Comparative analysis of sapovirus genetic diversity based on VP1 and NS6-7

Abstract A significant foodborne pathogen that causes acute gastroenteritis worldwide is sapovirus. Currently, there have been reports of certain recombinant strains of sapovirus, and the genetic diversity of this virus is continuously increasing. In this study, sapovirus nucleotide sequences with entire VP1 and NS6-7 regions were obtained from GenBank, and phylogenetic analysis and genetic distance calculations were performed to investigate the genetic diversity of the VP1 and NS6-7 regions of this virus. In addition to the 19 known genogroups, a small number of sequences were discovered to be beyond the range of known genogroups and were temporarily divided (Bat NA1-Bat NA3). This was based on the genetic diversity of the entire VP1 region. Based on the VP1 region, 38 key reference sequences were also suggested. Furthermore, for 33 sequences for which the genotyping tool mistyped, the genotype and genogroup information were modified. We also attempted to categorize sapovirus based on the genetic diversity of the nucleotide sequences of NS6-7 region. Phylogenetically, 17 P (polymerase)-groups (GI.P-GIII.P, GV.P-GVIII.P, GX.P-GXIX.P) and one tentative (GNA1.P) were identified based on the genetic diversity of nucleotide sequences in the entire NS6-7 region, and 35 related reference sequences were also suggested. Nine recombinant sequences, including six recombinant genotypes (GI.1[P4], GI.2[P1], GII.4[P1], GII.4[PNA1], GII.6[P2], and GV.5[P3]), were identified by genetic diversity differences between VP1 and NS6-7 of sapovirus. With this approach, sapovirus recombination events may be effectively characterized.