Whole genome analysis of multiple rotavirus strains from a single stool specimen using sequence-independent amplification and 454® pyrosequencing reveals evidence of intergenotype genome segment recombination

► The whole genomes of multiple rotavirus strains were characterized from a single stool sample. ► Sequence-independent amplification and 454® pyrosequencing were used. ► Four distinct rotavirus strains were identified. ► Intergenotype recombination occurred in VP6, NSP2 and NSP4 encoding genome segments. ► Some genome segments encoding VP6, VP7 and NSP2 shared ancestry with animal rotaviruses.