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

Phylogenetic analysis. To further investigate the genetic relationship between ChinaGD01 and other MERS-CoV strains whose genomes are available, we performed phylogenetic analyses using the complete genome, the ORF1ab gene, and the S gene. From the whole-genome phylogeny, all available MERS-CoV strains can be clustered into two clades, the earlier clade A and the more recent clade B ( Fig. 2A) . ChinaGD01 fell into group 3 of clade B ( Fig. 2A) . Within group 3, ChinaGD01 and the South Korean and Saudi Arabian strains from 2015 were closely clustered and formed a long branch, separate from others of group 3. The nearest strain to this branch was Hafr-Al-Batin-1-2013 (GenBank accession no. KF600628), isolated in August 2013. Phylogenetic analysis of the ORF1ab gene indicated a similar topology in which ChinaGD01 and the recent MERS-CoV strains identified in South Korea were closely adjacent to Hafr-Al-Batin-1-2013 in group 3 (Fig. 2B) . However, the phylogeny of the S gene differed in that the new viruses fell into group 5 and were closely related to viruses from both humans and dromedaries (Fig. 2C ). These findings are consistent with recombination, a phenomenon not uncommon in coronaviruses.