Sequence of the coding regions from the 3.0 kb and 3.9 kb mRNA. Subgenomic species from a virulent isolate of transmissible gastroenteritis virus

Downstream ribosomal entry for translation of coronavirus TGEV gene 3b

Gene 3b (ORF 3b) in porcine transmissible gastroenteritis coronavirus (TGEV) encodes a putative nonstructural polypeptide of 27.7 kDa with unknown function that during translation in vitro is capable of becoming a glycosylated integral membrane protein of 31 kDa. In the virulent Miller strain of TGEV, ORF 3b is 5'-terminal on mRNA 3-1 and is presumably translated following 5' cap-dependent ribosomal entry. For three other strains of TGEV, the virulent British FS772/70 and Taiwanese TFI and avirulent Purdue-116, mRNA species 3-1 is not made and ORF 3b is present as a non-overlapping second ORF on mRNA 3. ORF 3b begins at base 432 on mRNA 3 in Purdue strain. In vitro expression of ORF 3b from Purdue mRNA 3-like transcripts did not fully conform to a predicted leaky scanning pattern, suggesting ribosomes might also be entering internally. With mRNA 3-like transcripts modified to carry large ORFs upstream of ORF 3a, it was demonstrated that ribosomes can reach ORF 3b by entering at a distant downstream site in a manner resembling ribosomal shunting. Deletion analysis failed to identify a postulated internal ribosomal entry structure (IRES) within ORF 3a. The results indicate that an internal entry mechanism, possibly in conjunction with leaky scanning, is used for the expression of ORF 3b from TGEV mRNA 3. One possible consequence of this feature is that ORF 3b might also be expressed from mRNAs 1 and 2.

The major product of porcine transmissible gastroenteritis coronavirus gene 3b is an integral membrane glycoprotein of 31 kDa

The open reading frame potentially encoding a polypeptide of 27.7 kDa and located as the second of three ORFs (gene 3b) between the S and M genes in the genome of the Purdue strain of porcine transmissible gastroenteritis coronavirus (TGEV) was cloned and expressed in vitro to examine properties of the protein. Gene 3b has a postulated role in pathogenesis, but its truncated form in some laboratory-passaged strains of TGEV has led to the suggestion that it is not essential for virus replication. During synthesis in vitro in the presence of microsomes, the 27.7-kDa polypeptide became an integral membrane protein, retained its postulated hydrophobic N-terminal signal sequence, and underwent glycosylation on apparently two asparagine linkage sites to attain a final molecular mass of 31 kDa. A 20-kDa N-terminally truncated, nonglycosylated, nonanchored form of the protein was also made via an unknown mechanism. The existence of both transmembrane and soluble forms of the gene 3 product in the cell is suggested by immunofluorescence patterns showing both a punctuated perinuclear and diffuse intracytoplasmic distribution. No gene 3b product was found on gradient-purified Purdue TGEV by a Western blotting procedure that would have detected as few as 4 molecules/virion, indicating the protein probably is not a structural component of the virion.

Nucleotide sequence of the inter-structural gene region of feline infectious peritonitis virus

The sequence of the region located between the S and M glycoprotein genes of the 79-1146 strain of feline infectious peritonitis virus (FIPV) is presented. The inter-structural gene region encodes 3 open reading frames (ORFs), termed ORFs 3a, 3b and 4, with nucleotide sequences conforming to the minimum conserved transcription signal upstream of each. An additional ORF, 3x, partially overlaps the 3' end of ORF 3a. The FIPV interstructural gene region is identical in length when compared to the Insavc-1 strain of canine coronavirus (CCV) but differs from various strains of transmissible gastroenteritis virus (TGEV) by the presence of deletions and insertions. The sizes of ORF 3a and 4 are conserved in FIPV, TGEV and CCV. However, as with CCV, the FIPV ORF 3b is truncated in comparison with TGEV.

Sequence comparison of porcine respiratory coronavirus isolates reveals heterogeneity in the S, 3, and 3-1 genes

Four new porcine respiratory coronavirus (PRCV) isolates were genetically characterized. Subgenomic mRNA patterns and the nucleotide sequences of the 5' ends of the S genes, the open reading frame (ORF) 3/3a genes, and the ORF 3-1/3b genes of these PRCV isolates were determined and compared with those of other PRCV and transmissible gastroenteritis virus (TGEV) isolates. The S, ORF 3/3a, and ORF 3-1/3b genes are under intense study because of their possible roles in determining tissue tropism and virulence. Northern (RNA) blot analysis of subgenomic mRNAs revealed that mRNA 2, which encodes for the S gene, of the PRCV isolates migrated faster than the mRNA 2 of TGEV. The PRCV isolates AR310 and LEPP produced eight subgenomic mRNA species, the same number as produced by the virulent Miller strain of TGEV. However, the PRCV isolates IA1894 and ISU-1 produced only seven subgenomic mRNA species. All four of the PRCV isolates were found to have a large in-frame deletion in the 5' end of the S gene; however, the size and location of the deletion varied. Analysis of the ORF 3/3a gene nucleotide sequences from the four PRCV isolates also showed a high degree of variability in this area. The ORF 3 gene of the PRCV isolates AR310 and LEPP was preceded by a CTAAAC leader RNA-binding site, and the ORF 3 gene was predicted to yield a protein of 72 amino acids, the same size as that of the virulent Miller strain of TGEV. The PRCV isolates AR310 and LEPP are the first PRCV isolates found to have an intact ORF 3 gene. The ORF 3a gene of the PRCV isolate IA1894 was preceded by a CTAAAC leader RNA-binding site and was predicted to yield a truncated protein of 54 amino acids due to a 23-nucleotide deletion. The CTAAAC leader RNA-binding site and ATG start codon of ORF 3 gene of the PRCV isolate ISU-1 were removed because of a 168-nucleotide deletion. Analysis of the ORF 3-1/3b gene nucleotide sequences from the four PRCV nucleotides isolates also showed variability.

Characterization of the transmissible gastroenteritis virus (TGEV) transcription initiation sequence. Characterization of TGEV TIS

The ability of the TGEV transcription initiation sequence (TIS) to produce subgenomic RNAs was investigated by placing a reporter gene, chloramphenicol acetyltransferase (CAT) under the control of either the mRNA 6 or the mRNA 7 TISs. Both constructs only produced CAT in TGEV infected cells and the amount of CAT produced from the mRNA 7 TIS was less than from the mRNA 6 TIS. Mutations were made within and around the TISs and the effect on CAT production assayed. THe results showed that the TGEV TIS acted as a initiator of transcription for CAT, though the degree of base pairing between the TIS and leader RNA was not the only factor implicated in the control transcription.

Molecular characterization of attenuated vaccine strains of transmissible gastroenteritis virus

Previous studies in our laboratory demonstrated that 2 attenuated strains of transmissible gastroenteritis virus (TGEV) contain deletions affecting messenger (m) RNAs 2, 3, or 4. In this report, we have compared mRNAs of four modified-live virus vaccines for TGEV with the virulent Miller PP3 isolate to determine whether any transcriptional patterns are shared among attenuated strains. Using northern blot analysis, all vaccine viruses expressed mRNAs indistinguishable in size from those of Miller PP3. However, using S1 nuclease protection experiments, alterations in the regions of the genome from which mRNAs 2 and 3 are transcribed were detected in 2 of the vaccine strains. When genomic cDNA fragments derived from the coding region for mRNA 2 were sequenced, a 6-nucleotide deletion, also found in the attenuated strain Purdue-115, was discovered. The product of mRNA 2, a spike glycoprotein, was visualized by western blotting for each vaccine strain, and no profound differences in mobility were detected relative to Miller PP3. Alterations in the region of the genome from which mRNA 3 is transcribed appear to be identical or very similar to sequence alterations already described in this region for Purdue-115, one of which is likely to alter the polypeptide product of mRNA 3. Insertions or deletions in mRNAs 2 or 3 may contribute to attenuation but are not a prerequisite for this phenotype. The S1 nuclease protection analysis is a sensitive tool for differentiating particular strains of TGEV.

Genomic organisation of a virulent Taiwanese strain of transmissible gastroenteritis virus

Transmissible gastroenteritis (TGE) infection causes 65% of infectious piglet diarrhoea in Taiwan. A virulent Taiwanese strain, TFI, of transmissible gastroenteritis virus (TGEV) from a field outbreak was isolated in cell culture and plaque purified. Phenotypic differences were observed in the ability of TFI to infect certain cell lines. TGEV strains TLM-83 (PRCV Belgium), TO-163 (TGEV Japan) and Purdue-115 (TGEV USA) infected both ST (swine testis) and RPTG (pig kidney) cell lines whereas TFI infected ST but not RPTG cells. To investigate this phenotypic variation cDNA was generated from TFI genomic and amplified by PCR with oligonucleotides derived from published TGEV sequence data. An 8.4kb cDNA derived from the 3'-end of the TFI genome was sequenced. Eight ORFs, corresponding to the three structural protein genes, four potential genes and the 3'-end of an incomplete ORF whose amino acid sequence corresponded to the carboxyl end of the 1b subunit of the polymerase gene, were identified on the TFI sequence. The overall sequence similarity of TFI with the other TGEV strains was over 97%. However, several deletions, insertions and point mutations were found on the TFI sequence when compared with other TGEV strains. The TFI S protein was found to contain 1449 amino acids, as also identified for the FS772/70 and Miller TGEV strains, but two amino acids longer than the Purdue S protein. The TFI ORF-3a gene encodes 72 amino acids, however, a 37 nucleotide deletion was found 16 nucleotides downstream of the TFI ORF-3a stop codon.(ABSTRACT TRUNCATED AT 250 WORDS)

The use of PCR genome mapping for the characterisation of TGEV strains

Previous studies on different transmissible gastroenteritis virus (TGEV) strains, including porcine respiratory coronavirus (PRCV), have identified regions within the genome that are polymorphic as regards insertions and deletions. For example the 672 base deletion within the S gene and multiple deletions 5', within and 3' of the ORF-3a gene were detected in strains of PRCV. The presence of deletions may be associated with a change in the virulence, attenuation or tissue tropism of the isolate. The Nouzilly (188-SG) TGEV vaccine strain was attenuated by passage of a cell culture adapted virulent isolate D-52 188 times through swine testis cells after treatment with gastric juice. PCR amplification with oligonucleotides, corresponding to known TGEV sequences, were used to analyse D-52 and 188-SG for genetic variation. Results with several pairs of oligonucleotides within the first 1565 nucleotides of the S gene did not identify a deletion within this region of the genome from either strain. However, oligonucleotides directed against the ORF-3a/3b region detected a deletion of about 250 nucleotides within the 188-SG genome but not in the D-52 genome. Since all the attenuated TGEV strains so far sequenced, PRCV, Miller SP and 188-SG, contained deletions within the ORF-3a/3b, it would suggest that this region of the TGEV genome is involved in regulating viral virulence.

TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions

The coding potential of the open reading frame ORF4 (82 amino acids) of transmissible gastroenteritis virus (TGEV) has been confirmed by expression using a baculovirus vector. Five monoclonal antibodies (MAbs) raised against the 10K recombinant product immunoprecipitated a polypeptide of a similar size in TGEV-infected cells. Immunofluorescence assays performed both on insect and mammalian cells revealed that ORF4 was a membrane-associated protein, a finding consistent with the prediction of a membrane-spanning segment in ORF4 sequence. Two epitopes were localized within the last 21 C-terminal residues of the sequence through peptide scanning and analysis of the reactivity of a truncated ORF4 recombinant protein. Since the relevant MAbs were found to induce a cell surface fluorescence, these data suggest that ORF4 may be an integral membrane protein having a Cexo-Nendo orientation. Anti-ORF4 MAbs were also used to show that ORF4 polypeptide may be detected in TGEV virion preparations, with an estimated number of 20 molecules incorporated per particle. Comparison of amino acid sequence data provided strong evidence that other coronaviruses encode a polypeptide homologous to TGEV ORF4. Our results led us to propose that ORF4 represents a novel minor structural polypeptide, tentatively designated SM (small membrane protein).

Sequence analysis of human coronavirus 229E mRNAs 4 and 5: evidence for polymorphism and homology with myelin basic protein

Human coronaviruses (HCV) are important pathogens responsible for respiratory, gastrointestinal and possibly neurological disorders. To better understand the molecular biology of the prototype HCV-229E strain, the nucleotide sequence of the 5'-unique regions of mRNAs 4 and 5 were determined from cloned cDNAs. Sequence analysis of the cDNAs synthesized from mRNA 4 revealed a major difference with previously published results. However, polymerase chain reaction amplification of this region showed that the sequenced cDNAs were produced from minor RNA species, an indication of possible genetic polymorphism in this region of the viral genome. The mutated messenger RNA 4 contains two ORFs: (1) ORF4a consisting of 132 nucleotides which potentially encodes a 44-amino acid polypeptide of 4653 Da; this coding sequence is preceded by a consensus transcriptional initiation sequence, CUAAACU, similar to the ones found upstream of the N and M genes; (2) ORF4b of 249 nucleotides potentially encoding an 83-amino acid basic and leucine-rich polypeptide of 9550 Da. On the other hand, mRNA 5 contains one single ORF of 231 nucleotides which could encode a 77-amino acid basic and leucine-rich polypeptide of 9046 Da. This putative protein presents a significant degree of amino acid homology (33%) with its counterpart found in transmissible gastroenteritis coronavirus (TGEV). The proteins in the two different viruses exhibit similar molecular weights and are extremely hydrophobic. Interestingly, a sequence homology of five amino acids was found between the protein encoded by ORF4b of HCV-229E and an immunologically important region of human myelin basic protein.

The cloning and sequencing of the virion protein genes from a British isolate of porcine respiratory coronavirus: comparison with transmissible gastroenteritis virus genes

Previous analysis of porcine respiratory coronavirus (PRCV) mRNA species showed that mRNAs 2 and 3 were smaller than the corresponding transmissible gastroenteritis virus (TGEV) mRNA species (Page et al. (1991) J. Gen. Virol. 72, 579-587). Sequence analysis showed that mRNA 3 was smaller due to the presence of a new putative RNA-leader binding site upstream of the PRCV ORF-3 gene. However, this observation did not explain the deletion observed in PRCV mRNA 2. Polymerase chain reaction (PCR) was used to generate cDNA from the 3' coding region of the putative polymerase gene to the poly (A) tail of PRCV for comparison to the equivalent region from TGEV. The PRCV S protein was found to consist of 1225 amino acids, which had 98% similarity to the TGEV S protein. However, the PRCV S gene contained a 672 nucleotide deletion, corresponding to 224 amino acids (residues 21 to 245 in TGEV S protein), 59 nucleotides downstream of the S gene initiation codon. The PRCV genome from the ORF-3 gene to the poly (A) tail was sequenced for comparison to TGEV in order to identify other potential differences between the two viruses. Four ORFs were identified that showed 98% similarity to the TGEV ORF-4, M, N and ORF-7 genes. No other deletions or any PRCV specific sequences were identified.

Genetic analysis of porcine respiratory coronavirus, an attenuated variant of transmissible gastroenteritis virus

The genome and transcriptional pattern of a newly identified respiratory variant of transmissible gastroenteritis virus were analyzed and compared with those of classical enterotropic transmissible gastroenteritis virus. The transcriptional patterns of the two viruses indicated that differences occurred in RNAs 1 and 2(S) and that RNA 3 was absent in the porcine respiratory coronavirus (PRCV) variant. The smaller RNA 2(S) of PRCV was due to a 681-nucleotide (nt) deletion after base 62 of the PRCV peplomer or spike (S) gene. The PRCV S gene still retained information for the 16-amino-acid signal peptide and the first 6 amino acid residues at the N terminus of the mature S protein, but the adjacent 227 residues were deleted. Two additional deletions (3 and 5 nt) were detected in the PRCV genome downstream of the S gene. The 3-nt deletion occurred in a noncoding region; however, the 5-nt deletion shortened the potential open reading frame A polypeptide from 72 to 53 amino acid residues. Significantly, a C-to-T substitution was detected in the last base position of the transcription recognition sequence upstream of open reading frame A, which rendered RNA 3 nondetectable in PRCV-infected cell cultures.

Sequence of the S gene from a virulent British field isolate of transmissible gastroenteritis virus

Subgenomic mRNA from a virulent field isolate of porcine transmissible gastroenteritis virus (TGEV), strain FS772/70, was used to produce cDNA. The cDNA from three overlapping clones was sequenced by the chain termination method and two open reading frames (ORFs) were identified. The largest ORF, 4350bp, encoded a polypeptide of 1449 amino acids of relative molecular mass (Mr) 159811, which contained 33 potential N-linked glycosylation sites, a cysteine-rich region, and a potential transmembrane region. The C-terminal half of this ORF showed homology to the S proteins of four other coronaviruses. The other ORF consisted of the 3'-end of a gene with homology to the carboxyl terminus of the F2 subunit of infectious bronchitis virus (IBV) RNA polymerase.

Sequence analysis of the leader RNA of two porcine coronaviruses: transmissible gastroenteritis virus and porcine respiratory coronavirus

The leader RNA sequence was determined for two pig coronaviruses, transmissible gastroenteritis virus (TGEV), and porcine respiratory coronavirus (PRCV). Primer extension, of a synthetic oligonucleotide complementary to the 5' end of the nucleoprotein gene of TGEV was used to produce a single-stranded DNA copy of the leader RNA from the nucleoprotein mRNA species from TGEV and PRCV, the sequences of which were determined by Maxam and Gilbert cleavage. Northern blot analysis, using a synthetic oligonucleotide complementary to the leader RNA, showed that the leader RNA sequence was present on all of the subgenomic mRNA species. The porcine coronavirus leader RNA sequences were compared to each other and to published coronavirus leader RNA sequences. Sequence homologies and secondary structure similarities were identified that may play a role in the biological function of these RNA sequences.

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.