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.

The evolutions of clade A and clade B MERS-CoV are quite different from each other. Intriguingly, clade B MERS-CoV out-numbered clade A MERS-CoV strains (Figure 2 ). This may be a result of sampling bias or a genuine survival or transmission advantage of clade B MERS-CoV. As for the specific lineages, the S protein of lineage A2 MERS-CoV showed higher number of amino acid changes as compared to other lineages. After the virus has evolved into clades A and B, we speculate that lineage B5 diverged and evolved separately from the other clade B lineages, as demonstrated by its deep branch in the phylogenetic tree as well as the unique amino acid change at position 1020 of the S2 subunit in S protein (Figures 4 and 6) . Moreover, this residue at 1020 also distinguishes between clade A and B strains, and was positively selected among B and B5 strains, suggesting a role in the divergence of different lineages along the evolution of spike protein. Interestingly, this residue is located at the HR region of S2 which is responsible for virus-host fusion. Further studies have to be performed to understand whether clade B MERS-CoV have better survival advantages over clade A MERS-CoV, and the potential effect of amino acid substitution at codon 1020 on viral fusion.