Sequence Analysis of the Porcine Epidemic Diarrhea Virus Genome between the Nucleocapsid and Spike Protein Genes Reveals a Polymorphic ORF

Abstract

In order to investigate the genome organization of the porcine epidemic diarrhea virus (PEDV) further, cDNA clones covering the region between the nucleocapsid and the spike (S) protein genes were independently constructed and sequenced for the two virulent isolates Br1/87 and CV777. Of the three major ORFs identified, two were found to encode the major and minor coronavirus membrane proteins M and sM. A potentially single ORF, designated ORF3 according to the pattern of the viral subgenomic mRNAs, could be identified between the S and sM genes. A striking variability, essentially generated by short deletions clustered in a few loci, was observed in the ORF3 of both isolates. The largest predicted polypeptide of 223 amino acids showed homology with polypeptides potentially encoded by other members of the same genetic subset, including two shorter polypeptides of human respiratory virus HCV 229E and one of transmissible gastroenteritis virus TGEV. This homology suggests that the two HCV ORFs may have originated from a single precursor. The function of these polypeptides is not known, but the predicted products of the PEDV ORF3 and related ORFs share features suggestive of a membrane-associated protein.

A previously undescribed coronavirus associated with respiratory disease in humans

“…We observed sequence variation in ORF3 of HCoV-NL; in addition to RT-PCR fragments having a stretch of nine T residues from nucleotide position 24820 to 24828, we obtained RT-PCR fragments with deletions of one or two T residues. Considerable sequence variation was also observed in ORF3 of porcine epidemic diarrhea virus, potentially because this ORF is dispensable for, or incompatible with, virus replication in vitro (21). Analysis of nucleotide sequences of ORF3 homologues derived from other group 1 coronaviruses isolated in cell cultures revealed significant sequence variation as well.…”

Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus

“…Although no one can accurately predict the future impact of SARS-CoV on the global community, the past 25 years has seen the emergence and global spread of several new pathogenic CoVs in animals (23)(24)(25). Coupled with in vitro findings, CoVs are serious emerging pathogens capable of rapid evolution, cross species transmission, and colonization of new host species (26,27).…”

In Situ Hybridization for the Detection and Localization of Porcine Epidemic Diarrhea Virus in the Intestinal Tissues from Naturally Infected Piglets

“…The disease can appear similar to that caused by TGEV. 12,31 Although these two viral diseases can be difficult to distinguish clinically, PEDV differs antigenically from TGEV, and antigenic cross-reaction has been described only with feline infectious peritonitis. 32 Like TGEV, PEDV causes destruction of villus enterocytes and villus atrophy within the jejunum and ileum.…”