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2021Apr;592(7855):616-622。
doi:10.1038/s41586-021-03324-6。 Epub2021Feb10。

mRNA vaccine-elicited antibodies to SARS-COV-2and circulating variant

Zijun Wang # 1个单击功能区上Fabian Schmidt # 2单击功能区上Yiska Weisblum # 2单击功能区上Fruke Muecksch # 2单击功能区上Christopher O Barnes # 3单击功能区上Shlomo Finkin # 1个单击功能区上Dennis Schaefer-Babajew # 1个单击功能区上Melissa Cipolla # 1个单击功能区上Christian Gaebler # 1个单击功能区上Jenna A Lieberman # 4个单击功能区上Thiago Y Oliveira 1个单击功能区上Zhi Yang 3单击功能区上Morgan E Abernathy 3单击功能区上Kathryn E Huey-Tubman 3单击功能区上Arlene Hurley 5单击功能区上Martina Turroja 1个单击功能区上Kamille A West 6个单击功能区上Kristie Gordon 1个单击功能区上Katrina G Millard 1个单击功能区上Victor Ramos 1个单击功能区上Justin Da Silva 2单击功能区上Jianliang Xu 4个单击功能区上Robert A Colbert 7单击功能区上Roshni Patel 1个单击功能区上Juan Dizon 1个单击功能区上Cecille Unson-O'Brien 1个单击功能区上Irina Shimeliovich 1个单击功能区上Anna Gazumyan 1个单击功能区上Marina Caskey 1个单击功能区上Pamela J Bjorkman 8个单击功能区上拉斐尔Casellas 9 10单击功能区上Theodora Hatziioannou 11单击功能区上Paul D Bieniasz 12 13单击功能区上ichel C Nussenzweig 14 15
疲劳,疲劳

mRNA vaccine-elicited antibodies to SARS-COV-2and circulating variant

Zijun Wanget al。 自然,自然 2021Apr

Abstract

Here we report on the antibody and memory B cell responses of a cohort of 20 volunters who received the Moderna(mRNA-1273)or Pfizer-BioNTech(BNT162b2)vaccine against SARS-CoV-21-4.Eight weeks after the second injection of vaccine,volunters showed high levels of IgM and IgG anti-SARS-CoV-2spike protein(S)and receptor-binding-domain(RBD)binding titre。RBD-specific memory B cells of vaccinated volunters were equivalent to those of individuals who had recovered from natural infection5,6.However,activity against SARS-CoV-2variants that encode E484K-,N501Y-or K417N/E484K/N501-mutant S was reduced by asmall-but significant-margin.The monoclonal antibodies elicited by the vaccines potently neutralize SARS-CoV-2,and target a number of different RBD topiant in钢管接头5-8.However,neutralization by14 of the 17 most-potent monoclonal antibodies that we tested was reduced or abolished by the K417N,E484K or N501Y mutation.Notably,these mutations were selected when we cultured recombinant vesicular stomatitis virus expressing SARS-CoV-2S in the presence of the preselection of the monocies gether, these results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants,and that mRNA vaccines may need to be updated periodically to avoid a potential loss of clinical efficacy。

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组件:The Rockefeller University has filed a provisional patent application in connection with this work on which Z.W.and M.C.N.are inventors(USpatent63/199676)。

Figures

扩展数据Fig.1。
Extended Data Fig.1.Plasma antibodies against SARS-COV-2。
af,Results of ELISAS measuring plasma reactivity to S(a单击功能区上,c,e)and RBD protein(b、d、f)of20vaccinees(grey curves)and8controls(black curves)。a,Anti-S IgG。b,Anti-RBD IgG。c,Anti-S IgM。d,Anti-RBD IgM。e、e,Anti-S IgA。f,Anti-RBD IgA.Left,optical density at450nm(OD450nm)for the indicated reciprocal plasma dilutions。Right,normalized area under the curve(AUC)values for the 8controls and 20vaccinees。Horizontal bars indicate geometric mean.Statistical significance was determined using the two-tailed Mann–Whitney U-test.Average of two or more experiments。g-i,Correlations of plasma antibodies measurements。g,Normalized AUC for IgG anti-S(X axis)plotted against normalized AUC for IgG anti-RBD(Y axis)。h,Normalized AUC for IgM anti-S(X axis)plotted against normalized AUC for IgM anti-RBD(Y axis)。i,Normalized AUC for IgA anti-S(X axis)plotted against normalized AUC for IgA anti-RBD(Y axis)。Therand,andp气门,气门g-iwere determined with the two-tailed Spearman’s correlation test.Moderna vaccinees are in black and Pfizer-BioNTech in red。j-l,ELISAS measuring plasma reactivity to RBD in convalescent volunters 1.3 and 6.2 months after infection单击功能区上,and in 20vaccinees,who received the Moderna vaccine(black dots)and Pfizer-BioNTech vaccine(red dots)。j,Anti-RBD IgG。k,Anti-RBD IgM。l,Anti-RBD IgA.The normalized area under the curve(AUC)values are shown。Positive and negative controls were included for validation.Red horizontal bars and indicated values represent geometric mean.Statistical significance was determined using two-tailed Mann-Whitney U-test or Wilcoxon matched-pairs signed rank test。
扩展数据Fig.2:
Extended Data Fig.2:.Plasma neutralizing activity。
a,Anti-S IgM AUC(Y axis)plotted against NT50(X axis)r=0.12,p<0.62。b、,Anti-S IgA AUC(Y axis)plotted against NT50(X axis)r=0.79,p<0.0001。c,Anti-RBD IgM AUC(Yaxis)plotted against NT50(X axis)r=-0.079p=0.74。d,Anti-RBD IgA AUC(Yaxis)plotted against NT50(X axis)r=0.69p=0.0008。e、e,NT50(Yaxis)plotted against time between last dose and blood draw(X axis)r=-0.63p=0.0032。f,NT50(Yaxis)plotted against time between doses(X axis)r=0.03p=0.89。g,Anti-RBD IgG AUC(Y axis)plotted against time between last dose and blood draw(X axis)r=-0.57p=0.0084。h,Anti-S IgG AUC(Y axis)plotted against time between last dose and blood draw(X axis)r=-0.59p=0.0064。i,Age(Y axis)plotted against NT50(X axis)r=-0.06p=0.82。The r and p values were determined by two-tailed Spearman’s.Moderna vaccinees in black and Pfizer-BioNTech in red。j,NT50values for vaccinee plasma(n=15)neutralization of pseudotyped viruses with WT and the indicated RBD-mutant SARS-COV-2S proteins;p-values determined using one tailed t-test。
扩展数据Fig.3:
Extended Data Fig.3:.Flow cytometry。
a,Gating strategy used for cell sorting.Gating was on singlets that were CD20+and CD3-CD8-CD14-OVA-.Sorted cells were RBD-PE+and RBD-AF647+。b、,RBD-double positive memory B cells from apre-COVID-19 control(HD)and 15vaccinees,who received the Moderna vaccine are shown in black and Pfizer-BioNTech vaccine recipients are in red。c,the percentage of RBD-binding memory B cells in vaccinees(Y axis)plotted against time between first dose and blood draw(X axis)r=0.40p=0.087(left panel),and between last dose and blood draw(X axis)r=0.33p=0.17(right panel)。Moderna vaccinees in black and Pfizer-BioNTech in red.The r and p values for correlations were determined by two-tailed Spearman’s。d,Pie charts show the distribution of antibody sequences from 10 individuals inb。The number in the inner circle indicates the number of sequences analyzed.Pie slice size is proportional to the number of clonally related sequences.The black outline indicates the frequency of clonally expanded sequences.The r and p values for correlations incwere determined by the two-tailed Spearman correlation test。
扩展数据Fig.4:
Extended Data Fig.4:.Frequency distributions of human VL genes。
Graph shows relative abundance of human IGVK(left)and IgVL(right)genes of Sequence Read Archive accession SRP010970(orange),and vaccinees(blue)。Two-sided binomial tests with unequal variance were used to compare the frequency distributions.,significant differences are denoted with stars(*p<0.05,**p<0.01,***p<0.001,****=p<0.0001)。b。Sequences from14individuals(扩展数据表3)with clonal relationships。Interconnecting lines indicate the relationship between antibodies that share V and Jgene segment sequences at both IGH and IGL.Purple,green and grey lines connect related clones,clones and singles,and singles to each other,respectively。
扩展数据Fig.5:
Extended Data Fig.5:.Antibody somatic hypermutation,and CDR3 length。
a,Number of somatic nucleotide mutations in both the IGVH and IGVL in 14 participants(left)。Individuals who received the Moderna vaccine are shown in black and Pfizer-BioNTech vaccine recipients in red.For each individual,the number of the amino acid length of the CDR3 at the IGVH and IGVL is shown(right)。The horizontal bars indicate the mean.The number of antibody sequences(IGVH and IGVL)evaluated for each participant are n=68(MOD1),n=45(MOD2),n=117(MOD3),n=123(MOD4),n=110(MOD6),n=109(MOD7),n=144(MOD8),n=102(MOD9),n=132(PFZ10),n=109 78(C001),n=66(C003),andn=115(C004)。b、,Distribution of the hydrophobicity GRAVY scores at the IGH CDR3 compared to a public database(see Methods for statistical analysis)。The box limits are at the lower and upper quartiles,the center line indicates the median,the whiskers are1.5×interquartile range and the dots represent outliers。Statistical significance was determined using two-tailed Wilcoxon matched-pairs signed rank test(*****=p<0.0001)。
扩展数据Fig.6:
Extended Data Fig.6:.Monoclonal antibody ELISAS。
a,Graphs show anti-SARS-CoV-2RBD antibody reactivity.ELISA EC50values for all antibodies isolated from COVID-19convalescent individuals assayed at1.3and6.2 months after infection单击功能区上,and127 selected monoclonal antibodies isolated from4Moderna vaccinees(black dots)and4Pfizer-BioNTech vaccinees(red dots)measured at8weeks after the boost。Red horizontal bars and indicated values represent geometric mean.Statistical significance was determined using two-tailed Mann-Whitney U-test。b–c,Graphs show ELISA titration curves for 86 monoclonal antibodies isolated from Moderna vaccinees(b)and41 monoclonal antibodies isolated from Pfizer-BioNTech vaccinees(c)。d-l,Graphs show ELISA titrations for84antibodies isolated from Moderna vaccinees against the indicated RBD variants.Isotype control and low-binding antibodies are indicated in colors.C661is anon-binding antibody.Data are representative of two independent experiments。m,Relative change in EC50values for the indicated RBD variants over wt RBD of 84 antibodies isolated from Moderna vaccinees.Red horizontal bars represent geometric mean。n,电子商务50values for binding to wild type RBD and the indicated mutant RBDs for 17top neutralizing antibodies。
扩展数据Fig.7:
Extended Data Fig.7:.Neutralizing activity of monoclonal antibodies in clinical development against SARS-COV-2variants。
a,Results of a SARS-CoV-2pseudovirus neutralization assay.IC50values for6different monoclonal antibodies,alone or in their clinically designated combinations,for neutralization of wild type and the indicated mutant SARS-COV-2pseudotyped viruses.Antibodies with IC50values above1000ng/ml were plotted at1000ng/ml.Data are the mean of 2 independent experiments.Color gradient indicates IC50values ranging from0(white)to1000ng/ml(red)。Casirivimab and imdevimab,respectively,,has been granted emergency use authorization by the U.S.FDA,the combination of COV2-2196and COV2-2130(licensed to Astra Zeneca as AZD7442),and the combination of C135and C144(The Rockefeller University)are currently in clinical trials(NCT04507256and,andNCT04700163,respectively)。
扩展数据Fig.8:
Extended Data Fig.8:.Local resolution estimates of Fab-S cryo-EM reconstructions。
a-g,局部可回收的炉膛燃烧室SPARC for(a)C669-S,(b)C643-S,(c)C603-S,(d)C601-S,(e、e)C666-S,(f)C663-S,and(g)C670-S complexes。Fab-RBD interfaces are high lighted for(a)C669and(b)C643。h,Gold-standard Fourier shell correlation curves for Fab-S complexes.The0.5and0.143cutoffs are indicated by dashed lines。
Fig.1。
Fig.1.Plasma neutralizing activity。
a,SARS-COV-2pseudovirus neutralization assay.NT50values for COVID-19convalescent plasma measured at 1.3 months and 6.2 months after infection as well as plasma from vaccinees.NT50values lower than10were plotted at10.Mean of 2independent experiments.Red bars and indicated values represent geometric mean NT50values.Statistical significance was determined using the two-tailed Mann-Whitney U-test.Pre-COVID-19historical control plasma was analyzed as negative control and showed no detectable neutralization(NT50<10)。b,NT50values for Moderna mRNA-1273(black)and Pfizer-BioNTech BNT162b2(red)vaccine recipients。Red bars and indicated values represent geometric mean NT50values.Statistical significance was determined using the two-tailed Mann-Whitney U-test。c,Anti-RBD IgG AUC(Y axis)plotted against NT50(X axis)r=0.82,p<0.0001。d,Anti-S IgG AUC(Y axis)plotted against NT50(X axis)r=0.83,p<0.0001。e、e,Anti-RBD IgG AUC(Yaxis)plotted against time between first dose and blood draw(X axis)r=-0.59p=0.0058。f,Anti-S IgG AUC(Yaxis)plotted against time between first dose and blood draw(X axis)r=-0.62p=0.0038。g,NT50(Yaxis)plotted against time between first dose and blood draw(X axis)r=-0.69p=0.008。空气调节阀c-gwere determined by two-tailed Spearman correlation.Moderna vaccinees are in black and Pfizer-BioNTech in red。h。Examples of neutralization assays,comparing the sensitivity of pseudotyped viruses with WT and RBD mutant SARS-CoV-2S proteins to vaccinee plasma.MOD1and PFZ10indicate two representative individuals receiving the Moderna and Pfizer-BioNTech vaccine,respectively(for details ExtData)。i,NT50values for vaccinee plasma(n=15)neutralization of pseudotyped viruses with WT and the indicated RBD-mutant SARS-CoV-2S proteins。Pfizer-BioNTech vaccinees in red。j,NT50values for convalescent plasma(n=45)neutralization of pseudotyped viruses with WT and KEN(K417N/E484K/N501Y)SARS-COV-2S proteins。统计信号iniand,andjwas determined using one tailed t-test.All experiments were performed a minimum of 2times.Pseutotyped viruses containing the E484K mutation and corresponding WT controls contain the R683Gmutation(for details see methods)。
Fig.2。
Fig.2.Memory B cell antibodies。
a单击功能区上,Representative flow cytometry plots showing dual AlexaFluor-647-RBD and PE-RBD binding B cells for4vaccinees。b、,as in ina,RBD binding B cells in 19 vaccinees,in comparison to a cohort of infected individuals assayed 1.3 and 6.2 months after infection单击功能区上,.Individuals who received the Moderna vaccine are shown in black and Pfizer-BioNTech vaccine recipients in red.Red horizontal bars indicate mean values。Statistical significance was determined using two-tailed Mann–Whitney U-tests。c,Pie charts show the distribution of antibody sequences from the 4 individuals ina。The number in the inner circle indicates the number of sequences analyzed.Pie slice size is proportional to the number of clonally related sequences.The black outline indicates the frequency of clonally expanded sequences。d,as in inc,graph shows relative clonality among14vaccinees assayed,individuals who received the Moderna vaccine are shown in black and Pfizer-BioNTech vaccine recipients in red.Red horizontal bars indicate mean values.Statistical significance was determined using two-tailed Mann–WhitneyU-tests。e,Graph shows relative abundance of human IGVH genes Sequence Read Archive accession SRP010970(orange),and vaccinees(blue)。Atwo-sided binomial test was used to compare the frequency distributions,significant differences are denoted with stars(*p<0.05,**p<0.01,***p<0.001,****=p<0.0001)。f,来自14个vaccinated individuals(Moderna in black,Pfizer-BioNTech in red Extended Data Table3)and naturally infected individuals(in green,from单击功能区上,)。Interconnecting lines indicate the relationship between antibodies that share V and Jgene segment sequences at both IGH and IGL.Purple,green and grey lines connect related clones,clones and singles,and singles to each other,respectively。g,Number of somatic nucleotide mutations in the IGVH(top)and IGVL(bottom)in vaccinee antibodies(Extended Data Table3)compared to natural infection obtained 1.3 or 6.2 months after infection单击功能区上,.Statistical significance was determined using the two-tailed Mann–Whitney U-tests and red horizontal bars indicate mean values。h,as in ing,but for CDR3length。
Fig.3:
Fig.3:.Anti-SARS-CoV-2RBD monoclonal antibody neutralizing activity。
a,SARS-CoV-2pseudovirus neutralization assay.IC50从COVID-19 Convalescent patients measured at 1.3 and 6.2 months单击功能区上,after infection as well as antibodies cloned from Moderna mRNA-1273(black)and Pfizer-BioNTech BNT162b2(red)mRNA-vaccine recipients。防波堤开关50values above1000ng/ml were plotted at1000ng/ml.Mean of 2 independent experiments.Red bars and indicated values represent geometric mean IC50values in ng/ml.Statistical significance was determined using the two-tailed MannWhitney U-test.Isotype control antibody was analyzed in parallel and showed no detectable neutralization。b、,集成电路50values for 17selected mAbs for neutralization of wild type and the indicated mutant SARS-CoV-2pseudoviruses.Color gradient indicates IC50values ranging from0(white)to1000ng/ml(red)。c单击功能区上,Antibody selection pressure can drive emergence of S variants in cell culture;the percentage of sequence reads encoding the indicated RBD mutations after a single passage of rVSV/SARS-CoV-2 in the presence of the indicated antibodies is tabulated.Color gradient indicates percentage of sequence reads reads bearing the indiged(white)to100(red)。Positions for which no sequence read was detected are shown in grey.The percentages calculated for agiven position are based on all the reads,and not just the reads that include that position.K417N,E484K/R683G and N501are high lighted inband,andcas they constitute important circulating variants。
Fig.4。
Fig.4.Cryo-EM reconstructions of Fab-S complexes。
Cryo-EM densities for Fab-S complexes(a-e打开;k–l)and close-up views of antibody footprints on RBDs(f–j打开;m–n)are shown for neutralizing mAbs。As expected,due to Fab inter-domain flexibility,cryo-EM densities(a-e打开;k–l)were weak for the Fab CH-CL、Ldomains.Models of antibody footprints on RBDs(f–j打开;m–n)are presented as Fab VH–VL、Ldomains(cartoon)complexed with the RBD(surface)。To generate models,coordinates of stabilized S trimer(PDB6XKL)and representative Fab fragments(PDB6XCA or7K8P)with CDR3loops removed were fit by rigid body docking into the cryo-EM density maps。a,f,C669;b,g,C643;c,h,C603;d,i,C601;e,j,C670;k,m,C666;andl,n,C663.RBD residues K417,N439,N440,E484,and N501are high lighted as red surfaces.The N343glycan is shown as a teal sphere。o、,RBD-specific neutralizing mAbs(shown as V)H-VL、Ldomains in colors from panelsa-l)elicited from mRNA vaccines。

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  • mRNA vaccine-elicited antibodies to SARS-COV-2and circulating variants。
    Wang Z,Schmidt F,Weisblum Y,Muecksch F,Barnes CO,Finkin S,Schaefer-BabajewD,Cipolla M,Gaebler C,Lieberman JA,Oliveira TY,Yang Z,Abernathy ME,Huey-Tubman KE,Hurley A,Turroja M,West KA,Gordon K,Millard KG,RamosRA,Dalval,Patel R,Dizon J,Unson-O'Brien C,Shimeliovich I,Gazumyan A,Caskey M,Bjorkman PJ, Casellas R,Hatziioannou T,Bieniasz PD,Nussenzweig MC。 Wang Z,et al。 bioRxiv[Preprint]。2021 Jan30:2021.01.15.426911。doi:10.1101/2021.01.15.426911。 bioRxiv.2021。 PMID:33501451 Free PMC article。 Updated。 Preprint。

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