Isolation and genomic characterization of a reassortant G9P[8]-E2 rotavirus strain in China

Abstract Objective: To isolate a prevalent G9P[8] group A rotavirus (RVA) strain (N4006) in China and investigate its genomic and evolutionary characteristics, with the goal of facilitating the development of a new rotavirus vaccine. Methods: An RVA strain of the G9P[8] genotype from a diarrhea sample was passaged in MA104 cells. The strain was evaluated by SEM, polyacrylamide gel electrophoresis, and indirect immunofluorescence assay. The complete genome of the strain was obtained by RT-PCR and sequencing. The genomic and evolutionary characteristics of the strain were evaluated by nucleic acid sequence analysis with MEGA ver. 5.0.5 and DNASTAR software. The neutralizing epitopes of VP7 and VP4 (VP5* and VP8*) were analyzed using BioEdit ver. 7.0.9.0 and PyMOL ver. 2.5.2. Results: The N4006 strain (G9P[8] genotype) was adapted in MA104 cells with a high titer (105.5 PFU/mL). Whole-genome sequence analysis showed N4006 to be a reassortant rotavirus of Wa-like G9P[8] RVA and the NSP4 gene of DS-1-like G2P[4] RVA, with the genotype constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2). Phylogenetic analysis indicated that N4006 had a common ancestor with Japanese G9P[8]-E2 rotavirus strains. Neutralizing epitope analysis showed that VP7, VP5*, and VP8* of N4006 had low homology with vaccine strains of the same genotype and marked differences with vaccine strains of other genotypes. Conclusion: The G9P[8] genotype rotavirus with the G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2) constellation predominates in China and may originate from reassortment between Japanese G9P[8] with Japanese DS-1-like G2P[4] rotaviruses. The antigenic variation of N4006 with the vaccine strain necessitates evaluation of the effect of the rotavirus vaccine on G9P[8]-E2 genotype rotavirus.