A dual typing system establishment and global diversity analysis for sapoviruses

Abstract

Background: The genus Sapovirus in the family Caliciviridae comprises of a genetically diverse group of viruses that are responsible for causing acute gastroenteritis in both human and animals globally. As the number of sequences continues to grow and more recombinant sequences are identified, the classification criteria of genogroups and genotypes of sapovirus need to be further refined. In this study, we aimed to optimize the classification of sapoviruses.

Results: Through evolutionary clustering and genetic distance analysis, we have updated the classification criteria for VP1 genogroup and genotypes. We adjusted the original mean values ± 3 standard deviations (SD) of genetic distances to mean values ± 2.5SD, resulting the corresponding cutoff values for the same genotype and genogroup set at <0.161 and <0.503, respectively. Additionally, we established classification criteria for RdRp types and groups, referred to as P-types and P-groups,, with mean values ± 2SD and cutoff values of <0.266 and <0.531 for the same type and group, respectively. This refinement has expanded the VP1 genogroups to thirty-four and identified twenty-four P-groups. For human sapoviruses, the new criteria have resulted in the addition of one genotype, GV.PNA1. Moreover, the new criteria defined three P-groups and 21 P-types for human sapoviruses. Spatial-temporal analysis revealed no specific distribution pattern for human sapoviruses.

Conclusions: We established a dual typing system on classification based on VP1 and RdRp nucleotide sequences for sapoviruses.

Keywords: Classification; Dual-typing; Genetic distance; Genogroup; Genotype; Sapoviruses.

Fig. 1

Phylogenetic classification of sapoviruses based on VP1 and RdRp amino acid sequences. (A) VP1 genogroups. (B) P-groups. Phylogenetic analysis was performed using maximum likelihood method. RdRp groupings were generally consistent with those of VP1

Fig. 2

Pairwise distance distribution of major sapovirus strains using the VP1 and RdRp nucleotide sequences. (A) VP1; (B) RdRp. The horizontal bars indicated the mean value ± 2.5SD and mean value ± 2SD in the VP1 and RdRp for each distribution peaks of strain, genotype and genogroup, respectively

Fig. 3

Phylogenetic classification of clustered sapoviruses in pigs and bats. (A) porcine VP1. The original GVI genogroup should be divided into three genogroups and GVII genogroup into five. (B) porcine RdRp. No full RdRp sequences were available in GVI genogroup. (C) bat VP1. The original GXIX can be divided into two genogroups, and a total of four new genogroups were designated. (D) bat RdRp. The classification of bat P-group was strictly corresponded to its VP1 grouping

Fig. 4

Patristic distances comparison of the sapoviruses from pigs and bats with their phylogenetically closest cluster(s). (A, B) porcine VP1 and RdRp; (C, D) bat RdRp and VP1. After re-assigning GVI, GVII and GXIX into 3, 5 and 2 genogroups, respectively, no overlap of error bars within or in-between genogroups were present. Error bars represent 2.5 × SD in VP1 and 2 × SD in RdRp. Y-axis represented comparison of distances within and in-between genogroups. Red lines indicated the genogroups that did not meet the 2.5/2 × SD criterion

Fig. 5

Phylogenetic trees of GI/GI.P, GII/GII.P, and GV/GV.P genogroups based on nucleotide sequences of VP1 and RdRp. (A-C) genotypes in GI, GII and GV; (D-F) P types in GI.P, GII.P and GV.P. The red font indicated the newly designated genotypes/P-types

Fig. 6

Patristic distances comparison of the sapoviruses in GI/GI.P, GII/GII.P, and GV/GV.P with their phylogenetically closest cluster(s). (A, B) GI and GI.P; (C, D) GII and GII.P; (E, F) GV and GV.P. Original GI.P1 and GI.P4 were classified together and named as GI.P1; GII.P2 was split into GII.P2, GII.P9, and GII.PNA2; the RdRp from GV.4 not clustering within GV.P but instead clustering in GXIII.P, the remaining clusters correspond to GV genogroup. Error bars represent 2.5 × SD in VP1 and 2 × SD in RdRp. Y-axis represented comparison of distances within and between genogroups. Red lines indicated the genogroups that did not meet the 2.5/2 × SD criterion

Fig. 7

Temporal-spatial distributions of evolutionary clusters for human sapoviruses based on the VP1 nucleotide sequences. (A) temporal distribution. (B) spatial distribution. Results showed there was no obvious temporal or spatial specificity