FIG 3.

Phylogenetic analysis of the partial RNA-dependent RNA polymerase genes of all CoV genera. Shown are results of Bayesian analyses of an 853-nt alignment comprising unique partial RNA-dependent RNA polymerase gene sequences of 50 CoV strains representing all CoV species recognized by the International Committee on Taxonomy of Viruses (ICTV), as well as novel unassigned but putative CoV species. Three of the 43 CoV from this study were added to the data set to represent the genetic diversity of CoV circulating in Myotis emarginatus and Rhinolophus ferrumequinum populations in Luxembourg. The deltaCoV strains served as the outgroup for the phylogenetic analyses. Only the pp values of well-supported nodes (pp > 0.7) are shown, and if the nodes were also supported by ML inference (bootstrap confidence levels above 0.7), the bootstrap support is shown in parentheses. For each strain, the CoV genus assignment is shown. Assignment to recognized ICTV species is shown only for the study sequences displayed in red. A phylogenetic tree highlighting the CoV species of every strain can be found in the supplemental material (Fig. S3). The code for the country of origin of each strain is shown in boldface to stress the vast geographic spread of CoV. The sequences were named, if the information was available, according to the following nomenclature: abbreviated virus name/virus strain/host species/three-letter code of the country of origin/year of sampling_GenBank accession number. BtCoV, bat coronavirus; PEDV, porcine epidemic diarrhea virus; HCoV, human coronavirus; TGEV, transmissible gastroenteritis virus; PRCV, porcine respiratory coronavirus; FCoV, feline coronavirus; MiCoV, mink coronavirus; CiCoV, civet severe acute respiratory syndrome CoV; RatCoV, rat coronavirus; MHV, murine hepatitis virus; PHEV, porcine hemagglutinating encephalomyelitis virus; BCoV, bovine coronavirus; CaCoV, canine respiratory coronavirus; ECoV, equine coronavirus; DrCoV, dromedary camel coronavirus; WtDCoV, white-tailed deer coronavirus; GCoV, giraffe coronavirus; AnCoV, sable antelope coronavirus; WBkCoV, waterbuck coronavirus; SdCoV, Sambar deer coronavirus; RabCoV, rabbit coronavirus; HeCoV, hedgehog coronavirus; IBV, infectious bronchitis virus; CMCoV, common moorhen coronavirus; WECoV, wigeon coronavirus; BuCoV, bulbul coronavirus; ThCoV, thrush coronavirus; MuCoV, munia coronavirus; PCoV, porcine coronavirus; WiCoV, white-eye coronavirus; NHCoV, night heron coronavirus.