新冠Omicron变异株全基因组测序及ORF7a蛋白的生物信息学分析  

Whole genome sequencing and bioinformatic analysis of ORF7a protein in a strain of SARS-CoV-2 omicron variant

作　　者：李静虹 石强 朱晓莉 孙瑞贞 穆晋平 刘玲[2] Li Jinghong;Shi Qiang;Zhu Xiaoli;Sun Ruizhen;Mu Jinping;Liu Ling(Department of Laboratory,Jinzhong Center for Disease Control and Prevention,Jinzhong 030600,China;Shanxi Key Laboratory of Prevention,Control and Diagnosis of Major Infectious Diseases,Center for Disease Control and Prevention,Taiyuan 030000,China)

机构地区：[1]晋中市疾病预防控制中心疾病检验科,030600 [2]山西省疾病预防控制中心重大传染性疾病防控与诊治山西省重点实验室,太原030000

出　　处：《国际病毒学杂志》2024年第5期364-370,共7页International Journal of Virology

基　　金：“十三五”国家科技重大专项(2018ZX10201002);山西省卫生厅科技攻关项目(20211127)。

摘　　要：目的 了解晋中市新型冠状病毒(SARS-CoV-2)全基因组特征及变异情况,分析ORF7a蛋白的结构与功能.方法 对晋中市2023年4月份流感样病例进行新冠核酸检测,将获得的6例新冠阳性标本进行全基因测序,并对其进行变异分析,另外应用生物信息在线软件,分析预测ORF7a蛋自序列冠状病毒属同源性、理化性质、磷酸化位点、信号肽、糖基化修饰、亚细胞定位、二级结构和三级结构等.结果 共获得6例新冠病毒的全基因组序列,拼接后有效全长在 29 628 bp~29 668 bp 之间,与 SARS-COV-2(NC_045512.2)序列相对比,均属于 Omicron 变异株BF.7.14进化分支.6个毒株存在79~85个核苷酸变异位点,59~63个氨基酸变异位点,且在ORF7a区突变情况一致:核苷酸位点均为C27532T突变,氨基酸位点均为H47Y突变;进化树分析表明,ORF7a蛋白与马蹄蝠肌腺病毒(WMT59664.1)的ORF7a蛋白同源性最高;用在线软件进行生物信息学分析表明,ORF7a为不稳定蛋白,由121个19种氨基酸组成,摩尔系数以Leu(15个,占 12.30%)、Phe(10 个,占 8.20%)和 Thr(10个,占 8.20%)较高,Met(1 个,占 0.82%)较低,而Trp含量为0,存在4个磷酸化位点,未发现潜在的糖基化修饰位点,含有一个信号肽区切割位点位于C15-E16之间,疏水性较强;其二级结构以α螺旋和无规则卷曲为主,属于跨膜蛋白,在细胞外(包括细胞壁)、质膜中、内质网和高尔基体中存在的可能性依次为34.8%、30.4%、21.7%和13.0%.结论 对晋中市Omicron变异株及其ORF7a蛋白进行系统性分析,以全面了解ORF7a生物信息学特征,为新冠疫苗及抗新冠药物研制提供依据.Objective To investigate the whole genome characteristics and variation of Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)in Jinzhong city,and analyze the structure and function of ORF7a protein.Methods The influenza-like cases on April,2023 in Jinzhong city were tested for the nucleic acids of SARS-CoV-2.The 6 positive specimens were used for whole genome sequencing and mutation analysis.In addition,online bioinformatic software was applied to analyze and predict the similarity between amino acid sequences of ORF7a protein and that of Coronaviruses as well as the physical and chemical properties,phosphorylation site,signal peptide,glycosylation modification,subcellular localization,secondary structure and tertiary structure of the protein.Results The whole genome sequences of 6 SARS-CoV-2 cases were obtained,and the effective total length was between 29628bp and 29668bp after assmebly.Compared with the sequence of SARS-COV-2(NC_045512.2),all of strains belonged to the BF.7.14 clade of omicron variant.The 6 strains had 79-85 nucleotide mutation sites and 59-63 amino acid mutation sites.The mutations were consistent in the ORF7a region,including the nucleotide site as C27532T mutation and the amino acid site as H47Y mutation.Phylogenetic tree analysis showed that ORF7a protein had the highest similarity to that of horseshoe bat muscle adenovirus(WMT59664.1).Bioinformatic analysis by online software showed that ORF7a was an unstable protein,constituted by 121 amino acids residues of 19 types of amino acids.The molar coefficients of ORF7A were higher with Leu(15,12.30%),Phe(10,8.20%)and Thr(10,8.20%),and lower with Met(1,0.82%).The Trp content was zero.There were 4 phosphorylation sites and no potential glycosylation modification site was found.The cutting site of a signal peptide region located between C15-E16,with strong hydrophobicity.The secondary structures were mainlyαhelix and random coil.The protein was a transmembrane protein and the probability of existence in the extracellular(including cell

关 键 词：新型冠状病毒 全基因测序 ORF7a蛋白 生物信息学 

分 类 号：R373[医药卫生—病原生物学]