Fig 1.
Phylogenetic relationships among members of the subfamily Coronavirinae and taxonomic position of MERS-CoV. A rooted neighbor-joining tree was generated from amino acid sequence alignments of Coronaviridae-wide conserved domains in replicase polyprotein 1ab (ADRP, nsp3; Mpro, nsp5; RdRP, nsp12; Hel, nsp13; ExoN, nsp14; NendoU, nsp15; O-MT, nsp16) for MERS-CoV strain Hu/Jordan-N3/2012 (GenBank accession no. KC776174.1) and for 20 other coronaviruses, each a representative of a currently recognized coronavirus species (10); equine torovirus Berne served as the outgroup. Virus names are given with strain specifications; species and genus names are in italics as per convention. The tree shows the four main monophyletic clusters, corresponding to genera Alpha-, Beta-, Gamma-, and Deltacoronavirus (color coded) and the position of MERS-CoV. Also indicated are betacoronavirus lineages A through D (corresponding to former CoV subgroups 2A through D). Bootstrap values (1,000 replicates) are indicated at branch points. The tree is drawn to scale (scale bar, 0.2 amino acid substitutions per site).