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

Abstract

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

Keywords: Genetic diversity; Genotype; Reassortment; Recombination; Rotavirus.

Fig. 1

The temporal genotype distribution of rotavirus in different geographical levels. Temporal distribution bar chart of RVA genotypes in Global (A), in China (B), in Shenzhen and Zhuhai (C). Temporal distribution percentage stacked area chart of RVA genotypes in Global (D), in China (E), in Shenzhen and Zhuhai (F) Different norovirus genotypes are indicated by color

Fig. 2

Phylogenetic tree of complete genome sequence of VP7 gene. The background color of the tree represents the genotype, the color strip outside depicts the location, and the color of solid circle represents the time. The strains contributed in this study are indicated by red stars outside. Other sequences can be downloaded from the GenBank database, with accession numbers shown in the Table S2.

Fig. 3

Phylogenetic tree of complete genome sequence of VP4 gene. The background color of the tree represents the genotype, the color strip outside depicts the location, and the color of solid circle represents the time. The strains contributed in this study are indicated by red stars outside. Other sequences can be downloaded from the GenBank database, with accession numbers shown in the Table S2

Fig. 4

Reassortment analysis of the reassortant strain. Phylogenetic trees were presented for VP7 (A), VP2 (B), VP1 (C), and VP6 (D). The reassortant strain is indicated by red solid square outside. (E). Reassortment results verified by RDP. Reassortant strain name is highlighted in red. The colored lines represent the pairwise similarity between sequences

Fig. 5

Recombination analysis of rotavirus in NSP1 and NSP5/6. A. Event in NSP1. B Event in NSP5/6. The green line compares the minor parent to the recombinant, purple line compares the major parent to the recombinant, and the blue line compares the major parent to the minor parent. The gray areas represent the degree of confidence. Recombinant strain names are highlighted in red