Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2

Figures

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  Fig. 1. Preferred usage of IGHV3-53/3-66 among the potent neutralizing antibodies. a, b Lineage analysis for heavy and light chains in pie charts. The numbers in the center represent the number of RBD-specific antibodies. Each slice represents a unique clone and proportional to its own size. c, d Counts of various CDR3 length and somatic hypermutation from IGHV3-53 and IGHV3-66 as well as RBD binders. Source data are provided as a Source Data file.

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  Fig. 2. Structure and binding features of public antibodies to SARS-CoV-2 RBD. a The crystal structures of RBD and Fab complexes. RBD was colored in cyan. P22A-1D1 Fab was colored in slate and light blue, P5A-1D2 in hot pink and salmon, P5A-3C8 in yellow orange and light yellow, and P2C-1F11 (PDB ID: 7CDI) in violet and pink, for heavy chain and light chain, respectively. b The footprint of Fabs and ACE2 on SARS-CoV-2 RBD. The color of the epitope was depicted as in a. The epitope of ACE2 was colored by black. K417 was highlighted with blue. c Binding residues shared with ACE2 are listed. K417 was highlighted with blue box.

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  Fig. 3. Shared binding interface among the public antibodies. a Conserved HCDR1, HCDR2, and different HCDR3. RBD was colored in cyan and shown as surface. CDR loops of the heavy chain were shown as ribbon with the same color in Fig. 2. b The interactions between the three conserved tyrosine at HCDR1 and HCDR2. c The interactions between HCDR2 -SGGS- segment, and RBD. Hydrogen bonds were shown as black dashed line and P5A-3C8/RBD complex was used as an example in b, c.

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  Fig. 4. Susceptibility of SARS-CoV-2 K417 variants to binding and neutralization of public antibodies. Values indicate the fold changes in a binding affinity (KD) and b half-maximal inhibitory concentrations (IC50). The symbol “-” indicates increased resistance and “+” increased sensitivity. Those KD or IC50 values highlighted in red, resistance increased at least twofold; in blue, sensitivity increased at least twofold; and in white, resistance or sensitivity increased less than twofold. BDL (Below Detection Limit) indicates the highest concentration of mAbs failed to bind or reach 50% neutralization. c The individual antibodies were captured on protein A covalently immobilized onto a CM5 sensor chip followed by injection of purified soluble SARS-CoV-2 WT and K417/R/A/E/N/T mutant RBDs at five different concentrations. The black lines indicate the experimentally derived curves while the red lines represent fitted curves based on the experimental data. d Comparison of public antibodies’ neutralization against pseudovirus bearing WT, K417R, K417A, K417E, K417N, or K417T mutant SARS-CoV-2 spike on the pseudovirus. VRC01 is an HIV-1 specific antibody used here as a negative control. Data…

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  Fig. 5. Efficacy of P5A-3C8 prophylaxis against live SARS-CoV-2 infection in Syrian hamsters. a The hamsters were given a single intraperitoneal dose of 5 mg/kg of P5A-3C8 (n = 3), or VRC01, an anti-HIV-1 antibody as negative control (n = 3). On day 4 after viral challenge, the genomic viral RNA in the lung and nasal turbinate tissues were determined by qRT-PCR normalized by beta-actin. The differences between P5A-3C8 group and VRC01 group in lung tissues are statistically significant with two-tailed p value = 0.0064 (**p < 0.01, unpaired t test). b Subgenomic viral RNA in the lung and nasal turbinate tissues on day 4 after viral challenge were determined by qRT-PCR normalized by beta-actin (n = 3). c Infectious virions were tested by viral plaque assay in lung and nasal turbinate tissues. PFUs per mg of tissue extractions were compared between two groups (n = 3). d The body weights of hamsters were monitored over a 4-day time course (n = 3). All data from a–d are shown in mean value ± SD. e Representative images of hamster lung tissues detected for viral NP antigen by immunofluorescence. In the VRC01 group, diffuse NP expression was shown in large areas of alveoli. Sporadic NP…