Figure 1.

Genetic characterization of pangolin-CoVs in pangolin muscles

A: The five samples that yielded positive RT-PCR signals of SC2r-CoVs. The nomenclature of mitochondrial DNA (mtDNA) clusters used for inferring the possible geographic origins of the samples is given in reference (Hu et al., 2020). B: Sequencing depth of clean reads remapped to MP20 using nucleotide extraction and enrichment technologies. The genome organization of the SARS-CoV-2 reference strain MN908947 is shown. C: Sliding window analysis of nucleotide sequence similarity between SARS-CoV-2 and SC2r-CoVs/SARSr-CoVs from bats and pangolins. D: Maximum likelihood tree based on the alignment of the 22 genomes with the substitution model GTR+I+G4. Bootstrap values calculated from 1000 replicates are shown.