Amino acid sequence of the porcine rotavirus YM VP1 protein

Intra-genotypic diversity of archival G4P[8] human rotaviruses from Washington, DC

Group A human rotaviruses (RVs) remain the most frequently detected viral agents associated with acute gastroenteritis in infants and young children. Despite their medical importance, relatively few complete genome sequences have been determined for commonly circulating G/P-type strains (i.e., G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]). In the current study, we sequenced the genomes of 11 G4P[8] isolates from stool specimens that were collected in Washington, DC during the years of 1974-1991. We found that the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6-encoding genes of all 11 G4P[8] RVs have the genotypes of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees for each gene, extensive intra-genotypic diversity was revealed among the G4P[8] RVs, and new sub-genotype gene alleles were identified. Several of these alleles are nearly identical to those of G3P[8] isolates previously sequenced from this same Washington, DC collection, strongly suggesting that the RVs underwent gene reassortment. On the other hand, we observed that some G4P[8] RVs exhibit completely different allele-based genome constellations, despite being collected during the same epidemic season; there was no evidence of gene reassortment between these strains. This observation extends our previous findings and supports the notion that stable, genetically-distinct clades of human RVs with the same G/P-type can co-circulate in a community. Interestingly, the sub-genotype gene alleles found in some of the DC RVs share a close evolutionary relationship with genes of more contemporary human strains. Thus, archival human RVs sequenced in this study might represent evolutionary precursors to modern-day strains.

Human group C rotavirus: completion of the genome sequence and gene coding assignments of a non-cultivatable rotavirus

Genome segments 1 and 2 of human group C rotavirus 'Bristol' strain were sequenced and their gene-protein coding properties assigned. This work completed the genome sequence of a human group C rotavirus (17,910 bp) and allowed the full gene-protein coding assignment of the 11 segments of dsRNA. Gene 1 is 3309 bp in size and contains a single ORF of 3272 nucleotides, encoding a protein of 1090 amino acids in length with a predicted molecular mass of 125 kDa. Comparison of the translated sequence with cognate published mammalian group A, B and C rotavirus sequences showed 45.2, 26.4 and 92.6% identity, respectively. The sequence contains conserved amino acid motifs including the classic RNA-dependent RNA polymerase motif GDD, indicating that segment 1 encodes the group C rotavirus polymerase protein. Gene 2 is 2736 bp in size and contains a single ORF of 2655 nucleotides encoding a protein of 884 amino acids in length with a calculated molecular mass of 102 kDa. Database searches showed highest homology with VP2, the main structural component of the 'core' from group A rotaviruses (46% identity). Alignment of the human group C and A rotavirus VP2 proteins revealed several characteristics common to nucleic acid binding proteins. However, these features were not shared with group B rotavirus VP2.

Genetic relatedness of VP1 genes of Australian and Taiwanese rotavirus isolates

Gene 1 (which encodes the viral RNA-dependent RNA polymerase, VP1) of an atypical human reassortant rotavirus strain, E210 (serotype G2P1B), is unrelated to genes 1 of standard human rotaviruses. To ascertain the origin of this gene, we determined a partial sequence and found that it exhibited greatest identity to gene 1 of a Taiwanese isolate, TE83, which is representative of G2 strains that caused an epidemic of gastroenteritis in 1993. Limited sequence identity to genes 1 of standard human and animal viruses was observed. This was confirmed by phylogenetic analysis. However, hybridization analysis using an E210 gene 1-specific probe indicated that a related gene was found among other Australian G2 isolates and in a Japanese strain isolated in the 1970s.