Sequence analysis of group B rotavirus gene 1 and definition of a rotavirus-specific sequence motif within the RNA polymerase gene.

The complete nucleic acid sequence was determined for the largest genomic segment of the IDIR strain of group B rotavirus and compared with RNA polymerase genes of rotavirus groups A and C as well as other RNA viruses. IDIR gene 1 contained 3509 bases with a single, long open reading frame which encoded a deduced polypeptide of 1159 amino acids (MW = 131.6 kDa; pl 8.851). The deduced amino acid sequence of IDIR gene 1 shared 50% similar sequences and 27.6% identical sequences with VP1 of the RF strain of group A rotavirus. IDIR gene 1 also contained 45.4% similar and 26.5% identical amino acid sequences in comparison with gene 1 of the Cowden strain of group C rotavirus. Amino acids 643-689 of IDIR gene 1 corresponded to the conserved viral RNA polymerase domains, "SG . . . T . . . NS . . N" and "GDD." Within these domains, group A, B, and C rotaviruses displayed substantial homologies that were not shared with other RNA viruses. These sequences indicated the presence of highly conserved structural or functional components among groups of rotaviruses which were otherwise quite heterogeneous. The identification of rotavirus-specific residues within RNA polymerase sequence may prove valuable in devising strategies aimed at the control of rotavirus replication and infection.