Marked sequence variation between segment 4 genes of human RV-5 and simian SA 11 rotaviruses

Abstract

The complete nucleotide sequence of dsRNA gene segment 4 of a human serotype 2 rotavirus, RV-5, was determined by sequencing overlapping cloned DNA copies of the gene. Segment 4 is 2359 base pairs in length and contains a single long open reading frame of 2325 bases capable of coding for a protein of 775 amino acids, with 5′ and 3′ non coding regions of 9 and 25 nucleotides respectively. Comparison with SA 11 segment 4 sequence reveals a moderately conserved trypsin cut site and an overall amino acid homology of 69.8 percent. One localized region of 126 amino acids is only 37.8 percent homologous. Localized frame shifts account for some of this variation, but at the nucleotide level the segment 4 sequences show more variability than other rotavirus genes that have been studied so far.