title: The correct sequence of the porcine group C/Cowden rotavirus major inner capsid protein shows close homology with human isolates from Brazil and the U.K.
abstract: Amino acid sequence alignments between the human group C/Bristol and the published porcine group C/Cowden VP6 proteins have revealed a region of extreme sequence divergence. We have been unable to confirm the nucleotide sequence of the Cowden VP6 gene corresponding to this region of divergence. Direct sequencing of a PCR-amplified cDNA pool has revealed a frame shift, and three nucleotide changes, within the published sequence of the porcine (Cowden) VP6 gene. The corrected sequence of the porcine protein revealed a closer homology with VP6 from the Bristol strain and two new human group C rotavirus isolates. Atypical rotaviruses have been detected in the feces of children living in Belém, Brazil, and Preston, U.K. Direct sequencing of PCR-amplified cDNA corresponding to the VP6 gene of one isolate from each location confirmed the presence of a group C rotavirus. The complete nucleotide sequences of the VP6 genes from the group C/Belém and C/Preston rotaviruses contained an open reading frame of 1185 nucleotides (395 amino acids; deduced M(r) 44,669 Da). The Belém VP6 gene demonstrated 97.9% nucleotide homology with the human group C/Bristol VP6 gene and 83.4% nucleotide homology (91.6% deduced amino acid homology) with the corrected porcine group C/Cowden sequence. The Preston VP6 gene demonstrated 99.6% nucleotide homology with the human group C/Bristol VP6 gene and 84.0% nucleotide homology (91.6% deduced amino acid homology) with the corrected porcine group C/Cowden sequence. Remarkably, the deduced amino acid sequence of the Brazilian strain was identical to that of the U.K. isolates.
authors.affiliation: Department of Microbiology, University Medical School, Southampton General Hospital, U.K.
authors.forename: S J
authors.initials: SJ
authors.lastname: Cooke
authors.forename: I N
authors.initials: IN
authors.lastname: Clarke
authors.forename: R B
authors.initials: RB
authors.lastname: Freitas
authors.forename: Y B
authors.initials: YB
authors.lastname: Gabbay
authors.forename: P R
authors.initials: PR
authors.lastname: Lambden
mesh_terms: D000595:Amino Acid Sequence; D000956:Antigens, Viral; D001483:Base Sequence; D001938:Brazil; D002213:Capsid / Q000235:genetics*; D036022:Capsid Proteins; D004279:DNA, Viral; D006801:Humans; D008969:Molecular Sequence Data; D012401:Rotavirus / Q000235:genetics*; D012400:Rotavirus Infections / Q000382:microbiology*; D012689:Sequence Homology, Nucleic Acid; D006113:United Kingdom
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; D004279:DNA, Viral; C061332:VP6 protein, Rotavirus