SEQUENCE DIVERSITY WITHIN THE REOVIRUS S2 GENE - REOVIRUS GENES REASSORT IN NATURE, AND THEIR TERMINI ARE PREDICTED TO FORM A PANHANDLE MOTIF

To better understand genetic diversity within mammalian reoviruses, we determined S2 nucleotide and deduced sigma 2 amino acid sequences of nine reovirus strains and compared these sequences with those of proto type strains of the three reovirus serotypes. The S2 gene and sigma 2 protein are highly conserved among the four type 1, one type 2, and se ven type 3 strains studied. Phylogenetic analyses based on S2 nucleoti de sequences of the 12 reovirus strains indicate that diversity within the S2 gene is independent of viral serotype. Additionally, we found marked topological differences between phylogenetic trees generated fr om S1 and S2 gene nucleotide sequences of the seven type 3 strains. Th ese results demonstrate that reovirus ST and S2 genes have distinct ev olutionary histories, thus providing phylogenetic evidence for lateral transfer of reovirus genes in nature. When variability among the 12 s igma 2-encoding S2 nucleotide sequences was analyzed at synonymous pos itions, we found that approximately 60 nucleotides at the 5' terminus and 30 nucleotides al the 3' terminus were markedly conserved in compa rison with other sigma 2-encoding regions of S2. Predictions of RNA se condary structures indicate that the more conserved S2 sequences parti cipate in the formation of an extended region of duplex RNA interrupte d by a pair of stem-loops. Among the 12 deduced sigma 2 amino acid seq uences examined, substitutions were observed at only 11% of amino acid positions. This finding suggests that constraints on the structure or function of sigma 2, perhaps in part because of its location in the v irion core, have limited sequence diversity within this protein.