The coronavirus disease discovered in 2019 (COVID-19) is caused by recently discovered human Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). An initial step of the SARS-CoV-2 entrance into the host cell depends on the spike (S) protein which interacts with the angiotensin-converting enzyme 2 (ACE2) as a receptor, via the receptor binding domain (RBD). We compared the S proteins from SARS-CoV-2, SARS, bat and pangolin CoVs. The most striking fact firstly discovered in this study is that the relative proportion of the synonymous substitution rates between SARS-CoV-2 and pangolin CoV are significantly higher than the corresponding characteristics for other CoVs studied. By comparing with SARS and bat CoVs, the significantly higher rate of the synonymous substitutions between the human SARS-CoV-2 and the pangolin CoV puts several intriguing questions on an emergence and the duration of divergence of the SARS-CoV-2.