, there is discrepancy in cluster formation among the outcomes of phylogenetic analyses of different regions of the S gene. c, Phylogeny of coronaviruses closely related to SARS-CoV-2, based on full genome sequences. The phylogenetic tree was constructed using RAxML with the substitution model GTRGAMMAI and 1,000 bootstrap replicates. Numbers (>70) above or below branches are percentage bootstrap values for the associated nodes. The scale bar represents the number of substitutions per site. Red circles indicate the pangolin coronavirus sequences generated in this study, and blue triangles indicate SARS-CoV-2 sequences from humans.