Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UMLS:C0017160 (gastroenteritis)
 11,398 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The genetic information, carried on mRNA 6 of feline infectious peritonitis virus (FIPV) strain 79-1146, was determined by sequence analysis of cDNA clones derived from the 3' end of the FIPV genome. Two ORFs were found, encoding polypeptides of 11K (ORF-1) and 22K (ORF-2). The FIPV sequence was compared to the 3' end sequence of transmissible gastroenteritis virus (TGEV). ORF-1 has a homologous counterpart (ORF-X3) in the TGEV genome; both ORFs are located at the same position relative to the nucleocapsid gene. However, as a result of an in-frame insertion or deletion, ORF-1 is 69 nucleotides larger than ORF-X3. A similar event has occurred immediately downstream of ORF1: a 624-nucleotide segment, containing the complete ORF-2, is absent in the TGEV sequence. Most sequence similarity (98.5%) was found in the 3' noncoding sequences. ORF-X3 and ORF-1 are preceded by the sequence AACTAAAC, which is assumed to be the transcription-initiation signal in FIPV and TGEV (P.A. Kapke and D.A. Brian (1986) Virology 151, 41-49). By S1 nuclease analysis, the 5' end of FIPV RNA 6 was mapped immediately upstream of this sequence. A 700-nucleotide TGEV-specific RNA was found by cross-hybridization with an FIPV 3' end probe, suggesting that TGEV ORF-X3 is also carried on a separate mRNA. The differences at the 3' ends of the FIPV and TGEV genomes may be the result of RNA recombination events.
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PMID:Sequence analysis of the 3'-end of the feline coronavirus FIPV 79-1146 genome: comparison with the genome of porcine coronavirus TGEV reveals large insertions. 320 47

The application of the reverse transcriptase polymerase chain reaction (RT-PCR) has enabled several morphologically and physically similar small round structured viruses (SRSVs), including the prototype Norwalk virus (NV), to be classified within the Caliciviridae. This technique, using primers directed to the RNA-dependent RNA polymerase region within the ORF1 of NV, was used to characterise SRSVs associated with epidemic gastroenteritis in adults and sporadic paediatric gastroenteritis in South Africa. Genomic variation was investigated by sequence analysis of the amplified 209bp cDNA region from six isolates and comparison with other characterised SRSVs including NV. Antigenic variation was investigated by the use of the recombinant enzyme immunoassay described recently for the detection of Snow Mountain agent-like antigen in stool specimens. Two distinct antigenic groups were evident with NV-like viruses associated with adult gastroenteritis, and Mexico viruslike viruses associated with paediatric gastroenteritis. Viral isolates from two of the outbreaks of adult gastroenteritis showed a high degree of nucleotide sequence identity with NV, i.e., 84% and 98%, respectively, whereas the paediatric isolates showed 92-95% sequence similarity with the Snow Mountain-like virus, MxV. These data show concordance between antigenic and genomic analyses.
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PMID:Molecular characterisation of small round structured viruses associated with gastroenteritis in South Africa. 863 7

Five small round-structured viruses (SRSVs) associated with gastroenteritis in Victoria, Australia, from January to November 1994 were examined by sequencing cDNA prepared from faecal samples using RT-PCR. The sequence of the 3' half (3.8 kb) of the genome of one of these viruses, Camberwell, was determined. Camberwell virus was related most closely to Bristol and Lordsdale viruses, and belonged to the genetic group of SRSVs containing Bristol, Lordsdale, Toronto, OTH-25, Mexico, and Hawaii viruses. The amino acid identities between Camberwell and Bristol viruses for proteins encoded by ORF1 (partial), ORF2, and ORF3 were 99%, 98%, and 90%, respectively. A highly variable region in ORF3 corresponding to amino acid residues 123 to 169 (Bristol and Camberwell numbering) were identified. Short segments of ORF1 (polymerase region) and the highly variable ORF3 region was analysed for the other four viruses. The results obtained indicated the potential usefulness of the variable region in distinguishing between closely related viruses.
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PMID:Molecular characterization of Camberwell virus and sequence variation in ORF3 of small round-structured (Norwalk-like) viruses. 873 63

A total of 6,226 fecal samples collected from 1980 to 1996 in the Australian states of Victoria, New South Wales, and Tasmania from individuals with gastroenteritis were tested for small round-structured viruses (SRSVs) and classical human caliciviruses (ClHuCVs) by electron microscopy. There were 223 samples positive for SRSVs, and nine positive for ClHuCVs. SRSVs were detected in individuals of all ages and were commonly associated with gastroenteritis outbreaks in nursing homes and hospitals. SRSVs were detected throughout the year, but were more common in the period from late winter to early summer in Australia (August to December). There were peaks of virus activity in the early 1980s and more recently in 1995 and 1996. Analyses by RT-PCR and sequencing of a segment of ORF1 encoding the putative RNA polymerase for SRSVs and ClHuCVs showed the presence of viruses belonging to several genogroups. Viruses of genogroup 1 (Norwalk/Southampton-like) and genogroup 3 (ClHuCVs) were relatively rare. Viruses of genogroup 2 (Snow Mountain-like) were common, and could be divided into two subgroups, one containing Toronto/Mexico-like viruses, the other Lordsdale/Camberwell-like viruses. The majority of viruses detected belonged to this latter subgroup.
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PMID:Small round-structured (Norwalk-like) viruses and classical human caliciviruses in southeastern Australia, 1980-1996. 966 41

Genomic characterization of Norwalk-like human caliciviruses (NLVs) originating from outbreaks and sporadic cases of acute gastroenteritis has revealed surprisingly high levels of diversity, even in the RNA polymerase gene, which is anticipated to be highly conserved. Since information on antigenic relationship is limited, due to the lack of a tissue culture system for these viruses, strains mostly are described on the basis of their genetic relatedness. However, the lack of uniformly applied criteria has led to a confusing array of strains with different groups employing different names for similar genetic lineages. Our goal was to conduct a structured analysis of genomic relationships among NLV strains in an attempt to provide an interim framework for genotyping. We assembled a panel of 31 potentially distinct genogroup I (GGI) and genogroup II (GGII) NLVs that reflected the diversity seen in strains detected by our laboratories and in published sequences. Phylogenetic analysis of sequences from regions of the open reading frames (ORF) 1, 2 and 3 was performed in order to investigate genomic relationships. The strains sequenced fell into seven phylogenetic groups in GGI and at least five phylogenetic groups in GGII, based on greater than 80% nucleotide identity in the region of ORF2 encoding the N-terminus of the capsid protein, and consistent clustering with high bootstrap values irrespective of the method used. Analysis of the ORF1 and ORF3 regions supported for most strains the clustering as established for those derived from ORF2. In the ORF1 region, used by most laboratories for diagnostic RT-PCR, clustering was consistent when a putative genotype border was set at 15% nucleotide mismatches for viruses in GGI and at 10% for viruses in GGII. Two strains grouped within different clusters based on ORF1 and ORF2 indicating that recombination may have occurred. We discuss the implications of these observations for the classification and typing of NLVs.
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PMID:Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses". 1075 50

The molecular epidemiology of small round structured viruses (SRSVs) in Germany was studied using fecal specimens from 16 SRSV-associated gastroenteritis outbreaks in different parts of Germany during 1997/1998 by reverse transcription-polymerase chain reaction (RT-PCR) and by sequencing of the ORF1 and ORF3 amplicons. The majority of the isolates clustered in one subtype and were closely related to published SRSV sequences of genogroup II.
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PMID:Molecular epidemiology of outbreaks of gastroenteritis associated with small round structured viruses in Germany in 1997/98. 1079 14

Norwalk-like viruses (NLVs) are now established as the most important causative agents of epidemic gastroenteritis worldwide. The overall objective of this study was to determine the molecular epidemiology of Irish NLV isolates for the first time by obtaining sequence data from specimens originating from outbreaks and sporadic cases of gastroenteritis. Eight samples from sporadic cases of gastroenteritis and nine isolates from separate NLV outbreaks were examined. Of the sporadic isolates, six were shown to be genogroup 2 (G2) by RT-PCR, while two were G1. All of the outbreak isolates were G2. All isolates were partially sequenced within a highly conserved region of ORF1 (RNA-dependent RNA polymerase gene). Sequence data were aligned and a dendogram was constructed. The results indicated that the majority of G2 isolates were seen to cluster with Bristol and Lordsdale virus, while the two G1 specimens were related most closely to Southampton virus. Further downstream sequence analysis of a number of the isolates confirmed this result. It is concluded that the majority of NLV isolates circulating in Ireland belong to the Bristol/Lordsdale clade.
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PMID:Molecular detection and sequencing of "Norwalk-like viruses" in outbreaks and sporadic cases of gastroenteritis in Ireland. 1153 49

The sequence of the replicase gene of porcine epidemic diarrhoea virus (PEDV) has been determined. This completes the sequence of the entire genome of strain CV777, which was found to be 28,033 nucleotides (nt) in length (excluding the poly A-tail). A cloning strategy, which involves primers based on conserved regions in the predicted ORF1 products from other coronaviruses whose genome sequence has been determined, was used to amplify the equivalent, but as yet unknown, sequence of PEDV. Primary sequences derived from these products were used to design additional primers resulting in the amplification and sequencing of the entire ORF1 of PEDV. Analysis of the nucleotide sequences revealed a small open reading frame (ORF) located near the 5' end (no 99-137), and two large, slightly overlapping ORFs, ORF1a (nt 297-12650) and ORF1b (nt 12605-20641). The ORF1a and ORF1b sequences overlapped at a potential ribosomal frame shift site. The amino acid sequence analysis suggested the presence of several functional motifs within the putative ORF1 protein. By analogy to other coronavirus replicase gene products, three protease and one growth factor-like motif were seen in ORF1a, and one polymerase domain, one metal ion-binding domain, and one helicase motif could be assigned within ORF1b. Comparative amino acid sequence alignments revealed that PEDV is most closely related to human coronavirus (HCoV)-229E and transmissible gastroenteritis virus (TGEV) and less related to murine hepatitis virus (MHV) and infectious bronchitis virus (IBV). These results thus confirm and extend the findings from sequence analysis of the structural genes of PEDV.
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PMID:Completion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence. 1172 65

Human enteric caliciviruses have been assigned to two distinct genera: the Norwalk-like viruses (NLVs) and the Sapporo-like viruses (SLVs). During a 3-year surveillance of gastroenteritis in the South West of England during November 1997-2000, a total of 27 clinical samples containing SLVs were collected. PCR amplicons covering a region of the RNA polymerase gene were obtained from 18 of the SLV samples. Sequence analysis of the PCR products indicated that the SLV isolates could be assigned to one of the two major genetic groups represented by Sapporo and London/92 caliciviruses. One of these isolates belonging to the London/92 group (Bristol/98) was subjected to a complete genome sequence analysis. The full genomic sequence of the Bristol/98 isolate was determined from RNA extracted from a single stool sample and consists of 7490 nucleotides, excluding the poly(A) tail. The genome is organised into two open reading frames (ORFs), similar to that of Manchester SLV although the small ORF overlapping the region encoding the capsid protein observed in Manchester SLV is absent in Bristol/98 SLV. The polyprotein (ORF1) of Bristol/98 SLV consists of 2,280 amino acids and, as observed in all SLVs, the structural protein is encoded in frame and contiguous with the 3' terminus of the ORF1. Phylogenetic studies based on complete capsid sequences and genome arrangements within the SLVs indicate that the human enteric viruses within the "Sapporo-like" virus clade should be divided into two distinct genetic groups analogous to the assignment of the Norwalk-like viruses.
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PMID:Epidemiology of human Sapporo-like caliciviruses in the South West of England: molecular characterisation of a genetically distinct isolate. 1199 91

The Norwalk Virus (NV) is the prototype strain of human caliciviruses that cause epidemic outbreaks of foodborne and waterborne gastroenteritis. These viruses do not grow in cell culture and the mechanisms of virus replication are obscure. The NV genome is a 7.7 kb ssRNA molecule that encodes three open reading frames (ORFs). The first ORF is a 1789 amino acid polyprotein that is processed into nonstructural proteins by a viral protease similar to the picornavirus 3C protease. Primary cleavage sites in the ORF1 polyprotein of two Norwalk-like viruses have been identified as QG dipeptides. We studied primary cleavage sites in the NV polyprotein and residues surrounding the scissile bond that are important in substrate recognition. A series of mutations were made at amino acids occupying positions implicated as important in cleavage site recognition for chymotrypsin-like viral proteases. We determined that effective processing at amino acid 398 to release the N-terminal p48 protein is necessary for proteolytic release of the p41 protein, that the P4 position N-terminal to the scissile bond is important for efficient processing, and that substitution of large hydrophobic residues were tolerated at this position. Finally, we defined the acidic residue of the 3CL(pro) catalytic site.
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PMID:Substrate specificity of the Norwalk virus 3C-like proteinase. 1236 48


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