Evidence of Duplication and Deletion in Super Short Segment 11 of Rabbit Rotavirus Alabama Strain

The complete nucleotide sequence of genome segment 11, of the Alabama strain of rabbit rotavirus, was determined by sequencing dsRNA and mRNA using the dideoxy chain termination method. This strain has a "super short" RNA pattern. Its segment 11 is 1036 bp in length, 369 nucleotides longer than that reported for rotavirus strains with a "long" electropherotype. Sequence analysis indicated that the shift in genome segment 11 of Alabama strain to a "super short" RNA pattern results from a simple duplication followed by a simple deletion. The positive strand of segment 11 contains two non-overlapping open reading frames of 594 bases (198 amino acids) starting at base 22 and a second of 273 bases (91 amino acids) starting at base 712. The polypeptide from the latter reading frame is the result of a partial duplication of the nucleotide sequence encoding amino acids 110 to 198 of gene 11.