Whole genome classification of Rotavirus C and genetic diversity of porcine strains in the United States

Rotavirus C (RVC) is associated with acute diarrhea in both children and young animals. Because of its frequent occurrence, additional sequences have recently been generated. In this study, we have sequenced 31 complete genomes from porcine diarrhea samples and analyzed them together with all available reference sequences collected from the GenBank. Based on phylogenetic analysis and genetic distance calculation, the number of each segment identified as 31G, 26P, 13I, 5R, 5C, 5M, 12A, 10N, 9T, 8E and 4H, for genotypes encoding VP7, VP4, VP6, VP1, VP2, VP3 and NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. From the analysis, genotypes G18-G31, P[22]-P[26], R5, A9-A12, N9-N10, T7-T9 and E6-E8, were defined as newly identified genotypes and genotypes C6 and M6 were combined to C5 and M1, respectively, due to their closely related nature. Estimated with identity frequency ratio between inter-genotype and intragenotype, the nucleotide identity cutoff values for different genotypes were determined as 85%, 85%, 86%, 84%, 83%, 84%, 82%, 87%, 84%, 81% and 79% for VP7, VP4, VP6, VP1, VP2, VP3 and NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. Genotyping of the 49 US strains indicated possible segment reassortment in 9 of the 11 segments, except VP1 and NSP5, and the most prevalent genotypes for each segment genes in the US were G6/G5/G21/G9-P5/P4-I6/I5-R1-C5-M1-A8-N1/N10-T1-E1-H1. Our study updated the genotypes of RVC strains and provided more evidence of RVC strain diversity that may be relevant to better understand genetic diversity, and distribution and evolution of RVC strains.