Shared clusters between phylogenetic trees for genomic segments of Rotavirus A with distinct genotype constellations

Abstract

Rotavirus A (RVA) possesses a genome of 11-segmented, double-stranded RNAs, each of which is classified into genotypes. A variety of genotype constellations have been generated through reassortment, but reassortment does not appear to occur randomly. Here genomic sequences for 281 RVA strains with distinct genotype constellations retrieved from the International Nucleotide Sequence Database were analyzed to identify shared clusters between phylogenetic trees for genomic segments. The largest numbers of shared clusters were observed between the genomic segments encoding viral protein 1 (VP1) and VP2 as well as VP2 and VP3, suggesting that not only VP1 but also VP3 may interact with VP2 inside the core. Larger numbers were also associated with the segment encoding non-structural protein 5/6 (NSP5/6), which may be a hub for bundling genomic segments. Although VP7 and VP4 segments were associated with smaller numbers, reassortments between these segments as well as VP7 and VP6 segments appeared to be restricted due to interactions in constructing the virion. For VP4 segment, the number with NSP1 segment was significantly greater than those with other segments, possibly reflecting that specificities in receptor binding and interferon antagonism may define host range restriction. Overall, no cluster was shared by all genomic segments, supporting that RVA constituted a single species.