The close genetic and antigenic relatedness among the group 2 coronaviruses human coronavirus OC43 (HCoV-OC43), bovine coronavirus (BCoV), and porcine hemagglutinating encephalomyelitis virus (PHEV) suggests that these three viruses with different host specificities diverged fairly recently. In this study, we determined the complete genomic sequence of PHEV (strain PHEV-VW572), revealing the presence of a truncated group 2-specific ns2 gene in PHEV in comparison to other group 2 coronaviruses. Using a relaxed molecular clock approach, we reconstructed the evolutionary relationships between PHEV, BCoV, and HCoV-OC43 in real-time units, which indicated relatively recent common ancestors for these species-specific coronaviruses.Coronaviruses (family Coronaviridae, order Nidovirales) are large, enveloped, positive-stranded RNA viruses with a typical crown-like appearance. Their viral genomes (27 to 32 kb) are some of the largest known among all RNA viruses (12). Based on genetic and serological relationships, coronaviruses can be classified into three groups (8). Group 2 coronaviruses include murine hepatitis virus (MHV), bovine coronavirus (BCoV), human coronavirus OC43 (HCoV-OC43), rat sialodacryoadenitis virus, porcine hemagglutinating encephalomyelitis virus (PHEV), canine respiratory coronavirus, and equine coronavirus.PHEV was first isolated in 1962 in Canada from suckling piglets with encephalomyelitis (9, 18) and is now found to be widespread among swine worldwide, with frequent subclinical infections among swine. The virus has a strong tropism for epithelial cells of the upper respiratory tract and for the central nervous system (CNS) and is transmitted through nasal secretions (1). In addition to clinical signs of encephalomyelitis, vomiting and wasting disease can be another manifestation of PHEV infection in piglets (22). The clinical symptoms of vomiting and wasting are assumed to be centrally induced by infection of the vagus nerve, but a possible further dissemination of the virus into the CNS may lead to centrally induced motoric disorders.In this study, we determined the full-length genome sequence of the PHEV-VW572 strain and we reconstructed the common evolutionary history of PHEV and the closely related BCoV and HCoV-OC43. The PHEV-VW572 strain was isolated in Belgium in 1972 from the tonsils of two diseased pigs obtained from a litter in which an outbreak of vomiting and wasting disease occurred without further progression towards CNS motoric disorders (23). The isolate was propagated in a primary porcine kidney cell line. To determine the full-length genome sequence, primers developed for sequencing of group 2 coronaviruses, as described previously, were used (33).Multiple sequence alignments were prepared using ClustalX version 1.82 (30) and manually edited in GeneDoc (21). Maximum-likelihood phylogenetic analyses were conducted in Tree-Puzzle 5.1 using the VT (Mueller-Vingron 2000) model of amino acid substitution and a gamma distribution to model among-site rate heterogeneity (29). The SimPl...