Sequence analysis of normal and rearranged NSP5 genes from human rotavirus strains isolated in nature: implications for the occurrence of the rearrangement at the step of plus strand synthesis.

We determined the nucleotide sequences of normal and rearranged NSP5 genes from the human rotavirus strains (Mc323 and Mc345, respectively) which had previously been isolated from Thai infants with diarrhea in the same epidemic season. While the two strains shared G serotype 9 specificity and subgroup I specificity and they showed a high level of overall genomic relatedness to each other, they exhibited different RNA profiles; a long pattern for Mc323 and a super-short pattern for Mc345. Their NSP5 sequences were more closely related to those of porcine rotaviruses than to those of human rotaviruses. Mc345 NSP5 gene was shown to have concatemerization. In a head-to-tail orientation resulting in its length being 1182 bp, as compared with the Mc323 NSP5 sequence which was 664 bp in length. Sequence analysis suggested that the rearrangement found in the strain Mc345 occurred at the step of plus strand synthesis.