Intra-segmental recombinations between avian and mammalian VP4 genotypes in Rotavirus alphagastroenteritidis

Rotavirus alphagastroenteritidis (RVA), a pathogen causing acute gastroenteritis in young birds and mammals, possesses a genome of 11 segmented double-stranded RNAs, each of which is classified into genotypes. RVA has been divided into the avian and mammalian clusters as well as the basal group. Although the avian and mammalian clusters were considered to have evolved independently, genomic segment encoding viral protein 4 (VP4) of pheasant strain with genotype P[37] appeared to be transferred from mammalian cluster strain through reassortment. Here prototype sequences for all genotypes P[1]-P[58] of VP4 segment except for P[53] and P[54] retrieved from the International Nucleotide Sequence Database were analyzed to examine the possibility that P[37] was a product of intra-segmental recombinations between avian and mammalian cluster strains. In the sliding window analysis, different regions of P[37] appeared to have different relative similarities to avian and mammalian cluster strains. Using recombination detection programs, two regions of P[37] were identified to be derived from mammalian cluster strains and integrated into the background of avian cluster strain. These results were confirmed by phylogenetic analyses. Thus, even when genomic segments are not entirely compatible between strains, only compatible parts may be transferred through intra-segmental recombinations in RVA.