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. 2020 Aug;584(7821):437-442.
doi: 10.1038/s41586-020-2456-9. Epub 2020 Jun 18.

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

Affiliations
  • PMID: 32555388
  • PMCID: PMC7442695
  • DOI: 10.1038/s41586-020-2456-9
Free PMC article

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

Davide F Robbiani et al. Nature. 2020 Aug.
Free PMC article

Abstract

During the coronavirus disease-2019 (COVID-19) pandemic, severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has led to the infection of millions of people and has claimed hundreds of thousands of lives. The entry of the virus into cells depends on the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2. Although there is currently no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-21-5. Here we report on 149 COVID-19-convalescent individuals. Plasma samples collected an average of 39 days after the onset of symptoms had variable half-maximal pseudovirus neutralizing titres; titres were less than 50 in 33% of samples, below 1,000 in 79% of samples and only 1% of samples had titres above 5,000. Antibody sequencing revealed the expansion of clones of RBD-specific memory B cells that expressed closely related antibodies in different individuals. Despite low plasma titres, antibodies to three distinct epitopes on the RBD neutralized the virus with half-maximal inhibitory concentrations (IC50 values) as low as 2 ng ml-1. In conclusion, most convalescent plasma samples obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.

Figures

Extended Data Figure 1.
Extended Data Figure 1.. Clinical correlates.
a, Summary of the cohort’s characteristics. b, Age distribution (Y axis) for all males (n=83) and females (n=66) in the cohort; p=0.2074. c, Duration of symptoms in days (Y axis) for all males (n=83) and females (n=66) in the cohort; p=0.8704. d, Time between symptom onset and plasma collection (Y axis) for all males (n=83) and females (n=66) in the cohort; p=0.5514. e, Subjective symptom severity on a scale of 0–10 (Y axis) for all males (n=83) and females (n=66) in the cohort; p=0.1888. f, Age distribution (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.0305. g, Duration of symptoms in days (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.1241. h, Time between symptom onset and plasma collection in days (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.1589. i, Symptom severity (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.0550. j, Age distribution (Y axis) for all outpatient (n=138) and hospitalized (n=11) participants; p=0.0024. k, Duration of symptoms in days (Y axis) for all outpatient (n=138) and hospitalized (n=11) participants in the cohort; p=<0.0001. l, Time between symptom onset and plasma collection in days (Y axis) for all outpatient (n=138) and hospitalized (n=11) participants in the cohort; p=0.0001. m, Symptom severity (Y axis) for all outpatient (n=138) and hospitalized (n=11) participants in the cohort; p=<0.0001. Horizontal bars indicate median values. Statistical significance was determined using two-tailed Mann-Whitney U test.
Extended Data Figure 2.
Extended Data Figure 2.. Clinical correlates of plasma antibody titers.
a, Normalized AUC for IgG anti-RBD (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.0107. b, Normalized AUC for IgM anti-RBD (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.5371. c, Normalized AUC for IgG anti-S (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.0135. d, Normalized AUC for IgM anti-S (Y axis) for all cases (n=111) and contacts (n=38) in the cohort; p=0.7838. e, Normalized AUC for IgM anti-RBD (Y axis) for all males (n=83) and females (n=66) in the cohort; p=0.9597. f, Normalized AUC for IgG anti-S (Y axis) for all males (n=83) and females (n=66) in the cohort; p=0.0275. g, Normalized AUC for IgM anti-S (Y axis) for all males (n=83) and females (n=66) in the cohort; p=0.5363. h, Normalized AUC for IgM anti-RBD (Y axis) for all outpatient (=138) and hospitalized (n=11) participants in the cohort; p=0.0059. i, Normalized AUC for IgG anti-S (Y axis) for all outpatient (=138) and hospitalized (=11) participants in the cohort; p=0.0623. j, Normalized AUC for IgM anti-S (Y axis) for all outpatient (=138) and hospitalized (=11) participants in the cohort; p=0.2976. Horizontal bars indicate median values. Statistical significance was determined using two-tailed Mann-Whitney U test.
Extended Data Figure 3.
Extended Data Figure 3.. Additional clinical correlates of plasma antibody titers.
a, Time between symptom onset and plasma collection in days (X axis) plotted against normalized AUC for IgG anti-RBD (Y axis); r=−0.0261 p=0.7533. b, Time between symptom onset and plasma collection in days (X axis) plotted against normalized AUC for IgG anti-S (Y axis); r=−0.1495 p=0.0697. c, Time between symptom onset and plasma collection in days (X axis) plotted against normalized AUC for IgM anti-S (Y axis); r=0.1496 p=0.0695. d, Age (X axis) plotted against AUC for IgM anti-RBD (Y axis); r=0.0172 p=0.8355. e, Age (X axis) plotted against normalized AUC for IgG anti-S (Y axis); r=0.1523 p=0.0638. f, Age (X axis) plotted against normalized AUC for IgM anti-S (Y axis); r=0.0565 p=0.4934. g, Duration of symptoms in days (X axis) plotted against normalized AUC for IgG anti-RBD (Y axis); r=0.1525, p=0.0633. h, Duration of symptoms in days (X axis) plotted against normalized AUC for IgM anti-RBD (Y axis); r=−0.3187, p=<0.0001. i, Duration of symptoms in days (X axis) plotted against normalized AUC for IgG anti-S (Y axis); r=0.0329, p=0.6904. j, Duration of symptoms in days (X axis) plotted against normalized AUC for IgM anti-S (Y axis); r=0.0824, p=0.3177. k, Severity of symptoms (X axis) plotted against normalized AUC for IgG anti-RBD (Y axis); r=0.2679 p=0.0010. l, Severity of symptoms (X axis) plotted against normalized AUC for IgM anti-RBD (Y axis); r=−0.1943 p=0.0176. m, Severity of symptoms (X axis) plotted against normalized AUC for IgG anti-S (Y axis); r=0.1187 p=0.1492. n, Severity of symptoms (X axis) plotted against normalized AUC for IgM anti-S (Y axis); r=0.1597 p=0.0517. All correlations were analyzed by two-tailed Spearman’s.
Extended Data Figure 4.
Extended Data Figure 4.. Diagrammatic representation of the SARS-CoV-2 pseudovirus luciferase assay.
a, Co-transfection of pNL4-3ΔEnv-nanoluc and pSARS-CoV-2 spike vectors into 293T cells (ATCC) leads to production of SARS-CoV-2 Spike-pseudotyped HIV-1 particles (SARS-CoV-2 pseudovirus) carrying the Nanoluc gene. b, SARS-CoV-2 pseudovirus is incubated for 1 h at 37°C with plasma or monoclonal antibody dilutions. The virus-antibody mixture is used to infect ACE2-expressing 293T cells, which will express nanoluc Luciferase upon infection. c, Relative luminescence units (RLU) reads from lysates of ACE2-expressing 293T cells infected with increasing amounts of SARS-CoV-2 pseudovirus. Error bars represent standard deviation of triplicates, two experiments.
Extended Data Figure 5.
Extended Data Figure 5.. Clinical correlates of neutralization.
a, Normalized AUC for anti-RBD IgM (X axis) plotted against NT50 (Y axis); r=0.3119, p=0.0001. b, Normalized AUC for anti-S IgM (X axis) plotted against NT50 (Y axis); r=0.3211, p=<0.0001. c, Duration of symptoms in days (X axis) plotted against NT50 (Y axis); r=0.1997, p=0.0146. d, Time between symptom onset and plasma collection in days (X axis) plotted against NT50 (Y axis); r=−0.1344, p=0.1033. e, Symptom severity (X axis) plotted against NT50 (Y axis); r=0.2234, p=0.0062. f, Age (X axis) plotted against NT50 (Y axis); r=0.3005, p=0.0002. All correlations were analyzed by two-tailed Spearman’s. Dotted line (NT50=5) represents lower limit of detection (LLOD) of pseudovirus neutralization assay. Samples with neutralizing titers below 1:50 were plotted at LLOD.
Extended Data Figure 6.
Extended Data Figure 6.. Flow cytometry.
Gating strategy used for cell sorting. Gating was on singlets that were CD20+ and CD3CD8CD16Ova. Sorted cells were RBD-PE+ and RBD-AF647+.
Extended Data Figure 7.
Extended Data Figure 7.. Frequency distributions of human V genes.
The two-tailed t test with unequal variance was used to compare the frequency distributions of human V genes of anti-SARS-CoV-2 antibodies from this study to Sequence Read Archive SRP010970.
Extended Data Figure 8.
Extended Data Figure 8.. Analysis of antibody somatic hypermutation and CDR3 length.
a, For each individual, the number of somatic nucleotide mutations (Y axis) at the IGVH and IGVL are shown on the left panel, and the amino acid length of the CDR3s (Y axis) are shown on the right panel. The horizontal bars indicate the mean. The number of antibody sequences (IGVH and IGVL) evaluated in each participant are n=118 (COV107), n=127 (COV21), n=79 (COV47), n=54 (COV57), n=78 (COV72), n=78 (COV96). b, same as in a but for all antibodies combined (n=534 for both IGVH and IGVL). c, Distribution of the hydrophobicity GRAVY scores at the IGH CDR3 in antibody sequences from this study 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 are 1.5x interquartile range and the dots represent outliers.
Extended Data Figure 9.
Extended Data Figure 9.. Binding of the monoclonal antibodies to the RBD of SARS-CoV-2 and cross-reactivity to SARS-CoV.
a, EC50 values for binding to the RBD of SARS-CoV-2. Average of two or more experiments; n=89. b and c, Binding curves and EC50 values (average of two experiments) for binding to the RBD of SARS-CoV; n=20 and n=17 (excluding isotype and CR3022), respectively. d and e, SARS-CoV pseudovirus neutralization curves and IC50 values. Shown in d are the standard deviations of duplicates for one representative experiment and in e is the average of two experiments (n=10, excluding CR3022). Samples with IC50s above 1μg/ml were plotted at 1μg/ml.
Extended Data Figure 10.
Extended Data Figure 10.. Biolayer interferometry experiment.
Binding of antibodies C144, C101, C002, C121, C009, C119. Graphs show secondary antibody binding to preformed C121 IgG-RBD complexes. The table displays the shift in nanometers after second antibody (Ab2) binding to the antigen in the presence of the first antibody (Ab1). Values are normalized by the subtraction of the autologous antibody control.
Figure 1.
Figure 1.. Plasma antibodies against SARS-CoV-2.
a-d, Graphs show results of ELISAs measuring plasma reactivity to RBD (a, b) and S protein (c, d). Left shows optical density units at 450 nm (OD, Y axis) and reciprocal plasma dilutions (X axis). Negative controls in black; individuals 21, and 47 in blue and red lines and arrowheads, respectively. Right shows normalized area under the curve (AUC) for 8 controls and each of 149 individuals in the cohort. e, Symptom (Sx) onset to time of sample collection in days (X axis) plotted against normalized AUC for IgM binding to RBD (Y axis); r=0.5517 and p=<0.0001. f, Participant age in years (X axis) plotted against normalized AUC for IgG binding to RBD (Y axis); r=0.1827 and p=0.0258. The r and p values for the correlations in e and f were determined by two-tailed Spearman’s. g, Normalized AUC of anti-RBD IgG ELISA for outpatients (n=138) and hospitalized (n=11) individuals; p=0.0178. h, Normalized AUC of anti-RBD IgG ELISA for males (n=83) and females (n=66); p=0.0063. For g and h horizontal bars indicate median values. Statistical significance was determined using two-tailed Mann-Whitney U test.
Figure 2.
Figure 2.. Neutralization of SARS-CoV-2 pseudovirus by plasma.
a, Graph shows normalized relative luminescence values (RLU, Y axis) in cell lysates of 293TACE2 cells 48 hours after infection with nanoluc-expressing SARS-CoV-2 pseudovirus in the presence of increasing concentrations of plasma (X axis) derived from 149 participants (grey, except individuals 21 and 47 in blue and red lines, bars and arrowheads, respectively) and 3 negative controls (black lines). Mean of duplicates; representative of two independent experiments. b, Ranked average half-maximal inhibitory plasma neutralizing titer (NT50) for the 59 of 149 individuals with NT50s >500 and individual 107. Asterisks indicate donors from which antibody sequences were derived. c, Normalized AUC for anti-RBD IgG ELISA (X axis) plotted against NT50 (Y axis); r=0.6432, p=<0.0001. d, Normalized AUC for anti-S IgG ELISA (X axis) plotted against NT50 (Y axis); r=0.6721, p=<0.0001. The r and p values for the correlations in c and d were determined by two-tailed Spearman’s. e, NT50 for outpatients (n=138) and hospitalized (n=11) individuals; p=0.0495. f, NT50 for males (n=83) and females (n=66) in the cohort; p=0.0031. Statistical significance in e and f was determined using two-tailed Mann-Whitney U test and horizontal bars indicate median values. Dotted lines in c to f (NT50=5) represents lower limit of detection (LLOD). Samples with neutralizing titers below 1:50 were plotted at LLOD.
Figure 3.
Figure 3.. Anti-SARS-CoV-2 RBD antibodies.
a. Representative flow cytometry plots showing dual AF647- and PE-RBD binding B cells in control and 6 study individuals (for gating strategy see Extended Data Fig. 6). Percentages of antigen specific B cells are indicated. Control is a healthy sample obtained before COVID-19. b, Pie charts depicting the distribution of antibody sequences from 6 individuals. The number in the inner circle indicates the number of sequences analyzed for the individual denoted above the circle. White indicates sequences isolated only once, and grey or colored pie slices are proportional to the number of clonally related sequences. Red, blue, orange and yellow pie slices indicate clones that share the same IGHV and IGLV genes. c, Circos plot shows sequences from all 6 individuals with clonal relationships depicted as in b. Interconnecting lines indicate the relationship between antibodies that share V and J gene segment sequences at both IGH and IGL. Purple, green and gray lines connect related clones, clones and singles, and singles to each other, respectively. d, Sample sequence alignment for antibodies originating from different individuals that display highly similar IGH V(D)J and IGL VJ sequences including CDR3s. Amino acid differences in CDR3s to the bolded reference sequence above are indicated in red and dots represent identities.
Figure 4.
Figure 4.. Anti-SARS-CoV-2 RBD antibody reactivity.
a, Graph shows results of ELISA assays measuring monoclonal antibody binding to RBD. Optical density units at 450 nm (OD, Y axis) vs. antibody concentrations (X axis); 94 samples and 1 isotype control. C121, C135 C144 and isotype control in red, green, purple, and black respectively, in all panels. b, Graph shows normalized relative luminescence values (RLU, Y axis) in cell lysates of 293TACE2 cells 48 hours after infection with SARS-CoV-2 pseudovirus in the presence of increasing concentrations of monoclonal antibodies (X axis). 89 samples and 1 isotype control. c, Normalized RLU for SARS-CoV-2 pseudovirus neutralization (Y axis) vs. titration of monoclonal antibodies C121, C135 and C144. d, SARS-CoV-2 real virus neutralization assay. Normalized infected cells (Y axis, determined by dividing the amount of infection per well by the average of control wells infected in the absence of antibodies) vs. titration of monoclonal antibodies C121, C135 and C144. a to d show a representative of two independent experiments. In b and c is mean of duplicates and in d is mean with standard deviation of triplicates. e, IC50s for antibodies assayed in b and d, the average value of at least two experiments is shown. Samples with IC50s above 1μg/ml were plotted at 1μg/ml; n=89 (pseudovirus) and n=3 (virus), respectively. f, Diagrammatic representation of biolayer interferometry experiment. g, Graph shows binding of C144, C101, C121, C009, C135, and CR3022, to RBD. h-n, Secondary antibody binding to preformed IgG-RBD complexes (Ab1). The table displays the shift in nanometers after second antibody (Ab2) binding to the antigen in the presence of the first antibody (Ab1). Values are normalized by the subtraction of the autologous antibody control. Representative of two experiments. o-q, Representative 2D-class averages and 3D reconstructed volumes for SARS-CoV-S 2P trimers complexed with C002, C119, and C121 Fabs. 2D class averages with observable Fab density are boxed. r, Overlay of S-Fab complexes with fully-occupied C002 (blue), C121 (magenta) and C119 (orange) Fabs. The SARS-CoV-2 S model from PDB 6VYB was fit into the density and the SARS-CoV mAb S230 (PDB 6NB6) is shown as a reference (green ribbon).

Update of

  • Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals.
    Robbiani DF, Gaebler C, Muecksch F, Lorenzi JCC, Wang Z, Cho A, Agudelo M, Barnes CO, Gazumyan A, Finkin S, Hagglof T, Oliveira TY, Viant C, Hurley A, Hoffmann HH, Millard KG, Kost RG, Cipolla M, Gordon K, Bianchini F, Chen ST, Ramos V, Patel R, Dizon J, Shimeliovich I, Mendoza P, Hartweger H, Nogueira L, Pack M, Horowitz J, Schmidt F, Weisblum Y, Michailidis E, Ashbrook AW, Waltari E, Pak JE, Huey-Tubman KE, Koranda N, Hoffman PR, West AP Jr, Rice CM, Hatziioannou T, Bjorkman PJ, Bieniasz PD, Caskey M, Nussenzweig MC. Robbiani DF, et al. bioRxiv. 2020 May 22:2020.05.13.092619. doi: 10.1101/2020.05.13.092619. Preprint. bioRxiv. 2020. PMID: 32511384 Free PMC article. Updated.

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