STUDY OF GENOMIC REARRANGEMENT IN ROTAVIRUSES

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The complete nucleotide sequence of genomic double stranded RNA (dsRNA) 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 electrophoresis pattern. Its segment 11 is 1036 base pairs 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 (i.e., decreased mobility during electrophoresis) results from a simple duplication followed by a simple deletion. Two potential open reading frames (orf) frames are present. The first orf, 594 base pairs in length (encoding 198 amino acids), extends from nucleotide 22 to a stop codon (TAA) at nucleotides 616 to 618. A stretch of 92 nucleotides (from positions 619-711) separate the end of the first and the beginning of the second orf. Sixty-five of these nucleotides (from bases 625 to 690) are similar in sequence to the nucleotides from bases 169 to 234. In addition, 18 nucleotides from positions 691 to 708 are similar in sequence to those at positions 322 to 339. The second orf of gene 11 of Alabama strain extends from nucleotides 712 to 984 and is 272 base pairs in length. Of interest, this orf is a duplication of the sequence corresponding to nucleotides 349 to 615 and is followed by a 3' noncoding region of 52 nucleotides. This second orf, unique to the gene 11 of the Alabama strain, is capable of coding for a protein of 91 amino acids.