孙初阳;遇晓杰;蔡英桂;李丹丹;黄涵;曾祥洁;王如敏;陈海云;曾云婷;潘正帆;邝仕壮;甘晓婷;张亚淋;吴庆梓;陈言;

• 1:海南省疾病预防控制中心

摘要(Abstract)：

本文对2021年海南省2例感染引起本土轻型新冠肺炎病例的新冠病毒进行全基因组测定和序列分析，研究该病毒的分子特征和分子进化规律。通过荧光定量RT-PCR法检测ORF1ab和N靶基因，应用Illumina公司的MiSeq深度测序平台进行全基因组序列测定，使用MEGA 10.1.8和DNASTAR 7.0.1生物信息学软件进行多序列比对和分析，并采用邻位归并法（Neighbour-joining）绘制系统进化树。2例新冠病毒（HN0801和HN0802）均属于德尔塔变异株，与武汉参考序列（NC＿045512）基因序列相似性分别为99.7%和99.8%，系统进化树显示它们位于同一进化分支（B.1.617.2）的不同簇上，共有45个核苷酸突变位点，引起38个氨基酸位点改变，其中34个错义突变、6个同义突变、4个氨基酸位点缺失；刺突（S）糖蛋白发现B.1.617.2谱系共同突变特征L452R、T478K，以及T19R、G142D、D614G、P681R、D950N、R158G关键变异位点。HN0801同2021年7月江苏省南京市代表株基因序列100%相似，而HN0802与南京市疫情代表株基因组相似性较低。结合流行病学调查和基因组序列分析，这2例新冠病毒均属于新冠病毒德尔塔变异株，2例确诊病例之间没有明确的流行病学关联，为两条不同的传播链引起的相互独立的散发病例。本研究为海南省新冠病毒变异株的监测和新冠疫情防控提供了基础数据。

关键词(KeyWords)： 新型冠状病毒;德尔塔;全基因组;变异株

Abstract:

Keywords:

基金项目(Foundation):

作者(Authors): 孙初阳;遇晓杰;蔡英桂;李丹丹;黄涵;曾祥洁;王如敏;陈海云;曾云婷;潘正帆;邝仕壮;甘晓婷;张亚淋;吴庆梓;陈言;

DOI: 10.13242/j.cnki.bingduxuebao.004183

参考文献(References)：

• [1]Guruprasad L. Human SARS CoV-2 spike protein mutations[J/OL]. Proteins,2021,89(5):569-576.DOI:10.1002/prot.26042.
• [2]Xuemei He,Weiqi Hong,Xianyu Pan,Guangwen Lu,Xiawei Wei. SARS-CoV-2 Omicron variant:Characteristics and prevention[J/OL]. MedComm(2020), 2021, 2(4):838-845. DOI:10.1002/mco2.110.
• [3]Wu F,Zhao S,Yu B,Chen YM,Wang W,Song ZG,Hu Y,Tao ZW,Tian JH,Pei YY,Yuan ML,Zhang YL,Dai FH,Liu Y,Wang QM,Zheng JJ,Xu L,Holmes EC. A new coronavirus associated with human respiratory disease in China[J/OL]. Nature,2020,579(7798):265-269. DOI:10.1038/s41586-020-2008-3
• [4]Arya R,Kumari S,Pandey B,Mistry H,Bihani S C,Das A,Prashar V,Gupta G D,Panicker L,Kumar M.Structural insights into SARS-CoV-2 proteins[J/OL].J Mol Biol,2021,433(2):166725. DOI:10.1016/j.jmb.2020.11.024.
• [5]Campbell F,Archer B,Laurenson-Schafer H,Jinnai Y,Konings F,Batra N,Pavlin B,Vandemaele K,Kerkhove M, Jombart T, Mrogan O, Warous O.Increased transmissibility and global spread of SARSCoV-2 variants of concern as at June 2021[J/OL]. Euro Surveill,2021,26(24):2100509. DOI:10.2807/1560-7917.ES.2021.26.24.2100509.
• [6]Wall E C,Wu M,Harvey R,Kelly G,Warchal S,Sawyer C,Daniels R,Hobson P,Hatipoglu E,Ngai Y,Hussain S,Nicod J,Goldstone R,Ambrose K,Hindmarsh S,Beale R,Riddell A,Gamblin S,Howell M,Kassiotis G,Libri V,Williams B,Swanton C,Gandhi S, Bauer D. Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination[J/OL]. Lancet,2021,397(10292):2331-2333. DOI:10.1016/S0140-6736(21)01290-3.
• [7]Yurkovetskiy L,Wang X,Pascal K E,Tomkins-Tinch C,Nyalile T P,Wang Y T,Baum A,Diehl W E,Dauphin A, Carbone C, Veinotte K, Egri S B,Schaffner S F,Lemieux J E,Munro J B,Rafique A,Barve A,Sabeti P C,Kyratsous C A,Dudkina N V,Shen K,Luban J. Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant[J/OL].Cell,2020,183(3):739-751. e8. DOI:10.1016/j.cell.2020.09.032.
• [8]Xia S,Liu M Q,Wang C,Xu W,Lan Q S,Feng S L,Qi F F,Bao L L,Du L Y,Liu S W,Qin C,Sun F,Shi Z L,Zhu Y,Jiang S B,Lu L. Inhibition of SARSCoV-2(previously 2019-nCoV)infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion[J/OL]. Cell Res,2020,30(4):343-355. DOI:10.1038/s41422-020-0305-x.
• [9]郑宝路，高鑫，庄志超，苏承，邹明，于爱萍，谭昭麟，李晓燕．天津滨海新区本土疫情新型冠状病毒全基因组测序和溯源分析[J/OL]．中华微生物学和免疫学杂志，2021,41(8):581-587. DOI:10.3760/cma. J.cn112309-20210519-00165.
• [10]Davis C,Logan N,Tyson G,Orton R,Harvey W T,Perkins J S,Mollett G,Blacow R M,Peacock T P,Barclay W S,Cherepanov P,Palmarini M,Murcia P R,Patel A H,Robertson D L,Haughney J,Thomson E C,Willett B J. Reduced neutralization of the Delta(B.1.617.2)SARS-CoV-2 variant of concern following Vaccination[J/OL]. PLoS Pathog, 2021, 17(12):e1010022. DOI:10.1371/journal.ppat.1010022.
• [11]Lazarevic I, Pravica V, Miljanovic D, Cupic M.Immune evasion of SARS-CoV-2 emerging variants:what have we learnt so far?[J/OL]. Viruses,2021,13(7):1192. DOI:10.3390/v13071192.
• [12]Mohammadi M, Shayestehpour M, Mirzaei H. The impact of spike mutated variants of SARS-CoV-2[Alpha,Beta,Gamma,Delta,and Lambda]on the efficacy of subunit recombinant vaccines[J/OL]. Braz J Infect Dis,2021,25(4):101606. DOI:10.1016/j.bjid.2021.101606.
• [13]Andersen K G,Rambaut A,Lipkin W I,Holmes E C,Garry R F. The proximal origin of SARS-CoV-2[J/OL]. Nat Med,2020,17:1-3. DOI:10.1038/s41591-020-0820-9.
• [14]Walls A C, Park Y-J, Tortorici M A, Wall A,McGuire A T, Veesler D. Structur, function, and antigenicity of the SARS-CoV-2 spike glycoprotein[J/OL]. Cell,2020,181(2):281-92.e6. DOI:10.1016/j.cell.2020.02.058.
• [15]Tai W,He L,Zhang X J,Pu J,Voronin D,Jiang S B,Zhou Y S,Du L Y. Characterization of the receptorbinding domain(RBD)of 2019 novel coronavirus:implication for development of RBD protein as a viral attachment inhibitor and vaccine[J/OL]. Cell Mol Immunol,2020,17(6):613-620. DOI:10.1038/s41423-020-0400-4.
• [16]Tchesnokova V,Kulakesara H,Larson L,Bowers V,Rechkina E,Kisiela D,Sledneva Y,Choudhury D,Maslova I,Deng K,Kutumbaka K,Geng H,Fowler C,Greene D,Ralston J,Samadpour M,Sokurenko E.Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-CoV-2 variants[J/OL]. J Clin Microbiol,2021,59(11):e00921-21. DOI:10.1128/JCM.00921-21.
• [17]Cherian S,Potdar V,Jadhav S,Yadav P,Gupta N,Das M,Rakshit P,Singh S,Abraham P,Panda S,Team N. SARS-CoV-2 Spike mutations,L452R,T478K, E484and PQ681R in the second wave of COVID-19 in Maharashtra, India[J/OL].Microorganisms,2021,9(7):1542. DOI:10.3390/microorganisms9071542.
• [18]Greaney A J, Starr T N, Gilchuk P, Zost S J,Binshtein E,Loes A N,Hilton S K,Huddleston J,Eguia R,Crawford K H D,Dingens A S,Nargi R S,Sutton R E,Suryadevara N,Rothlauf P W,Liu Z M,Whelan A P J,Carnahan R H,Crowe Jr E C,Bloom J D.Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition[J/OL]. Cell Host Microbe,2021,29(1):44-57.e9. DOI:10.1016/j.chom.2020.11.007.
• [19]L Kirola. Genetic emergence of B.1.617.2 in COVID_19[J/OL]. New Microbe and New Infect, 2021, 43:100929. DOI:10.1016/j.nmni.2021.100929.
• [20]Korber B,Fischer W M,Gnanakaran S,Yoon H,Theiler J,Abfalterer W,Hengartner N,Giorgi E E,Bhattacharya T,Foler B,Hastie K M,Parker M D,Partridge D G,Evans C M,Freeman T M,de Silva T I. Tracking changes in SARS-CoV-2 Spike:Evidence that D614G increases infectivity of the COVID-19 virus[J/OL]. Cell,2020,182(4):812-827. e19. DOI:10.1016/j.cell.2020.06.043.
• [21]Torjesen I. COVID-19:Delta variant is now UK's most dominant strain and spreading through schools[J/OL]. BMJ,2021,n1445. DOI:10.1136/bmj.n1445.
• [22]Kunal S,Aditi,Gupta K,Ish P. COVID-19 variants in India:potential role in second wave and impact on vaccination[J/OL]. Heart Lung,2021,50(6):784-787. DOI:10.1016/j.hrtlng.2021.05.008.
• [23]Fontanet A,Autran B,Lina B,Kieny M P,Abdool Karim S S,Sridhar D. SARS-CoV-2 variants and ending the COVID-19 pandemic[J/OL]. Lancet,2021,397(10278):952-954. DOI:10.1016/S0140-6736(21)00370-6.