human coronavirus spike protein  (Sino Biological)

Journal: Biosensors & Bioelectronics

Article Title: Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients

doi: 10.1016/j.bios.2020.112643

Figure Lengend Snippet: Response of a commercial anti-SARS-CoV-2 rabbit polyclonal antibody (pAb) on the array. (A) Array exposed 20% FBS + 10% PNHS; (B) Array exposed to 1 μg/mL anti-SARS-CoV-2 pAb in 20% FBS + 10% PNHS. Strong responses to SARS-CoV-2 S1+S2 ECD, S1, and RBD are observed, as well as smaller cross-reactive responses to HCoV-229E, HCoV-OC43, and MERS spike proteins; (C) quantitative data for the titration. Concentrations of pAb are provided at the top of each column in ng/mL; response values at each concentration for each antigen are provided in Ångstroms of build. (D) Titration curves for the four SARS-CoV-2 antigens with standard deviation of replicate probe spots at each concentration.

Article Snippet: At the highest concentrations, significant cross-reactive binding to the HCoV-229E spike protein was observed, as well as some binding to the HCoV-OC43 spike protein and MERS S1.

Techniques: Titration, Concentration Assay, Standard Deviation

Journal: International Journal of Infectious Diseases

Article Title: High prevalence of pre-existing serological cross-reactivity against SARS-CoV-2 in sub-Sahara Africa

doi: 10.1016/j.ijid.2020.10.104

Figure Lengend Snippet: Immunofluorescence assay (IFA) against SARS, MERS, HCoV-OC43, HCoV-HKU-1, HCoV-NL63 and HCoV-229E spike or nucleocapsid expressing cells. Representative pictures of IFA with pre-COVID-19 pandemic cross-reactive plasma samples 21854. Sample 21854 strongly recognized the spike protein of HCoV-OC43, HCoV-HKU-1, HCoV-NL63 and HCoV-229E, but not SARS and MERS. Sample 21854 only recognized the nucleocapsid of HCoV-NL63 and not the other human coronaviruses. White arrows indicate positive cells. Scale bar represent 50 µm.

Article Snippet: Immunofluorescence assay against SARS-CoV-2 and other human coronaviruses To detect the presence of serological cross-reactivity against SARS-CoV-2 and other human coronaviruses, we used an immunofluorescence assay (IFA) against the spike and nucleocapsid proteins of SARS, SARS-CoV-2, MERS, HCoV-OC43, HCoV-HKU-1, HCoV-NL63 and HCoV-229E.

Techniques: Immunofluorescence, Expressing

Journal: International Journal of Infectious Diseases

Article Title: High prevalence of pre-existing serological cross-reactivity against SARS-CoV-2 in sub-Sahara Africa

doi: 10.1016/j.ijid.2020.10.104

Figure Lengend Snippet: Percent prevalence of serological cross-reactivity against SARS, MERS, HCoV-OC43, HCoV-HKU-1, HCoV-NL63 and HCoV-229E. (A) Spike. (B) Nucleocapsid.

Article Snippet: Immunofluorescence assay against SARS-CoV-2 and other human coronaviruses To detect the presence of serological cross-reactivity against SARS-CoV-2 and other human coronaviruses, we used an immunofluorescence assay (IFA) against the spike and nucleocapsid proteins of SARS, SARS-CoV-2, MERS, HCoV-OC43, HCoV-HKU-1, HCoV-NL63 and HCoV-229E.

Techniques:

Journal: bioRxiv

Article Title: Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients

doi: 10.1101/2020.06.15.153064

Figure Lengend Snippet: Response of a commercial anti-SARS-CoV-2 rabbit polyclonal antibody (pAb) on the array. (A) array exposed to array exposed to 20% FBS + 10% PNHS; (B) array exposed to 1 μg/mL anti-SARS-CoV-2 pAb in 20% FBS + 10% PNHS. Strong responses to SARS-CoV-2 S1+S2 ECD, S1, and RBD are observed, as well as smaller cross-reactive responses to HCoV-229E, HCoV-OC43, and MERS spike proteins; (C) quantitative data for the titration. Concentrations of pAb are provided at the top of each column in ng/mL; response values at each concentration for each antigen are provided in Angstroms of build. (D) Titration curves for the four SARS-CoV-2 antigens with standard deviation of replicate probe spots at each concentration.

Article Snippet: At the highest concentrations, significant cross-reactive binding to the HCoV-229E spike protein was observed, as well as some binding to the HCoV-OC43 spike protein and MERS S1.

Techniques: Titration, Concentration Assay, Standard Deviation

Journal: bioRxiv

Article Title: A human coronavirus evolves antigenically to escape antibody immunity

doi: 10.1101/2020.12.17.423313

Figure Lengend Snippet: The evolution of the 229E spike is clock-like, with the number of substitutions per site proportional to time. (A) Phylogenetic tree exactly like that in Figure 1 but with branch lengths proportional to divergence (not re-scaled based on tip isolation date). (B) A plot produced by TreeTime ( Sagulenko et al., 2018 ) showing the correlation between the distance of tip nodes from the root and sampling date. The fact that all points fall on a line indicates that the evolution is clock-like.

Article Snippet: Specifically, the 229E spike binds to human aminopeptidase N (APN) to initiate viral entry ( ).

Techniques: Isolation, Produced, Sampling

Journal: bioRxiv

Article Title: A human coronavirus evolves antigenically to escape antibody immunity

doi: 10.1101/2020.12.17.423313

Figure Lengend Snippet: The 229E spikes with a cytoplasmic tail deletion pseudotype lentiviral particles that efficiently infect 293T cells expressing the spike’s receptor aminopeptidase N (APN) and the activating protease TMPRSS2. (A) Titer in transduction units per ml as determined using flow cytometry of lentiviral particles pseudotyped with the full-length 2016 spike or that spike with a deletion of the last 19 residues in spike (the end of the cytoplasmic tail) on 293T cells transfected with a plasmid expressing APN. The dotted gray line is the limit of detection, and the titers in the absence of spike were below this line (undetectable). (B) Efficient entry by the pseudotyped virions depends on expression of APN and to a lesser extent TMPRSS2. Virions pseudotyped with the 2016 spike with the C-terminal deletion were infected into 293T cells transfected with plasmids expressing one or both of APN and TMPRSS2, and titers were determined by luciferase luminescence. Titers are normalized to one. (C) All of the 229E spikes and chimeras used in this study mediated efficient viral entry. Lentiviral particles were pseudotyped with the indicated spike (in all cases with the C-terminal deletion) and titers were determined using luciferase luminescence on 293T cells transfected with plasmids expressing APN and TMPRSS2.

Article Snippet: Specifically, the 229E spike binds to human aminopeptidase N (APN) to initiate viral entry ( ).

Techniques: Expressing, Transduction, Flow Cytometry, Transfection, Plasmid Preparation, Infection, Luciferase

Journal: bioRxiv

Article Title: A human coronavirus evolves antigenically to escape antibody immunity

doi: 10.1101/2020.12.17.423313

Figure Lengend Snippet: Although there is some evidence of recombination among closely related 229E spikes, this recombination does not alter the relative phylogenetic relationships among the spikes used in the experiments. Specifically, GARD ( Kosakovsky Pond et al., 2006 ; Spielman et al., 2019 ) was used to analyze the same set of 229E spike sequences used in Figure 1 with a nucleotide substitution model and three gamma-distributed rate classes. The best-fitting model had a single recombination breakpoint at nucleotide 1089 that improved the AIC by 60 units. The trees for each partition were then rooted and branch-re-scaled using TreeTime ( Sagulenko et al., 2018 ), and the resulting tanglegram was rendered using dendextend ( Galili, 2015 ). As can be seen above, the recombination is all between closely related sequences and does not alter the relative position of the 1984, 1992, 2001, 2008, and 2016 spikes used in the experiments. See https://github.com/jbloomlab/CoV_229E_antigenic_drift/blob/master/results/gard_tanglegram.md for details of the analysis steps described above.

Article Snippet: Specifically, the 229E spike binds to human aminopeptidase N (APN) to initiate viral entry ( ).

Techniques:

Journal: bioRxiv

Article Title: A human coronavirus evolves antigenically to escape antibody immunity

doi: 10.1101/2020.12.17.423313

Figure Lengend Snippet: Antigenic evolution is primarily due to changes in the spike’s receptor binding domain (RBD). (A) At top is a schematic of the 229E spike. Within the S1 subunit, the schematic indicates the N-terminal domain (NTD, also known as S1-A) and the RBD (also known as S1-B). The three loops in the RBD that bind the virus’s APN receptor are indicated ( Li et al., 2019 ). Below the schematic is a plot of sequence variability across the alignment of 229E spikes in Figure 1A . Variability is quantified as the effective number of amino acids at a site ( Echave and Wilke, 2017 ), with a value of one indicating complete conservation and larger values indicating more sequence variability. (B) Neutralizing titers of sera collected between 1985 and 1990 against either the full spike of “future” viruses or chimeras consisting of the 1984 spike containing the RBD from “future” viruses. The plot format and the black circles (full spike) are repeated from Figure 2A with the addition of the orange triangles showing the titers against the chimeric spikes.

Article Snippet: Specifically, the 229E spike binds to human aminopeptidase N (APN) to initiate viral entry ( ).

Techniques: Binding Assay, Sequencing

Journal: bioRxiv

Article Title: A human coronavirus evolves antigenically to escape antibody immunity

doi: 10.1101/2020.12.17.423313

Figure Lengend Snippet: Spikes used in this study. (A) Phylogenetic tree of 229E spikes, with tips colored by the country from which the virus was isolated. The spikes used in the experiments are indicated with black text and square shapes. The tree is a maximum-likelihood inference with IQ-TREE ( Minh et al., 2020 ) with a codon-substitution model and re-scaled with TreeTime ( Sagulenko et al., 2018 ) to position tips by to date of isolation. Figure S1 shows a tree with branch lengths proportional to divergence rather than time, and validates clock-like evolution. Figure S2 shows recombination does not substantially affect the phylogenetic placements of the spikes used in the experiments. (B) Protein sequence divergence of the spikes used in the experiments, computed over just the receptor-binding domain (RBD) or the full sequence. Divergence is the Levenshtein distance between the amino-acid sequences divided by the number of sites.

Article Snippet: Specifically, the 229E spike binds to human aminopeptidase N (APN) to initiate viral entry ( ).

Techniques: Isolation, Sequencing, Binding Assay

Journal: bioRxiv

Article Title: A human coronavirus evolves antigenically to escape antibody immunity

doi: 10.1101/2020.12.17.423313

Figure Lengend Snippet: Neutralization curves for all assays. Each facet is a serum, with titles indicating the year the serum was collected. Each point is the fraction infectivity at that serum concentration averaged across at least two replicates (error bars are standard error), with colors indicating the virus. The fits are 2-parameter Hill curves with baselines fixed to 1 and 0, and were fit using neutcurve ( https://jbloomlab.github.io/neutcurve/ ). IC50s are in File S3. The curves are also at https://github.com/jbloomlab/CoV_229E_antigenic_drift/blob/master/exptl_data/results/all_neut_by_sera.pdf

Article Snippet: Specifically, the 229E spike binds to human aminopeptidase N (APN) to initiate viral entry ( ).

Techniques: Neutralization, Infection, Concentration Assay