It is unclear whether respiratory and enteric bovine coronavirus (BoCV) strains are distinctive in biological, antigenic and genetic characteristics. In the present study, we analyzed the nucleotide and amino acid sequence of the S I subunit of the S glycoprotein, including the cleavage site, of both respiratory (n = 5) and enteric (n = 3) BoCV isolates including two paired isolates from the same feedlot animals and compared them with the prototype Mebus and two enteric and one respiratory BoCV strains from Quebec. A total of 75 polymorphic nucleotides were identified in the Sl subunit of the spike glycoprotein of BoCV isolates compared with the Mebus strain. These polymorphisms led to 42 amino acid changes at 38 distinct sites. The amino acid changes were distributed throughout the Sl subunit with clustering around residues 40-118, 146-179, and 458-531. Among these variations, only 19 amino acid substitutions altered the charge, hydrophobicity and surface probability of the protein. Based on phylogenetic analysis, our respiratory and enteric isolates clustered into two major groups with two subgroups. Although, there were only a few amino acid changes between the respiratory and enteric paired isolates, the other two respiratory isolates, one isolated from the same farm as a paired strain and the other from a different farm, showed more sequence diversity, Amino acid alterations in residues 113, 115, 118, 146, 148, 501, 510 and 531 of respiratory isolates conferred significant changes in the predicted secondary structure compared with the prototype winter dysentery (WD) and the calf diarrhea (CD) strains of BoCV. In conclusion, the data suggests that respiratory strains of BoCV may differ genetically from the classical calf enteric and adult WD strains. (C) 2002 Elsevier Science B.V. All rights reserved.