Norovirus GII.2[P16] strain in Shenzhen, China: a retrospective study

Jing Wang,Yaqing He,Guifang Hu,Yanan Zhu,Hong Yang,Miao Jin,Zhaojun Duan,Xiangjie Yao,Long Chen,Jun Meng,Hailong Zhang

doi:10.1186/s12879-021-06746-9

Abstract

BackgroundNorovirus (NoV) is the main cause of non-bacterial acute gastroenteritis (AGE) outbreaks worldwide. From September 2015 through August 2018, 203 NoV outbreaks involving 2500 cases were reported to the Shenzhen Center for Disease Control and Prevention.MethodsFaecal specimens for 203 outbreaks were collected and epidemiological data were obtained through the AGE outbreak surveillance system in Shenzhen. Genotypes were determined by sequencing analysis. To gain a better understanding of the evolutionary characteristics of NoV in Shenzhen, molecular evolution and mutations were evaluated based on time-scale evolutionary phylogeny and amino acid mutations.ResultsA total of nine districts reported NoV outbreaks and the reported NoV outbreaks peaked from November to March. Among the 203 NoV outbreaks, 150 were sequenced successfully. Most of these outbreaks were associated with the NoV GII.2[P16] strain (45.3%, 92/203) and occurred in school settings (91.6%, 186/203). The evolutionary rates of the RdRp region and the VP1 sequence were 2.1 × 10–3 (95% HPD interval, 1.7 × 10–3–2.5 × 10–3) substitutions/site/year and 2.7 × 10–3 (95% HPD interval, 2.4 × 10–3–3.1 × 10–3) substitutions/site/year, respectively. The common ancestors of the GII.2[P16] strain from Shenzhen and GII.4 Sydney 2012[P16] diverged from 2011 to 2012. The common ancestors of the GII.2[P16] strain from Shenzhen and previous GII.2[P16] (2010–2012) diverged from 2003 to 2004. The results of amino acid mutations showed 6 amino acid substitutions (*77E, R750K, P845Q, H1310Y, K1546Q, T1549A) were found only in GII.4 Sydney 2012[P16] and the GII.2[P16] recombinant strain.ConclusionsThis study illustrates the molecular epidemiological patterns in Shenzhen, China, from September 2015 to August 2018 and provides evidence that the epidemic trend of GII.2[P16] recombinant strain had weakened and the non-structural proteins of the recombinant strain might have played a more significant role than VP1.

Highlights

Norovirus (NoV) is the main cause of non-bacterial acute gastroenteritis (AGE) outbreaks worldwide
The P2 region is considered a hypervariable part of the genome because the domain encodes the receptor-binding domain, which is responsible for histoblood group antigen (HBGA) binding, and important epitopes targeted by antibodies that inhibit binding [9, 10]
Phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) region and VP1 To evaluate the evolution of the NoV GII.2[P16] strain in Shenzhen, the full-length RdRp region or VP1 sequence from this study and all the sequences of the full-length RdRp region or VP1 sequence we found in GenBank as of September 2016 were collected

Summary

Introduction

Norovirus (NoV) is the main cause of non-bacterial acute gastroenteritis (AGE) outbreaks worldwide. Norovirus (NoV), which is the main cause of non-bacterial acute gastroenteritis (AGE) worldwide, can infect all age groups, especially children under 5 years of age. The first 5 kb closest to the 5’ end of the genome is ORF1, which encodes non-structural proteins, including N-terminal protein (P48), NTPase, 3A protein (P22), VPg (viral genomic junction protein), 3 C-like protein (Pro) and RNA-dependent RNA polymerase (RdRp) [6]. These proteins are important for the replication of NoV. ORF3 is 0.6 kb and encodes the minor structural protein (VP2) [11]

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Discussion

Conclusion