The origin and underlying driving forces of the SARS-CoV-2 outbreak

Shu-Miaw Chaw; Jui-Hung Tai; Shi-Lun Chen; Chia-Hung Hsieh; Sui-Yuan Chang; Shiou-Hwei Yeh; Wei-Shiung Yang; Pei-Jer Chen; Hurng-Yi Wang

After cross-referencing with the haplotype network and the phylogeny, all mutations 158 listed as high frequency in Table 2 and Fig. 1a were re-assigned to the other side of the 159 frequency spectra. We only see an excess of singleton mutations, consistent with a recent reaching approximately 30% by 1/23/2020, suggesting that 84S may exhibit some advantage 168 over 84L. If genomes carrying 84S were ancestral, it would be a challenge to explain its 169 absence in early samplings. In addition, as mentioned above, C-T transitions are dominant in 170 coronavirus evolution and multiple hits were observed in SARS-CoV-2 (Fig. 2 ). It is 171 therefore possible that 28814C mutated to T after ancestral SARS-CoV-2 diverged from the 172 common ancestor with RaTG13 and recently changed back to C. Finally, if 84L is indeed a 173 derived haplotype and has rapidly increased in its frequency by positive selection, we would 174 expect haplotypes carrying 84L to have accumulated more derived mutations than haplotypes 175 with 84S. However, after correcting for mutational direction, the two haplotypes exhibited In addition to L84S, a G-T transversion at 26114 which caused an amino acid change 180 in orf3 protein (G251V) is also at intermediate frequency (Table 2) . 251V was first seen on 181 1/22/2020 and gradually increased its frequency to 13% by our sampling date (Fig. 3) . We 182 note that the emergence of 84S in orf8 and 251V in orf3 are consistent with the lockdown of 183 Wuhan on 1/23/2020. The former first appeared in early January, gradually increased its 184 frequency, and reached a plateau around 1/23/2020. The latter showed up on 1/22/2020 and 185 rapidly increased its frequency within two weeks. (Table 1) , such inflation would have a large effect on dN/dS estimates. 193 We therefore excluded singletons from dN and dS estimation.