a, Sliding window analysis of changing patterns of sequence similarity between human SARS-CoV-2, pangolin and bat coronaviruses. The potential recombination breakpoints are shown in pink dash lines, and regions separated by the breakpoints are alternatively shaded in yellow. These potential breakpoints subdivide the genomes into eight regions (regions with fewer than 200 bp were omitted), indicated by the red bars at the bottom of the analysis boxes. The names of the query sequences are shown vertically to the right of the analysis boxes. The similarities to different reference sequences are indicated by different colours. Guangdong pangolin-CoV GD/P1L and pangolin-CoV GD/P2S were merged for this analysis. The blue arrows at the top indicate the position of the ORFs in the alignment. b, Phylogenetic trees of different genomic regions. SARS-CoV- and SARS-CoV-2-related lineages are shown in blue and red tree branches, respectively. Branch supports obtained from 1,000 bootstrap replicates are shown. Branch scale bars are shown as 0.1 substitutions per site.