Double nomenclature of sapovirus based on complete VP1 and NS6-7 nucleotide sequences

A significant foodborne pathogen that causes acute gastroenteritis worldwide is sapovirus (SaV). Currently, SaV genotyping is primarily based on the VP1 gene. The single naming method based on the VP1 region can no longer suit the needs of SaV research due to the emergence of recombinant strains. Therefore, SaV nucleotide sequences with entire VP1 and NS6-7 genes sections were gathered in Genbank, and genetic distance calculations and phylogenetic analyses were carried out to investigate the double nomenclature based on SaV VP1 and NS6-7 genes. They can be further subdivided into genotypes and various genogroups based on the genetic diversity of the entire VP1 region, and 12 genogroups and 30 genotypes were found, including tentative genotypes and genogroups. The work is noteworthy for having discovered a novel genogroup, GNA1. There was an interesting discovery of a class of sequences known as bat-related sequences. The genetic distance between these sequences approached the inter-genogroup genetic distance, which in this study was classified as the bat genogroup. Thirty significant reference sequences are proposed based on the VP1 genotypes. Phylogenetically, twelve P (polymerase)-groups and 29 P-types (Including tentative genotypes and genogroup) were identified based on the genetic diversity of nucleotide sequences in the entire NS6-7 region, and related P-type reference sequences were also suggested. Nine recombinant sequences, comprising six recombinant genotypes (GI.1[P4], GI.2[P1], GII.4[P1], GII.4[PNA1], GII.6[P2], and GV.NA1[P3]), were found as a result of the dual nomenclature of the VP1 and NS6-7 genes. Dual nomenclature based on VP1 and NS6-7 genes can effectively characterize SaV recombination.