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Group A rotavirus (RVA), an etiological agent of gastroenteritis in young mammals and birds, possesses a genome of 11 double-stranded RNA segments. Although it is believed that the RVA virion contains one copy of each genomic segment and that the positive-strand RNA (+RNA) is incorporated into the core shell, the packaging mechanisms of RVA are not well understood. Here, packaging signals of RVA were searched for by analyzing genomic sequences of mammalian and avian RVA, which are considered to have evolved independently without reassortment. Assuming that packaging is mediated by direct interaction between +RNA segments via base-pairing, co-evolving complementary nucleotide sites were identified within and between genomic segments. There were two pairs of co-evolving complementary sites within the segment encoding VP7 (the VP7 segment) and one pair between the NSP2 and NSP3 segments. In the VP7 segment, the co-evolving complementary sites appeared to form stem structures in both mammalian and avian RVA, supporting their functionality. In contrast, co-evolving complementary sites between the NSP2 and NSP3 segments tended to be free from base-pairings and constituted loop structures, at least in avian RVA, suggesting that they are involved in a specific interaction between these segments as a packaging signal.

A possible packaging signal in the rotavirus genome