Molecular Evolution of MERS Coronavirus: Dromedaries as a Recent Intermediate Host or Long-Time Animal Reservoir?

Lau, Susanna K. P.; Wong, Antonio C. P.; Lau, Terrence C. K.; Woo, Patrick C. Y.

When the 15 MERS-CoV genomes that showed different clustering in the ORF1ab and S phylogenetic trees were subject to multiple alignment analysis, it was shown that for the five strains with possible recombination revealed by bootscan analysis, the possible recombination sites were confirmed by multiple alignments. For four strains (accession No. KT368829, KT368830, KT368831 and KT368832), sequences upstream to the possible recombination site were similar to that of KT368875 from lineage B5, while those downstream to the possible recombination site were similar to that of KT368860 from lineage B3 ( Figure S1A ). As for the remaining strain (accession No. KT368887), sequence upstream to the possible recombination site was similar to that of KT368878 from lineage B3, while sequence downstream to the possible recombination site was similar to that of KT368890 from lineage B4 ( Figure S1B ).