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 was further performed using BEAST with the complete genome, the nonrecombinant region (positions 1 to 17,300), and the potential recombinant region (positions 17,301 to 24,000), respectively (Fig. 4) . The phylogenies revealed by the BEAST trees were consistent with those from the maximum-likelihood trees. In the trees constructed using the complete genome and the nonrecombinant region, ChinaGD01 fell within group 3; however, trees constructed using the recombinant region clustered with the group 5 sequences. To date the recombination event, we estimated the time to most recent common ancestor for the novel MERS-CoV from 2015. Although there was a slight difference among results from different models, the time to most recent common ancestor of the 2015 cluster was estimated to be between 0.5 and 0.7 years before the identification of the imported case in the latter months of 2014 (Table 2) . Given the observation of similar recombination events in the newly released South Korean strains and the latest strains prevalent in Saudi Arabia, the travel histories of patients, and potential opportunities for virus exposure, we surmise that the recombination likely occurred in the Arabian Peninsula.