Selection of sequence data

The complete genomes of different MERS and MERS related isolates were retrieved from GenBank (http://www.ncbi.nlm.nih.gov/nuccore/?term=Middle+East+respiratory+syndrome+coronavirus%3B+complete+genome, and http://www.ncbi.nlm.nih.gov). Then the sequences were selected according to their geographical distribution, the isolation date, and the host species [46–50]. To analyse the codon usage bias of MERS strains, we selected only those viruses with complete genome and complete CDS information. Detailed information about the 71 MERS and MERS related strains, including their accession number, the date they were isolated, and their place of isolation listed in the supplementary materials (Supplementary Table 1). The edited data were then aligned using the MEGA7, the BioEdit (version 7.0.9.0) sequence analysis program and the Clustal W method.

For all selected and analysed sequences, short (<300bp of the corresponding gene) and abnormal sequences were removed from the datasets, and only six viral genes were studied because the short length and insufficient codon usage diversity of the other genes might have biased the results. The six genes analysed were the E, M, N, S, ORF1ab and ORF3, and all these genes were classified according to their viral isolation date and location.