Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis

Wang, Yanqun; Liu, Di; Shi, Weifeng; Lu, Roujian; Wang, Wenling; Zhao, Yanjie; Deng, Yao; Zhou, Weimin; Ren, Hongguang; Wu, Jun; Wang, Yu; Wu, Guizhen; Gao, George F.; Tan, Wenjie

The genome sequence of this virus, referred to as ChinaGD01, had high levels of nucleotide identity (99.33% to 99.79%) to previously published MERS-CoV genomes (Fig. 2) , with 99.31% to 99.78% sequence identity in the open reading frame 1a and -b (ORF1ab) gene segment and 98.91% to 99.60% identity in the S gene. The E, M, and N genes had 98.93% to 100% identity with previously described MERS-CoV strains. In total, ChinaGD01 possessed 11 nonsynonymous nucleotide substitutions (Table 1) , which occurred in the ORF1ab (n Ï­ 8), ORF3 (n Ï­ 1), ORF4b (n Ï­ 1), and M (n Ï­ 1) genes, respectively (Table 1) . Although there were five nucleotide substitutions in the S gene, no amino acid change was discovered. Of note, in comparison with previously published MERS-CoV genomes, the ChinaGD01 genome shows 11 unique amino acid substitutions, and 8 of them were shared with the newly released South Korean strains and the latest strains prevalent in Saudi Arabia (Table 1) .