Fig. 1.

A phylogeny of spike gene nucleotide sequences from SCoV isolated from humans, civets and raccoon dogs. This phylogeny was modified and adopted from Lam et al. (2008a). Sequences from humans, civets, raccoon dogs and bats were indicated with symbols ■, ○, ▴ and ♦, respectively. The tree was constructed using ML method, with confidences of topology summarized from 5000 trees sampled from ML and NJ bootstrap replicates and BMCMC samples. Only confidence values of major clusters were shown (ML/NJ/BMCMC, in the parenthesis). The human epidemic cluster (2002–2003) was divided into late, early and middle phases according to a previous study (CSMEC, 2004). Accession numbers of the sequences are shown within round brackets after their strain names (in bold). The distance unit was substitutions/site. Rp3 isolated from bats (♦) was used as an out-group to root the tree, and the genetic distance of its branch is not shown.