Evolution of the GII.3[P12] Norovirus from 2010 to 2019 in Jiangsu, China

Jianguang Fu,Changjun Bao,Jing Ai,Zheng Xing,Jianli Hu,Jun Zhang,Qingbin Wu,Liguo Zhu

doi:10.1186/s13099-021-00430-8

Abstract

ObjectivesNorovirus genotype GII.3[P12] strains have been an important pathogen for sporadic gastroenteritis infection. In previous studies of GII.3[P12], the number of specimens and time span are relatively small, which is difficult to truly reflect the infection and evolution of this type of norovirus. Here we report a molecular epidemiological study of the NoVs prevalent in Jiangsu between 2010 and 2019 to investigate the evolution of the GII.3[P12] strains in China.MethodsIn this study 60 GII.3[P12] norovirus strains were sequenced and analyzed for evolution, recombination, and selection pressure using bioanalysis software.ResultsThe GII.3[P12] strains were continuously detected during the study period, which showed a high constituent ratio in males, in winter and among children aged 0–11 months, respectively. A time-scaled evolutionary tree showed that both GII.P12 RdRp and GII.3 VP1 sequences were grouped into three major clusters (Cluster I–III). Most GII.3[P12] strains were mainly located in sub-cluster (SC) II of Cluster III. A SimPlot analysis identified GII.3[P12] strain to be as an ORF1-intragenic recombinant of GII.4[P12] and GII.3[P21]. The RdRp genes of the GII.3[P12] showed a higher mean substitution rate than those of all GII.P12, while the VP1 genes of the GII.3[P12] showed a lower mean substitution rate than those of all GII.3. Alignment of the GII.3 capsid sequences revealed that three HBGA binding sites of all known GII.3 strains remained conserved, while several amino acid mutations in the predicted antibody binding sites were detected. The mutation at 385 was within predicted antibody binding regions, close to host attachment factor binding sites. Positive and negative selection sites were estimated. Two common positively selected sites (sites 385 and 406) were located on the surface of the protruding domain. Moreover, an amino acid substitution (aa204) was estimated to be near the active site of the RdRp protein.ConclusionsWe conducted a comprehensive analysis on the epidemic and evolution of GII.3[P12] noroviruses and the results suggested that evolution was possibly driven by intergenic recombination and mutations in some key amino acid sites.

Highlights

Human norovirus has been recognized as the major cause for non-bacterial epidemic gastroenteritis [1, 2]
Residues in the P2 domain are involved in the interaction with antibodies and histo-blood group antigens (HBGAs), which are supposed to be receptors or co-receptors of norovirus [4]
Norovirus-positive samples were detected with a region of 1095 bp targeted in the ORF1/ ORF2 junction of the viral genome by one-step reverse transcription polymerase chain reaction (RT-PCR) for norovirus genotyping [12]

Summary

Introduction

Human norovirus has been recognized as the major cause for non-bacterial epidemic gastroenteritis [1, 2]. Noroviruses are phylogenetically classified into 10 genogroups (GI-GX) and, among them, at least five genogroups (GI, GII, GIV, GVIII and GIX) could infect humans [5]. GII. is a common cause for sporadic infection in infants and children as the second major genotype after GII. in China [6, 7]. Studies on the evolution of GII.3[P12] in detail are scarce [8,9,10,11] In these studies, the number of specimens and time span are relatively small, making it difficult to truly reflect the infection and evolution of this type of norovirus. We performed a molecular evolutionary study on the GII.P12 RdRp and GII. VP1 regions of the noroviruses from fecal samples collected from pediatric patients from 2010 to 2019

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