question: Two transmissible gastroenteritis virus (TGEV, Miller strain) cDNA clones were identified and their nucleotide sequences determined. The clones were non-overlapping and were located in the 5' region of the S glycoprotein gene. The TGEV clone pE21 contained 381 bp of the S glycoprotein gene and had > 98% nucleotide and amino acid sequence homology with the Purdue (P115) strain of TGEV and over 87% sequence homology with feline infectious peritonitis virus (FIPV). The TGEV clone, pD24, contained 267 bp of the S glycoprotein gene. It had > 98% nucleotide and amino acid sequence homology with P115 but only a 49% nucleotide sequence homology and a 24% amino acid sequence homology with FIPV. Using dot blot hybridization, a probe prepared from pD24 could differentiate TGEV from the antigenically related coronaviruses, FIPV, feline enteric coronavirus and canine coronavirus. This probe could also differentiate TGEV from porcine respiratory coronavirus (PRCV). Using polymerase chain reaction amplified regions of PRCV isolates and nucleotide sequencing, a 681 bp deletion in the 5' region of the S gene from PRCV isolate ISU-1 was identified. This deletion was located in the area of the S glycoprotein gene identified by the pD24 probe.