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赵云, 纪峰, 林小娟, 刘尧, 徐爱强, 陶泽新, 温红玲. 基于下一代测序的污水中人星状病毒分子流行病学研究[J]. 中国公共卫生, 2023, 39(11): 1475-1479. DOI: 10.11847/zgggws1139435
引用本文: 赵云, 纪峰, 林小娟, 刘尧, 徐爱强, 陶泽新, 温红玲. 基于下一代测序的污水中人星状病毒分子流行病学研究[J]. 中国公共卫生, 2023, 39(11): 1475-1479. DOI: 10.11847/zgggws1139435
ZHAO Yun, JI Feng, LIN Xiaojuan, LIU Yao, XU Aiqiang, TAO Zexin, WEN Hongling. Diversity of human astroviruses in untreated domestic sewage: a next generation sequencing analysis in Jining city, Shandong province[J]. Chinese Journal of Public Health, 2023, 39(11): 1475-1479. DOI: 10.11847/zgggws1139435
Citation: ZHAO Yun, JI Feng, LIN Xiaojuan, LIU Yao, XU Aiqiang, TAO Zexin, WEN Hongling. Diversity of human astroviruses in untreated domestic sewage: a next generation sequencing analysis in Jining city, Shandong province[J]. Chinese Journal of Public Health, 2023, 39(11): 1475-1479. DOI: 10.11847/zgggws1139435

基于下一代测序的污水中人星状病毒分子流行病学研究

Diversity of human astroviruses in untreated domestic sewage: a next generation sequencing analysis in Jining city, Shandong province

  • 摘要:
      目的  了解生活污水中人星状病毒(HAstV)的型别分布及遗传多样性。
      方法  2018年1月 — 2019年6月在山东省济宁市按季度采集6份生活污水样本,通过阴离子膜吸附洗脱法进行浓缩后,提取核酸,进行ORF2完整编码区的RT-PCR扩增及扩增产物下一代测序,对产生的干净数据使用CLC Genomics Workbench 12.0 软件de novo 组装后,进行基因定型、同源性比较和系统发生学分析。
      结果   检测地区生活污水中HAstV的检出率为100%,共获得HAstV序列43条,分属9种基因型,分别为HAstV-1、HAstV-2、HAstV-3、HAstV-4、HAstV-5等经典型和MLB1、VA1、VA2、VA3等新型HAstV,其中HAstV-5(47.53%)占比最高;基于ORF2完整编码区的系统发生学显示山东株与国内外其他参考株在一些分支上聚集在一起,表明不同型别在世界不同地区的传播。
      结论   本研究证实了基于NGS的环境监测有助于提高对HAstV遗传多样性的认识。

     

    Abstract:
      Objective  To investigate the prevalence and genetic diversity of human astrovirus (HAstV) strains in untreated domestic sewage.
      Methods  We collected six domestic sewage samples (one liter for each) at an inlet of an urban sewage treatment plant quarterly from January 2018 to June 2019 in Jining city, Shandong province. After concentrated via anion membrane adsorption elution method, the viral nucleic acid in the samples was extracted with MagMAX Pathogen RNA/DNA Kit and complete open reading frame 2 (ORF2) region of HAstV was amplified using real-time reverse transcription PCR (RT-PCR). Then the amplicons were subjected to next generation sequencing (NGS). Clean data of NGS were assembled de novo to form contigs using CLC Genomics Workbench 12.0 (QIAGEN, USA) with default parameters for homology and phylogenetic analysis.
      Results  All the six sewage samples were positive for HAstV. Totally 43 ORF2 sequences of HAstV were obtained and classified into 9 genotypes including classic HAstV-1 to HAstV-5 and novel MLB1 and VA1-3. HAstV-5 was the most common genotype (47.53%). Phylogenetic analysis revealed that local and foreign sequences clustered together in some branches, indicating the transmission of various genotypes of HAstV among different regions in the world.
      Conclusion  The analysis results demonstrates that NGS-based environmental surveillance could greatly improve the understanding on HAstV genetic diversity.

     

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