Phylogenetic tree of 47 S gene sequences from human patients and animals. The evolutionary process of S proteins during whole epidemic was simplified into three epidemic groups: 02–04 interspecies, 03-early-mid, and 03-late epidemic groups. Each group includes 15 unique S gene sequences after deleting all duplicate sequences (Table S1, see additional file 2). Two sequences isolated from bats were used as the outgroup in phylogenetic tree construction. The tree was constructed by the maximum likelihood method with 1000 bootstrap replicates using PHYML v2.4.4. Only the branch bootstrap values ≥ 50% are shown. PC, palm civet; HP, human patient.