Comparison of genomic and predicted amino acid sequences of respiratory and enteric bovine coronaviruses isolated from the same animal with fatal shipping pneumonia

The complete genome sequences are reported here of two field isolates of bo vine coronavirus (BCoV), which were isolated from respiratory and intestina l samples of the same animal experiencing fatal pneumonia during a bovine s hipping fever epizootic. Both genomes contained 31028 nucleotides and inclu ded 13 open reading frames (ORFs) flanked by 5'- and 3'-untranslated region s (UTRs). ORF1a and ORF1 b encode replicative polyproteins pp1a and pp1ab, respectively, that contain all of the putative functional domains documente d previously for the closest relative, mouse hepatitis virus. The genomes o f the BCoV isolates differed in 107 positions, scattered throughout the gen ome except the 5'-UTR. Differences in 25 positions were non-synonymous and were located in all proteins except pp 1 b. Six replicase mutations were id entified within or immediately downstream of the predicted largest pp1a-der ived protein, p195/p210. Single amino acid changes within p195/p210 as well as within the S glycoprotein might contribute to the different phenotypes of the BCoV isolates.