G Ⅱ.17[P17]型诺如病毒基因系统发育聚类特征分析
Phylogenetic clustering characteristics of different genes of norovirus G Ⅱ.17[P17]
李楚楚 1艾静 1秦圆方 1朱立国 1胡建利 1鲍倡俊 1付建光1
作者信息
- 1. 江苏省疾病预防控制中心卫健委肠道病原微生物重点实验室,南京 210009
- 折叠
摘要
目的 了解GⅡ.17[P17]型诺如病毒不同基因的发育聚类特征,为GⅡ.17[P17]序列的准确聚类提供依据.方法 收集2023年3月至5月聚集性疫情中的GⅡ.17[P17]阳性标本,二代测序获得全基因组序列,与GenBank下载的参考株序列共同构建进化树,分别对各基因(Nterm、NTP、P22、VPg、Pro、RdRp、VP1和VP2)序列进行系统发育聚类分析及熵值分析.结果16个G Ⅱ.17[P17]阳性标本中共14个获得了全基因组序列,测序深度及覆盖度均较高.首先构建RdRp及VP1基因的系统发育进化树,发育聚类均为6个簇(Cluster Ⅰ～Ⅵ),其中ClusterⅠ～Ⅳ聚类相同,Cluster V～Ⅵ聚类有少量差异.2023年的标本株序列位于Cluster V.以RdRp聚类为基准,对病毒的8个基因片段进行聚类分析,发现NTP、RdRp和VP1基因聚类效果较好,6个簇均未形成新的分支.此外,这三个基因的熵值位点构成比也处于较低水平.结论 诺如病毒GⅡ.17[P17]型别不同基因的系统发育聚类有一定差异,其中NTP、RdRp和VP1基因聚类效果较好.
Abstract
Objective To understand the evolutional clustering characteristics of different genes of GⅡ.17[P 17]norovirus,so as to provide a basis for accurate clustering of GⅡ.17[P 17]sequences.Methods The GⅡ.17[P17]positive specimens in the outbreaks from March to May,2023 were collected.The whole genome sequences were obtained by second-generation sequencing.The phylogenetic tree was constructed with the reference sequences from GenBank.Phylogenetic clustering analysis and entropy value analysis were performed on each gene(Nterm,NTP,P22,VPg,Pro,RdRp,VP1 and VP2)sequence respectively.Results Whole genome sequences were obtained from 14 of the 16 GⅡ.17[P17]positive specimens,with high sequencing depth and coverage.Phylogenetic trees of RdRp and VP1 genes were firstly constructed,and both had 6 phylogenetic clusters(Cluster Ⅰ-Ⅵ).The Cluster Ⅰ-Ⅳ were the same while few differences existed in Cluster Ⅴ-Ⅳ.The sequence of strains obtained from samples of 2023 was in Cluster V.Taking the RdRp clustering as a benchmark,clustering analysis for the 8 gene fragments of the virus were performed,and revealed that NTP,RdRp and VP1 genes had better clustering results,and none of the six clusters formed new branches.In addition,the entropic site composition ratio of these three genes was also at a low level.Conclusions The phylogenetic clustering of different genes of norovirus type GⅡ.17[P17]had some differences,and NTP,RdRp and VP1 genes clustered better.
关键词
诺如病毒/基因/系统发育/聚类Key words
Norovirus/Gene/Phylogeny/Clustering引用本文复制引用
出版年
2024
NETL
NSTL
万方数据