Three new isolates of porcine respiratory coronavirus (PRCV) were isolated and characterized. Two of the PRCV isolates, AR310 and LEPP, were shown to produce moderate interstitial pneumonia, whereas the third PRCV isolate, IA1894, was only mildly pathogenic in five-week-old specific pathogen free pigs. The previously described PRCV isolate ISU-1, a mildly pathogenic PRCV isolate, was also included in this study. These PRCV isolates with varying pathogenicity provided an opportunity to determine if there are certain genes that correlate with virulence, as the genes 3 and 3-1 have been hypothesized to be virulence determinants for transmissible gastroenteritis virus (TGEV) isolates. Using Northern blot analysis, the numbers and sizes of the subgenomic mRNAs produced by the PRCV isolates in infected swine testicular cells were shown to vary. The PRCV isolates all had a mRNA 2 that was smaller than the mRNA 2 of TGEV. The PRCV isolates AR310 and LEPP both had two mRNA species that comigrated with the mRNAs 3 and 3-1 of TGEV. The PRCV isolate IA1894 had only mRNA 3 present, whereas the PRCV isolate ISU-1 had only mRNA 3-1 present. Nucleotide sequence analysis revealed that the PRCV isolates AR310 and LEPP both had identical S gene deletions of 621 nucleotides. The PRCV isolates IA1894 and ISU-1 had S gene deletions of 678 and 681 nucleotides, respectively. The 3 gene of the PRCV isolates AR310 and LEPP was predicted to yield a protein of 72 amino acids, the same size as that of the virulent Miller strain of TGEV. The 3a gene of the PRCV isolate IA1894 was predicted to yield a truncated protein of 53 amino acids due to a 23 nucleotide deletion in 3a gene. The CTAAAC leader-RNA-binding site and ATG start codon for the 3 gene of the PRCV isolate ISU-1 was removed due to a 168 nucleotide deletion. The fact that the PRCV isolates AR310 and LEPP were more pathogenic than the PRCV isolate IA1894 indicates that the presence of an intact gene 3 may be important in determining the pathogenicity of PRCV isolates.