The spike proteins of CoVs are responsible for receptor binding and host species adaptation, and their genes therefore constitute one of the most variable regions within CoV genomes (10,11). The phylogenetic tree based on the amino acid sequences of spike protein (Figure 2) suggests that the selected betacoronaviruses were mainly divided into 5 clusters: SARS cluster; bat SARS-like cluster; civet SARS-like cluster; human betacoronavirus cluster; and EMC cluster. Bat Rp-coronavirus/Shaanxi2011 and Bat Cp-coronavirus/Yunnan2011 shared 89.4% aa identity in spike proteins, which consisted of 1,240 aa and 1,241 aa, respectively. The spike proteins of the CoVs in our analysis have 89.8%–92.7% aa identity with those of bat SARS-like CoVs, with substantial similarity in the receptor-binding domain. The close relationship also was observed with the SARS-CoVs (79.2%–79.4% aa identity) and civet SARS-like CoVs (78.9%–79.1% aa identity). In contrast, the human betacoronaviruses and EMC cluster formed separate clusters distinct from SARS-related CoVs that showed only 27.8%–29.4% aa and 28.8%–30.5% aa identities with the betacoronaviruses, respectively, in our analysis. The genome sequences reported here have been deposited into GenBank (accession nos. JX993987–JX993988).