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。
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 NGSbased environmental surveillance could greatly improve the understanding on HAstV genetic diversity.
作者
赵云
纪峰
林小娟
刘尧
徐爱强
陶泽新
温红玲
ZHAO Yun;JI Feng;LIN Xiaojuan;LIU Yao;XU Aiqiang;TAO Zexin;WEN Hongling(Department of Microbiological Laboratory Technology,School of Public Health,Shandong University,Ji′nan 250012,China;Shandong Center for Disease Control and Prevention,Ji′nan 250012,China)
出处
《中国公共卫生》
CAS
CSCD
北大核心
2023年第11期1475-1479,共5页
Chinese Journal of Public Health
基金
国家自然科学基金面上项目(81573209)
山东省自然科学基金面上项目(ZR2020MH337)
泰山学者青年专家计划项目(tsqn202103187)
关键词
人星状病毒
下一代测序
环境监测
human astrovirus
next generation sequencing
environmental surveillance
作者简介
第一作者:赵云(1994–),硕士,研究方向:人星状病毒环境污水监测;通信作者:陶泽新,E-mail:sdcdctzx@163.com;通信作者:温红玲,E-mail:whling@sdu.edu.cn
