Fig. 2

ML phylogenetic trees based on indicated genomic fragments of 166 PDCoV strains. (A) ORF 1a/b complete nucleotide sequences; (B) ORF Spike complete nucleotide sequences; (C) ORFs E-N complete nucleotide sequences. Multiple sequence alignment was performed using ClustalW. The phylogenetic trees were constructed in IQ-TREE multicore version 1.6.12 using the best-fitting model GTR + F + I + G4 for (A), TN + F + I + G4 for (B), and TNe + I + G4 for (C) with 1000 bootstraps. The China PDCoV viruses are indicated in red branches or red circles. The human Haiti PDCoV strains are indicated in blue circles. The scale bar represents nucleotide substitutions per site. The information on each virus in (A), (B), and (C) is detailed in Supplementary Figs. 2, 3, and 4, respectively