Genetic characteristics of rotavirus a in Shenzhen and Zhuhai, China, 2020-2023

Rotavirus A group (RVA) is a leading cause of viral diarrhea, posing a substantial economic and public health burden. Compared to other enteric viruses, RVA possesses diverse genetic mechanisms, making it more challenging to control and prevent. Moreover, surveillance and evolutionary studies on RVA remain limited in Southern China.

We collected diarrheal stool samples from sentinel hospitals in Shenzhen and Zhuhai between 2020 and 2023. RVA-positive samples were identified via RT-PCR, followed by RNA extraction, sequencing, and genome assembly, yielding 57 RVA strains, comprising 604 sequences. Genotype trends were analyzed statistically. For phylogenetic analysis, global sequences were curated by CD-HIT, aligned with contributed sequences by MAFFT, and analyzed using IQ-TREE. Recombination and reassortment events were detected via RDP4.

We analyzed the temporal distribution and genetic diversity of 57 newly sequenced strains from Shenzhen and Zhuhai in the context of global sequences. Our findings reveal that the prevalent genotypes of RVA in China have undergone changes over time with the decreasing of G9P[8] and the rising of G8P[8]. Phylogenetic analysis focusing on the VP7 and VP4 genes revealed distinct evolutionary patterns among different genotypes across temporal and geographical dimensions. Additionally, we discovered one reassortment event in the VP7 gene and two recombination events in the NSP1 and NSP5/6 gene.

we observed significant variability and complexity in the evolutionary characteristics of RVA in Shenzhen and Zhuhai. These insights enhance our understanding of global evolution and transmission of RVA and provide guidance for future research and vaccine development.