Genetic basis for the pathogenesis of transmissible gastroenteritis virus

Intracellular RNAs of an avirulent small-plaque (SP) transmissible gastroenteritis virus variant and the parent virulent Miller strain of transmissible gastroenteritis virus were compared. Northern RNA blotting showed that the Miller strain contained eight intracellular RNA species. RNAs 1, 2(S), 5, 6(M), 7(N), and 8 were similar in size for both viruses; however, the SP variant lacked subgenomic RNAs 3 and 4. Instead, the SP virus contained an altered RNA species (delta 4) that was slightly smaller than RNA 4. S1 nuclease protection experiments showed a deletion of approximately 450 nucleotides in the SP genome downstream of the peplomer S gene. Sequencing of cDNA clones confirmed that SP virus contained a 462-nucleotide deletion, eliminating the transcriptional recognition sequences for both RNAs 3 and 4. These RNAs encode open reading frames A and B, respectively. An alternative consensus recognition sequence was not readily apparent for the delta 4 RNA species of SP virus. Since open reading frame A is missing in SP virus, it is not essential for a productive infection. The status of the potential protein encoded by open reading frame B is not clear, because it may be missing or just truncated. Nevertheless, these genes appear to be the contributing entities for transmissible gastroenteritis virus virulence, SP morphology, tissue tropism, and/or persistence in swine leukocytes.