Abstract:At the end of December 2019,an outbreak of pneumonia caused by SARS-CoV-2 occurred in Wuhan,Hubei Province.So far,the epidemic caused by the virus is still circulating globally,infecting more than 180 million people in total.With the continuous spread of SARS-CoV-2 among populations,its genome has continued to mutate,from the first discovery of D614G mutation of the S protein in SARS-CoV-2 to Alpha,Beta,Gamma,Delta listed as concerns by the World Health Organization and some other variants of interest.The continuous emergence of new variants has aroused widespread public concern.Therefore,this article will briefly summarize the genome structure and function of SARS-CoV-2,some of the characteristics of the main international variants,the protection results of SARS-CoV-2 vaccines against the variants, and the vaccine strategies to deal with SARS-CoV-2 mutations.
蒋潘虹, 阮嘉雯, 俞慕华, 卢次勇. 新型冠状病毒(SARS-CoV-2)变异的研究进展[J]. 中国人兽共患病学报, 2022, 38(2): 157-164.
JIANG Pan-hong, RUAN Jia-wen, YU Mu-hua, LU Ci-yong. Research progress on the mutation of SARS-CoV-2. Chinese Journal of Zoonoses, 2022, 38(2): 157-164.
[1] 周烨真,张世豪,陈嘉仪,等.新型冠状病毒SARS-CoV-2的变异和进化分析[J].南方医科大学学报,2020,40(2):152-158. [2] World Health Organization.Naming the coronavirus disease (COVID-19) andthe virus that causes it[EB/OL].(2021-04-12)[2021-06-22].https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it [3] Korber B,Fischer WM,Gnanakaran S,et al.Tracking changes in SARS-CoV-2 spike:evidence that D614G increases infectivity of the COVID-19 virus[J].Cell,2020,182(4):812-827e19.DOI:101016/j.cell.2020.06.043 [4] World Health Organization. SARS-Cov-2 Variants[EB/OL].(2021-04-12)[2021-06-22].https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/zh/# [5] World Health Organization.Weekly epidemiological update on COVID-19-25 February2021[EB/OL].(2021-09-9)[2021-09-9].https://www.who.int/publications/m/item/covid-19-weekly-epidemiological-update [6] World Health Organization.Weekly epidemiological update on COVID-19-29 June 2021[EB/OL].(2021-06-29)[2021-06-30].https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19-29-june-2021 [7] 冯晔囡,陈志肖,梦遥,等.新型冠状病毒变异株VOC 202012/01的全球早期传播与刺突蛋白进化特征分析[J].病毒学报,2021,37(2):267-273. [8] Verma BK,Verma M, Verma VK,et al.Global lockdown: An effective safeguard in responding to the threat of COVID-19[J].J Eval Clin Pract,2020,26:1592-1598.DOI:10.1111/jep.13483 [9] Alfano V,Ercolano S.The efficacy of lockdown against COVID-19:a cross-country panel analysis[J].Appl Health Econ Health Policy,2020,18(4):509-517.DOI:10.1007/s40258-020-00596-3 [10] 刘彬,秦照玲,戚中田.新型冠状病毒基因组结构与蛋白功能[J].微生物与感染,2020,15(1):52-57. [11] 李悦,林昶东.新型冠状病毒(SARS-CoV-2)概述[J].生命的化学,2021,41(3):413-419. [12] Li F.Structure,function,and evolution of coronavirus spike proteins[J].Annu Rev Virol,2016,3(1):237-261.DOI:10.1146/annurev-virology-110615-042301 [13] Letko M,Marzi A,Munster V.Functional assessment ofcell entry and receptor usage for SARS-CoV-2 and otherlineage B betacoronaviruses[J].Nat Microbiol,2020,5(4):562-569.DOI: 10.1038/s41564-020-0688-y [14] Volz E,Hill V,McCrone JT,et al.Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity[J].Cell,2021,184(1):64-75.DOI:10.1016/j.cell.2020.11.020 [15] Zhang L,Jackson CB,Mou H,et al.SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity[J].Nat Commun.,2020,11(1):6013.DOI:10.1038/s41467-020-19808-4 [16] Hou YJ,Chiba S,Halfmann P,et al.SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo[J].Science,2020,370(6523):1464-1468.DOI:10.1126/science.abe8499 [17] Zhou B,Thao TTN,Hoffmann D,et al.SARS-CoV-2 spike D614G change enhances replication and transmission[J].Nature,2021,592(7852):122-127.DOI:10.1038/s41586-021-03361-1 [18] Ahmadpour D,Ahmadpoor P,Rostaing L.Impact of circulating SARS-CoV-2 mutant G614 on the COVID-19 pandemic[J].Iran J Kidney Dis,2020,14(5):331-334. [19] Mueller NF,Wagner C,Frazar CD,et al.Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State[J].Sci Transl Med,2021,13(595):eabf0202.DOI:10.1126/scitranslmed.abf0202 [20] Lorenzo-Redondo R,Nam HH,Roberts SC,et al.A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways[J].EBio Medicine,2020,62:103112.DOI:10.1016/j.ebiom.2020.103112 [21] Weissman D,Alameh MG,de Silva T,et al.D614G spike mutation increases SARS CoV-2 susceptibility to neutralization[J].Cell Host Microbe,2021,29(1):23-31.DOI:10.1016/j.chom.2020.11.012 [22] Klumpp-Thomas C,Kalish H,Hicks J,et al.Effect of D614G spike variant on immunoglobulin G,M,or a spike seroassay performance[J].J Infect Dis,2021,223(5):802-804.DOI:10.1093/infdis/jiaa743 [23] Gomez CE,Perdiguero B,Esteban M.Emerging SARS-CoV-2 variants and impact in global vaccination programs against SARS-CoV-2/COVID-19[J].Vaccines,2021,9(3):243.DOI:10.3390/vaccines9030243 [24] Davies NG,Abbott S,Barnard RC,et al.Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England[J].Science,2021,372(6538):eabg3055.DOI:10.1126/science.abg3055 [25] Kidd M,Richter A,Best A,et al.S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR[J].J Infect Dis,2021,223(10):1666-1670.DOI: 10.1093/infdis/jiab082 [26] Arif TB.The 501.V2 and B.1.1.7 variants of coronavirus disease2019 (COVID-19):a new time-bomb in the making[J].Infect Control Hosp Epidemiol,2021 Jan 11:1-2.DOI:10.1017/ice.2020.1434 [27] Davies NG,Jarvis CI,CMMID COVID-19 Working Group,et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7[J].Nature,2021,593(7858):270-274.DOI: 10.1038/s41586-021-03426-1 [28] Nuñez IA,Lien CZ,Selvaraj P,et al.SARS-CoV-2 B.1.1.7 infection of syrian hamster does not cause more severe disease,and naturally acquired immunity confers protection[J].mSphere,2021,6(3):e0050721.DOI:10.1128/mSphere.00507-21 [29] Wang P,Nair MS,Liu L,et al.Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7[J].Nature,2021,593(7857):130-135.DOI:10.1038/s41586-021-03398-2 [30] Supasa P,Zhou D,Dejnirattisai W,et al.Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera[J].Cell,2021,184(8):2201-2211.DOI:10.1016/j.cell.2021.02.033 [31] Tegally H,Wilkinson E,Giovanetti M,et al.Detection of a SARS-CoV-2 variant of concern in South Africa[J]. Nature,2021,592(7854):438-443.DOI:10.1038/s41586-021-03402-9 [32] Li Q,Nie J,Wu J,et al.SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape[J].Cell,2021,184(9):2362-2371.DOI:10.1016/j.cell.2021.02.042 [33] Kuzmina A,Khalaila Y,Voloshin O,et al.SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera[J].Cell Host Microbe,2021,29(4):522-528.DOI:10.1016/j.chom.2021.03.008 [34] Cele S,Gazy I,Jackson L,et al.Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma[J].Nature,2021,593(7857):142-146.DOI:10.1038/s41586-021-03471-w [35] Madhi SA,Baillie V,Cutland CL,et al.Efficacy of the ChAdOx1 nCoV-19 COVID-19 vaccine against the B.1.351 variant[J].N Engl J Med,2021,384(20):1885-1898.DOI:10.1056/NEJMoa2102214 [36] Edara VV,Norwood C,Floyd K,et al.Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant[J].Cell Host Microbe,2021,29(4):516-521.DOI:10.1016/j.chom.2021.03.009 [37] Faria NR,Mellan TA,Whittaker C,et al.Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus,Brazil[J].Science,2021,372(6544):815-821.DOI:10.1126/science.abh2644 [38] Coutinho RM,Marquitti FMD,Ferreira LS,et al.Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant[J].medRxiv,[2021-03-03].DOI: 10.1101/2021.03.03.21252706 [39] Wang P,Casner RG,Nair MS,et al.Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization[J].Cell Host Microbe,2021,29(5):747-751.DOI: 10.1016/j.chom.2021.04.007 [40] Dejnirattisai W,Zhou D,Supasa P,et al.Antibody evasion by the P.1 strain of SARS-CoV-2[J].Cell,2021,184(11):2939-2954.DOI:10.1016/j.cell.2021.03.055 [41] Hoffmann M,Arora P,Gross R,et al.SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies[J].Cell,2021,184(9):2384-2393.DOI:10.1016/j.cell.2021.03.036 [42] Arora P,Kempf A,Nehlmeier I,et al.Increased lung cell entry of B.1.617.2 and evasion of antibodies induced by infection and BNT162b2 vaccination[J/OL].bioRxiv,[2021-06-22].https://doi.org/10.1101/2021.06.23.449568 [43] World Health Organization.Weekly epidemiological update on COVID-19-11 May 2021[EB/OL].(2021-04-12)[2021-06-22].https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19-11-may-2021 [44] Ito K,Piantham C,Nishiura H.Predicted domination of variant Delta of SARS-CoV-2 before Tokyo Olympic games,Japan[J/OL].Med Rxiv,[2021-06-22].https://www.medrxiv.org/content/10.1101/2021.06.12.21258835v2.article-info [45] Chaudhari AM,Kumar D,Joshi M,et al.E156G and Arg158, Phe-157/del mutation in NTD of spike protein in B.1.617.2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape[J/OL].bioRxiv,[2021-06-22].https://doi.org/10.1101/2021.06.07.447321 [46] Planas D,Veyer D,Baidaliuk A,et al.Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals[J/OL].bioRxiv,[2021-06-22].https://doi.org/10.1101/2021.05.26.445838 [47] Yadav PD,Sapkal GN,Ella R,et al.Neutralization against B.1.351 and B.1.617.2 with sera of COVID-19 recovered cases and vaccinees of BBV152[J/OL].bioRxiv,[2021-06-22].https://doi.org/10.1101/2021.06.05.447177 [48] Deng X,Garcia-Knight MA,Khalid MM,et al.Transmission,infectivity,and neutralization of a spike L452R SARS-CoV-2 variant[J].Cell,2021,184(13):3426-3437.DOI: 10.1016/j.cell.2021.04.025 [49] McCallum M,Bassi J,De Marco A,et al.SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern[J].Science,2021,373(6555):648-654.DOI:10.1126/science.abi7994 [50] Zhou H,Dcosta BM,Samanovic MI,et al.B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies[J].mBio,2021,12(4):e0138621.DOI:10.1128/mBio.01386-21 [51] Annavajhala MK,Mohri H,Zucker JE,et al.A novel SARS-CoV-2 variant of concern,B.1.526,identified in New York[J/OL].medRxiv,[2021-02-25].DOI:10.1101/2021.02.23.21252259 [52] Zhou H,Dcosta BM,Samanovic MI,et al.B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies[J/OL].bioRxiv, [2021-03-24].DOI:10.1101/2021.03.24.436620 [53] Fillatre P, Dufour M-J,Behillil S,et al.A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples,with high lethality[ J/OL].medRxiv, [2021-05-10].DOI:https://doi.org/10.1101/2021.05.05.21256690 [54] World Health Organization.Weekly epidemiological update on COVID-19-27 July 2021[EB/OL].(2021-07-30)[2021-08-1].https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19-27-july-2021 [55] Bian L,Gao F,Zhang J,et al.Effects of SARS-CoV-2 variants on vaccine efficacy and response strategies[J].Expert Rev Vaccines,2021,20(4):365-373.DOI:10.1080/14760584.2021.1903879 [56] Lopez Bernal J,Andrews N,Gower C,et al.Effectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) variant[J/OL].N Engl J Med,[2021-08-1].https://pubmed.ncbi.nlm.nih.gov/34289274/ [57] Chemaitelly H,Yassine HM,Benslimane FM,et al.mRNA-1273 COVID-19 vaccine effectiveness against the B.1.1.7 and B.1.351 variants and severe COVID-19 disease in Qatar[J/OL].Nat Med,[2021-08-1].https://pubmed.ncbi.nlm.nih.gov/34244681/Abu-Raddad [58] Abu-Raddad LJ,Chemaitelly H,Butt AA,et al.Effectiveness of the BNT162b2 Covid-19 vaccine against the B.1.1.7 and B.1.351 variants[J].N Engl J Med, 2021,385(2):187-189.DOI:10.1056/NEJMc2104974 [59] Hitchings MD,Ranzani OT,Torres MSS,et al.Effectiveness of CoronaVac in the setting of high SARS-CoV-2 P.1 variant transmission in Brazil:a test-negative case-control study[J/OL]. medRxiv,[2021-08-011].https://doi.org/10.1101/2021.04.07.21255081 [60] 孟子延,马丹婧,高雪,等.mRNA疫苗及其作用机制的研究进展[J].中国生物制品学杂志,2021,34(6):740-744. [61] Rojas-Pérez-Ezquerra P,Crespo Quirós J,Tornero Molina P,et al.Safety of new mRNA vaccines against COVID-19 in severely allergic patients[J].J Investig Allergol Clin Immunol,2021,31(2):180-181.DOI:10.18176/jiaci.0683 [62] Lazarevic I,Pravica V,Miljanovic D,et al.Immune evasion of SARS-CoV-2 emerging variants: what have we learnt so far[J].Viruses,2021,13(7):1192.DOI:10.3390/v13071192 [63] Maeda DLNF,Tian D,Yu H,et al.Killed whole-genome reduced-bacteria surface-expressed coronavirus fusion peptide vaccines protect against disease in a porcine model[J].Proc Natl Acad Sci U S A, 2021,118(18):e2025622118.DOI: 10.1073/pnas.2025622118 [64] Plante JA,Mitchell BM,Plante KS,et al.The variant gambit:COVID-19's next move[J].Cell Host Microbe,2021,29(4):508-515.DOI:10.1016/j.chom.2021.02.020 [65] 史庆丰,高晓东,胡必杰.Delta新冠病毒变异株的特性及流行现状与防控研究进展[J].中华医院感染学杂志,2021,31:1-5. [66] Eyal Leshem,Benjamin Alan Lopman.Population immunity and vaccine protection against infection[J].The Lancet,2021,397(10286):1685-1687.DOI:10.1016/S0140-6736(21)00870-9