Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003

Vega, Vinsensius B; Ruan, Yijun; Liu, Jianjun; Lee, Wah Heng; Wei, Chia Lin; Se-Thoe, Su Yun; Tang, Kin Fai; Zhang, Tao; Kolatkar, Prasanna R; Ooi, Eng Eong; Ling, Ai Ee; Stanton, Lawrence W; Long, Philip M; Liu, Edison T

Our proposed mutation filter, which is based on these observations, seems to be stable and effective. Using this filter, reconstruction of molecular phylogenetic relations of the 54 SARS-CoV genomes revealed at least three major branches composed of cases related to Hotel M (Hong Kong), cases reported in North China, and cases found in Taiwan. Moreover, we show that these molecular sequence associations can be effectively used to more precisely reconstruct contact tracing. Our estimated the daily substitution rate of SARS-CoV to be 0.1722 nucleotides, or 5.7 × 10 -6 nucleotide substitutions per site, a mutation rate similar to other RNA viruses [13, 14] . Taking the SARS-CoV isolated from palm civet cat as the putative originating SARS-CoV, our calculations suggest that the earliest possible date for SARS emergence is predicted to be Oct 21, 2002. During the final preparation of this manuscript two reports were published addressing the muta- Figure 3 Molecular relationship between 54 SARS-CoV genomes. The phylogenetic tree reconstructed using PAUP* on nucleotide variations shared by more than two isolates. The tree was re-rooted on the earliest reported case, i.e. TOR2. Four major branches can be observed in the tree, each largely belonging to a certain geographical origin. Two of which encompass the Singapore cases, indicating the possibility of separate infection sources of the Singapore cases.