2020年深圳地区4株冠状病毒HCoV-NL63基因组特征分析

Whole-genome sequence analysis of four human coronavirus NL63 strains regionally prevalent in Shenzhen,2020

目的了解2020年深圳市冠状病毒HCoV-NL63全基因组序列的遗传特征和变异。方法对HCoV-NL63核酸检测阳性的咽拭子标本进行全基因组测序、系统发生树重建和生物信息学分析。结果获得4株HCoV-NL63全基因组序列,均属于B基因型B2亚型,株间核苷酸(氨基酸)同源性为99.80%~99.98%(99.64%~99.93%),在进化树上处于同一分支,与广州2018年肺炎病人中获得的MK334046.1毒株距离最近。氨基酸变异分析表明结构蛋白中S、M蛋白变异性较大。与B基因型参考株对比发现,S蛋白中发现2处氨基酸位点变异:位于散发疫情毒株S1蛋白NTR区L196F和位于聚集性疫情毒株S2蛋白A946S。N-糖基化位点预测发现S蛋白N-糖基化位点有10个,M蛋白N-糖基化位点有2个。结论本研究中的4株冠状病毒源自广州毒株的可能性大,在一定程度上可为HCoV-NL63防控工作提供生物学溯源依据。

In this study,the genomic RNA of HCoV-NL63 from throat swab samples obtained from cases of respiratory tract infection was sequenced.The cases were collected from clustered or sporadic epidemics in the Nanshan district of Shenzhen City in 2020.Four whole genomes of HCoV-NL63 strains were obtained and analyzed with phylogenetic tree reconstruction and other bioinformatics analyses.The sequence similarity among the four strains was 99.80%~99.98%for nucleotides and 99.64%~99.93%for amino acids.The four strains of HCoV-NL63 belonged to the B genotype,B2 subgenotype,which were on the same branch of the phylogenetic tree and were genetically closest to MK334046.1.Analysis of the amino acid variation sites of the S protein indicated that L196 F was present in the strains obtained from sporadic epidemic cases,and A946 S was present in the strains acquired from clustered epidemic cases.The prediction of N-glycosylation sites indicated ten N-glycosylation sites in S protein and two N-glycosylation sites in M protein.Through whole genome sequencing and feature analysis,we determined that the HCoV-NL63 obtained in this study probably originated from the Guangzhou virus strain.Our current results provide some clues as to the basis for biological traceability,and might facilitate future epidemic prevention and control.