Background With the help of an existing citywide comprehensive surveillance on gastroenteritis outpatients, although norovirus genogroup II (NoV GII) was tested routinely, its genotypes were never investigated systematically on a municipal level. This study aimed to understand the prevalence, major genotypes and evolutional trends of NoV GII in Shanghai during the period of 2016-2018, and to provide molecular bases for early warning for any potential NoV outbreaks. Methods 27 sentinel hospitals from all 16 districts were recruited by stratified probability proportional to size (PPS) method in Shanghai comprehensive diarrhea surveillance programme. Stool samples were collected and screened for NoV GII by real-time reverse transcription polymerase chain reaction (qRT-PCR). For samples that were positive in qRT-PCR, conventional RT-PCR was performed to amplify the ORF1-ORF2 junction of NoV GII gene. Generated sequences were typed by RIVM online genotyping tool, and then strains of interest were analyzed phylogenetically using MEGA 6.0. Results A total of 7883 stool samples were collected from diarrhea outpatients, among which 6474 were from adults and 1409 were from children. 13.66% (1077 cases) were screened positive in qRT-PCR for NoV GII, from which 71.96% (775 cases) were sequenced successfully. The top three genotypes were GII.Pe/GII.4 (37%), GII.P17/GII.17 (26%) and GII.P16/GII.2 (17%). While GII.Pe/GII.4 detection rate decreased significantly over the 3 years (from 48.4 to 20.9%); GII.P16/GII.2 appeared for the first time in October 2016 and rose rapidly to 27.0% in 2017, but fell back to 23.4% in 2018. Meanwhile there was a significant increase for both GII.P12/GII.3 and GII.P7/GII.6 recombinant genotypes detected in adult population in 2018. Phylogenic analysis revealed the existence of multiple gene clusters within both of these recombinant genotypes. Conclusion Unlike the alternating circulation of GII.4 and non-GII.4 NoV observed in 2016 or 2017, the genotype profile of NoV GII in 2018 was characterized by the co-prevalence of multiple recombinant genotypes. A recent increase in detection rate in less reported recombinant genotypes such as GII.P12/GII.3 and GII.P7/GII.6 among adult population calls for a continuing close monitoring on NoV GII genotypes in case of potential local outbreaks.

中文翻译：

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2016-2018年上海市胃肠炎门诊患者诺如病毒GII基因型流行情况

背景 在现有的全市范围内胃肠炎门诊患者综合监测的帮助下，虽然诺如病毒基因组 II (NoV GII) 进行了常规检测，但其基因型从未在市级进行系统调查。本研究旨在了解2016-2018年上海NoV GII的流行情况、主要基因型和进化趋势，为任何潜在的NoV暴发预警提供分子基础。方法在上海市腹泻综合监测项目中，采用分层概率与规模成正比（PPS）方法招募16个区的27家哨点医院。收集粪便样本并通过实时逆转录聚合酶链反应 (qRT-PCR) 筛选 NoV GII。对于 qRT-PCR 呈阳性的样本，进行常规RT-PCR以扩增NoV GII基因的ORF1-ORF2连接。生成的序列通过 RIVM 在线基因分型工具进行分型，然后使用 MEGA 6.0 对感兴趣的菌株进行系统发育分析。结果共采集腹泻门诊患者粪便样本7883份，其中成人6474份，儿童1409份。13.66%（1077例）在qRT-PCR中筛查出NoV GII阳性，其中71.96%（775例）测序成功。前三个基因型是 GII.Pe/GII.4 (37%)、GII.P17/GII.17 (26%) 和 GII.P16/GII.2 (17%)。而 GII.Pe/GII.4 检出率在 3 年内显着下降（从 48.4% 降至 20.9%）；GII.P16/GII.2于2016年10月首次出现，2017年快速上升至27.0%，2018年回落至23.4%。同时，2018年在成年人群中检测到的GII.P12/GII.3和GII.P7/GII.6重组基因型均显着增加。系统发育分析显示，这两种重组基因型均存在多个基因簇。结论 与 2016 年或 2017 年观察到的 GII.4 和非 GII.4 NoV 的交替循环不同，2018 年 NoV GII 的基因型谱以多种重组基因型的共存为特征。最近报告较少的重组基因型（如 GII.P12/GII.3 和 GII.P7/GII.6）在成年人群中的检出率有所提高，因此需要继续密切监测 NoV GII 基因型，以防潜在的局部暴发。系统发育分析揭示了这两种重组基因型中存在多个基因簇。结论 与 2016 年或 2017 年观察到的 GII.4 和非 GII.4 NoV 的交替循环不同，2018 年 NoV GII 的基因型谱以多种重组基因型的共存为特征。最近报告较少的重组基因型（如 GII.P12/GII.3 和 GII.P7/GII.6）在成年人群中的检出率有所提高，因此需要继续密切监测 NoV GII 基因型，以防潜在的局部暴发。系统发育分析揭示了这两种重组基因型中存在多个基因簇。结论 与 2016 年或 2017 年观察到的 GII.4 和非 GII.4 NoV 的交替循环不同，2018 年 NoV GII 的基因型谱以多种重组基因型的共存为特征。最近报告较少的重组基因型（如 GII.P12/GII.3 和 GII.P7/GII.6）在成年人群中的检出率有所提高，因此需要继续密切监测 NoV GII 基因型，以防潜在的局部暴发。