1. Epidemiology and Global Health
  2. Microbiology and Infectious Disease
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Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

  1. Nikhil Faulkner
  2. Kevin W Ng
  3. Mary Y Wu
  4. Ruth Harvey
  5. Marios Margaritis
  6. Stavroula Paraskevopoulou
  7. Catherine Houlihan
  8. Saira Hussain
  9. Maria Greco
  10. William Bolland
  11. Scott Warchal
  12. Judith Heaney
  13. Hannah Rickman
  14. Moria Spyer
  15. Daniel Frampton
  16. Matthew Byott
  17. Tulio de Oliveira
  18. Alex Sigal
  19. Svend Kjaer
  20. Charles Swanton
  21. Sonia Gandhi
  22. Rupert Beale
  23. Steve J Gamblin
  24. John W McCauley
  25. Rodney Stuart Daniels
  26. Michael Howell
  27. David Bauer
  28. Eleni Nastouli
  29. George Kassiotis  Is a corresponding author
  1. Retroviral Immunology, United Kingdom
  2. National Heart and Lung Institute, Imperial College London, United Kingdom
  3. High Throughput Screening STP, United Kingdom
  4. Worldwide Influenza Centre, United Kingdom
  5. Advanced Pathogen Diagnostics Unit UCLH NHS Trust, United Kingdom
  6. Division of Infection and Immunity, United Kingdom
  7. RNA Virus Replication Laboratory, United Kingdom
  8. Department of Population, Policy and Practice, United Kingdom
  9. School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, South Africa
  10. KwaZulu-Natal Research Innovation and Sequencing Platform, South Africa
  11. Centre for the AIDS Programme of Research in South Africa, South Africa
  12. Department of Global Health, University of Washington, United States
  13. Africa Health Research Institute, South Africa
  14. Max Planck Institute for Infection Biology, Germany
  15. Structural Biology STP, United Kingdom
  16. Cancer Evolution and Genome Instability Laboratory, United Kingdom
  17. Neurodegradation Biology Laboratory, United Kingdom
  18. Cell Biology of Infection Laboratory, United Kingdom
  19. Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, United Kingdom
  20. Department of Infectious Disease, St Mary's Hospital, Imperial College London, United Kingdom
Research Article
Cite this article as: eLife 2021;10:e69317 doi: 10.7554/eLife.69317
2 figures, 1 table and 3 additional files

Figures

Figure 1 with 6 supplements
Recognition of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoproteins by antibodies in D614G and B.1.1.7 sera.

(a-c) Correlation of IgG (a), IgM (b), and IgA (c) antibody levels to D614G and B.1.1.7 or B.1.351 spikes in the indicated groups of donors infected either with the D614G or B.1.1.7 strains. Each symbol represents an individual sample and levels are expressed as a percentage of the positive control. Black lines denote complete correlation and grey lines a 25% change in either direction. (d-f) Comparison of IgG (d), IgM (e), and IgA (f) antibody levels to the indicated spikes in groups of donors acutely infected either with the D614G or B.1.1.7 strains. Connected symbols represent individual donors. Numbers above the plots denote the average binding to each spike, expressed as a percentage of binding to the infecting spike.

Figure 1—figure supplement 1
Flow cytometric detection of spike-binding antibodies.

HEK293T cells were transfected with expression plasmids encoding each severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant spike and were used for flow cytometric analysis 2 days later. (a) Gating of HEK293T cells and of single cells in these mixed cell suspensions. (b) Example of IgG, IgM, and IgA staining in a positive sample and a negative control. Numbers within the plots denote the percentage of positive cells. (c) Staining of HEK293T cells transfected to express the Wuhan spike, with titrated amounts of the S2-specific D001 monoclonal antibody. Numbers above the plots denote the final D001 antibody concentration. (d) Median fluorescence intensity (MFI) of stained cells in c, according to the D001 antibody concentration.

Figure 1—figure supplement 2
Recognition of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoproteins by antibodies in D614G and B.1.1.7 sera.

Correlation of IgG antibody levels to Wuhan, D614G, B.1.1.7, and B.1.351 spikes in the indicated groups of donors infected either with the D614G or B.1.1.7 strains. Each symbol represents an individual sample and levels are expressed as a percentage of the positive control. Black lines denote complete correlation and grey lines a 25% change in either direction.

Figure 1—figure supplement 3
Recognition of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoproteins by antibodies in D614G and B.1.1.7 sera.

Correlation of IgM antibody levels to Wuhan, D614G, B.1.1.7, and B.1.351 spikes in the indicated groups of donors infected either with the D614G or B.1.1.7 strains. Each symbol represents an individual sample and levels are expressed as a percentage of the positive control. Black lines denote complete correlation and grey lines a 25% change in either direction.

Figure 1—figure supplement 4
Recognition of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoproteins by antibodies in D614G and B.1.1.7 sera.

Correlation of IgA antibody levels to Wuhan, D614G, B.1.1.7, and B.1.351 spikes in the indicated groups of donors infected either with the D614G or B.1.1.7 strains. Each symbol represents an individual sample and levels are expressed as a percentage of the positive control. Black lines denote complete correlation and grey lines a 25% change in either direction.

Figure 1—figure supplement 5
Matrix of correlation coefficients between binding and neutralising antibodies.

Levels of binding IgG, IgM, and IgA antibodies to the indicated spikes and levels of neutralising antibodies to the indicated strains were correlated using all the samples described in this work (n=83).

Figure 1—figure supplement 6
Kinetics and magnitude of the antibody response to D614G and B.1.1.7 infection.

(a) Levels of IgG antibodies to the spike of the infecting strain in sera from donors infected with the D614G or B.1.1.7 strains, over time since onset of symptoms (for symptomatic cases) or the first positive RT-qPCR diagnosis (for asymptomatic cases). Levels are expressed as a percentage of the positive control. (b) Neutralising antibody levels (IC50) against the closest infecting strain (Wuhan for D614G infection and B.1.1.7 for B.1.1.7 infection) in sera from donors infected with the D614G or B.1.1.7 strains, over time since onset of symptoms or since the first positive RT-qPCR diagnosis. (c) Correlation of binding IgG and neutralising antibody levels from a and b, respectively. (d) Comparison of binding IgG, IgM, and IgA antibody levels and of neutralising antibody levels (IC50) between B.1.1.7-infected asymptomatic donors and those with mild COVID-19 symptoms. Antibody binding and virus neutralisation were tested against the homologous B.1.1.7 spike and virus, respectively. Differences between the two groups were not statistically significant. Grey horizontal lines denote the lower and upper limit of detection. In (a-d), each symbol represents an individual sample.

Figure 2 with 5 supplements
Neutralisation of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains by antibodies in D614G and B.1.1.7 sera.

(a) Correlation of neutralising antibody levels (IC50) against the Wuhan, B.1.1.7, or B.1.351 strains in the indicated groups of donors infected either with the D614G or B.1.1.7 strains. Each symbol represents an individual sample. Black lines denote complete correlation and grey lines a 50% (twofold) change in either direction. (b) Comparison of neutralising antibody levels (IC50) to the indicated SARS-CoV-2 strains in groups of donors acutely infected with either the D614G or B.1.1.7 strains. Connected symbols represent individual donors. Numbers above the plots denote the average IC50 against each strain, expressed as a percentage of IC50 against the infecting strain. Grey horizontal lines denote the lower and upper limit of detection.

Figure 2—figure supplement 1
Neutralisation of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains by antibodies in D614G sera, according to severity of infection.

Comparison of neutralising antibody levels (IC50) to the indicated SARS-CoV-2 strains in donors acutely infected with the D614G strain, grouped according to the severity of the outcome. Connected symbols represent individual donors. Numbers above the plots denote the average IC50 against each strain, expressed as a percentage of IC50 against the infecting strain. Grey horizontal lines denote the lower and upper limit of detection.

Figure 2—figure supplement 2
Binding and neutralising antibodies at a 3-month follow-up of mild/asymptomatic D614G infection.

(a) Levels of IgG, IgM, and IgA antibodies (expressed as a percentage of the positive control) to the D614G spike in sera from D614G-infected donors at 1 and 3 months post infection. (b) Neutralising antibody levels (IC50) against the Wuhan, B.1.1.7, or B.1.351 strains in same donors described in a. In a and b, connected symbols represent individual donors.

Figure 2—figure supplement 3
Neutralisation of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains by antibodies in D614G and B.1.1.7 sera from mild/asymptomatic infection.

Comparison of neutralising antibody levels (IC50) to the indicated SARS-CoV-2 strains in subgroups of donors acutely infected with either the D614G (n=11) or B.1.1.7 (n=11) strains, selected for comparable disease outcome and time since infection. Connected symbols represent individual donors. Numbers above the plots denote the average IC50 against each strain, expressed as a percentage of IC50 against the infecting strain. Grey horizontal lines denote the lower and upper limit of detection.

Figure 2—figure supplement 4
Spike sequence distance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

Distance was calculated based on the sequence alignment of the full-length spike amino acid sequences of the indicated SARS-CoV-2 variants. Mutations of amino acid residues that are shared by at least two strains or are unique to specific strains are indicated in different colours. Mutations were considered shared if they affected the same amino acid position even if the change was not identical.

Figure 2—figure supplement 5
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralisation assay setup.

The 96-well racks of serum samples including controls are serially diluted after an initial dilution of 1:10 to generate four total dilution plates. These are used to treat pre-seeded Vero E6 cells in 384-well assay plates in duplicate before infection with SARS-CoV-2 virus. After immunostaining with DAPI and a 488-conjugated monoclonal antibody against SARS-CoV-2 nucleoprotein, each well is imaged and infection area per area of cells calculated, followed by automated curve fitting and identification of serum dilution factor to achieve 50% neutralisation (IC50).

Tables

Key resources table
Reagent type
(species) or
resource
DesignationSource or
reference
IdentifiersAdditional
information
AntibodyBV421 anti-human IgG (monoclonal)BiolegendRRID:AB_2562176; Cat# 409318FACS (1:200)
AntibodyAPC anti-human IgM (monoclonal)BiolegendRRID:AB_493011; Cat# 314510FACS (1:200)
AntibodyPE anti-human IgA (monoclonal)Miltenyi BiotechRRID:AB_2733860; Cat# 130-114-002FACS (1:200)
AntibodyAnti-SARS-CoV-2 S2 clone D001 (monoclonal)SinoBiologicalRRID:AB_2857932; Cat# 40590-D001FACS
AntibodyAlexa488 anti-SARS-CoV-2 nucleoprotein (monoclonal)Produced in-houseCR3009IF
Recombinant DNA reagentpcDNA3-SARS-CoV-2_WT spikeDr Massimo Pizzato, University of Trento, ItalyWuhan spike sequenceTransfected construct
Recombinant DNA reagentpcDNA3-SARS-CoV-2_D614G spikeDr Massimo Pizzato, University of Trento, ItalyWuhan spike sequence with D614G mutation and cytoplasmic tail deletionTransfected construct
Recombinant DNA reagentpcDNA3-SARS-CoV-2_B.1.1.7 spikeThis paperB.1.1.7 spike sequenceTransfected construct
Recombinant DNA reagentpcDNA3-SARS-CoV-2_ B.1.351 spikeThis paperB.1.351 spike sequenceTransfected construct
Cell line (Homo sapiens)HEK293TCell Services facility at the Francis Crick InstituteRRID:CVCL_0063; CVCL_0063
Cell line
(Chlorocebus sp.)
Vero E6Dr Björn Meyer, Institut Pasteur, Paris, FranceCRL-1586
Cell line
(Chlorocebus sp.)
Vero V1Prof. Steve Goodbourn, St. George’s, University of London, London, UKCCL-81
OtherSARS-CoV-2hCoV-19/England/02/2020Respiratory Virus Unit, Public Health England, UKWuhan strain
OtherSARS-CoV-2hCoV-19/England/204690005/2020Public Health England (PHE), UK, through Prof. Wendy Barclay, Imperial College London, London, UKB.1.1.7 strain
OtherSARS-CoV-2501Y.V2.HV001
Cele et al., 2021
B.1.351 strain

Additional files

Source data 1

Binding and neutralising titre values.

https://cdn.elifesciences.org/articles/69317/elife-69317-data1-v2.xlsx
Supplementary file 1

Donor and patient characteristics.

This table lists the number, median age (and range), gender proportion, and the median time (and range) post infection for the donors and patients studied.

https://cdn.elifesciences.org/articles/69317/elife-69317-supp1-v2.docx
Transparent reporting form
https://cdn.elifesciences.org/articles/69317/elife-69317-transrepform-v2.pdf

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