SARS-CoV-2 epitope mapping on microarrays highlights strong immune-response to N protein region

Musicò, Angelo; Frigerio, Roberto; Mussida, Alessandro; Barzon, Luisa; Sinigaglia, Alessandro; Riccetti, Silvia; Gobbi, Federico; Piubelli, Chiara; Bergamaschi, Greta; Chiari, Marcella; Gori, Alessandro; Cretich, Marina

doi:10.1101/2020.11.09.374082

Cited by 6 publications

(14 citation statements)

References 17 publications

(17 reference statements)

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“…The present investigation expands on previous reports that recognize various regions of the RNA binding domain of N protein as focal sites for anti-SARS-CoV-2 antibody response. For example, the phage display-based VirScan identified an epitope region spanning residues 141-196 and microarrays further isolated peptides including residues 134-171, 155-171, 153-190, and 153-171 (18,19,21). The above investigations, however, do not find correlations between any these epitopes and disease severity.…”

Section: Discussionmentioning

confidence: 95%

“…Previously, α N IgGs have been recognized as a focal site for an antibody response (18,19,21,36) and associated with disease severity and poor outcomes (11,36,37).…”

Section: Discussionmentioning

confidence: 99%

“…The epitopes for N, M or E proteins are less well-characterized than for S protein. Several studies have reported comprehensive epitope mapping of the antibody response to SARS-CoV-2 (18)(19)(20)(21). Here, we sought to characterize epitopes from SARS-CoV-2 and their correlations with disease severity.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score

Sen

Sanders

Gabriel

et al. 2020

Preprint

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Characterization of antibody response to SARS-CoV-2 is urgently needed to predict COVID-19 disease trajectories. Ineffective antibodies or antibody-dependent enhancement (ADE) could derail patient immune responses, for example. ELISA and coronavirus antigen microarray (COVAM) analysis epitope-mapped plasma from 86 COVID-19 patients. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including ICU stay, requirement for ventilators, and death. Furthermore, anti-Ep9 antibodies correlate both with various comorbidities and ADE hallmarks, including increased IL-6 levels and early IgG response. Importantly, anti-Ep9 antibodies can be detected within five days post-symptom onset and sometimes within one day. The results lay the groundwork for a new type of COVID-19 diagnostic for the early prediction of disease severity to guide more effective therapeutic interventions.

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Section: Discussionmentioning

confidence: 95%

“…Previously, α N IgGs have been recognized as a focal site for an antibody response (18,19,21,36) and associated with disease severity and poor outcomes (11,36,37).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score

Sen

Sanders

Gabriel

et al. 2020

Preprint

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“…Illustration of the predicted Spike protein epitopes which have overlapped with one or more frequently mutated Spike protein residues (Cun, Li et al 2020, He, Huang et al 2020, Li, Lai et al 2020, Mishra, Huang et al 2020, Poh, Carissimo et al 2020, Shomuradova, Vagida et al 2020, Wang, Wu et al 2020, Yarmarkovich, Warrington et al 2020, Yi, Ling et al 2020, Musico, Frigerio et al 2021). The countries in which they were found to be prevalent post lockdown have been mentioned alongside.…”

Section: Resultsmentioning

confidence: 99%

“…A number of studies have been carried out for speedy engineering of vaccines against the SARS-CoV-2 virus. We selected eight studies which have experimentally determined potential immune-responsive epitopes owing to several viral proteins, of which we are interested especially with the epitopes delegated towards the Spike protein (Farrera-Soler, Daguer et al 2020, Li, Lai et al 2020, Mishra, Huang et al 2020, Poh, Carissimo et al 2020, Shomuradova, Vagida et al 2020, Wang, Wu et al 2020, Yi, Ling et al 2020, Musico, Frigerio et al 2021) ( Supplementary Table 5a) . Several studies have used in-silico approaches to predict T-cell and B-cell epitopes that could potentially be employed to trigger immune responses in the host.…”

Section: Methodsmentioning

confidence: 99%

Country specific mutational profile of SARS-CoV-2 in pre- and post-international travel ban: Effect on vaccine efficacy

Laha

Chatterjee

2021

Preprint

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In order to curb the rapid transmission of SARS-CoV-2, nation-wide lockdowns were implemented as a preliminary measure. Since most countries enforced travel-bans during end of March 2020, the country-specific patterns should be discernible in the subsequent months. We identified frequently mutated non-synonymous mutations in 2,15,000 SARS-CoV-2 sequences during pre and post-travel-ban periods in 35 countries. We further investigated the mutational profile on a bi-monthly basis and traced the progress over the time. Several new mutations have emerged post-travel-ban and on the rise in specific countries, chief among them being A222V and S477N in Spike, and A220V in Nucleocapsid protein. Consequently, we examined the Spike protein epitopes to inspect whether any of these country-specific mutations overlapped with these epitopes. Several mutations were found to be contained within one or more epitopes, including the highly mutated residues of Spike protein, advocating the requirement of active monitoring of vaccine efficacies in respective countries.

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Immunoinformatics and Pepscan strategies on the path of a peptide-based serological diagnosis of COVID19

Lorenzo

Pachón

Maier

et al. 2021

Journal of Immunological Methods

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Several diagnostic tools have been developed for clinical and epidemiological assays. RT-PCR and antigen detection tests are more useful for diagnosis of acute disease, while antibody tests allow the estimation of exposure in the population. Currently, there is an urgent need for the development of diagnostic tests for COVID-19 that can be used for large-scale epidemiological sampling. Through a comprehensive strategy, potential 16 mer antigenic peptides suited for antibody-based SARS-CoV-2 diagnosis were identified. A systematic scan of the three structural proteins (S,N and M) and the non-structural proteins (ORFs) present in the SARS-CoV-2 virus was conducted through the combination of immunoinformatic methods, peptide SPOT synthesis and an immunoassay with cellulose-bound peptides (Pepscan). The Pepscan filter paper sheets with synthetic peptides were tested against pools of sera of COVID-19 patients. Antibody recognition showed a strong signal for peptides corresponding to the S, N and M proteins of SARS-CoV-2 virus, but not for the ORFs proteins. The peptides exhibiting higher signal intensity were found in the C -terminal region of the N protein. Several peptides of this region showed strong recognition with all three immunoglobulins in the pools of sera. The differential reactivity observed between the different immunoglobulin isotypes (IgA, IgM and IgG) within different regions of the S and N proteins, can be advantageous for ensuring accurate diagnosis of all infected patients, with different times of exposure to infection. Few peptides of the M protein showed antibody recognition and no recognition was observed for peptides of the ORFs proteins.

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SARS-CoV-2 epitope mapping on microarrays highlights strong immune-response to N protein region

Cited by 6 publications

References 17 publications

Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score

Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score

Country specific mutational profile of SARS-CoV-2 in pre- and post-international travel ban: Effect on vaccine efficacy

Immunoinformatics and Pepscan strategies on the path of a peptide-based serological diagnosis of COVID19

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