Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
A deeper understanding of the molecular determinants that drive humoral responses to coronaviruses, and in particular severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is critical for improving and developing diagnostics, therapies and vaccines. Moreover, viral mutations can change key antigens in a manner that alters the ability of the immune system to detect and clear infections. In this study, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses of asymptomatic or recovered COVID-19-positive patients relative to COVID-19-negative patients. We made use of a novel high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 and endemic human coronaviruses to rapidly identify B cell epitopes recognized by distinct antibody isotypes in patients’ blood sera. Using our integrated computational pipeline, we then evaluated the fine immunological properties of detected SARS-CoV-2 epitopes and relate them to their evolutionary and structural properties. While some epitopes are common across all CoVs, others are private to specific hCoVs. We also highlight the existence of hotspots of pre-existing immunity and identify a subset of cross-reactive epitopes that contributes to increasing the overall humoral immune response to SARS-CoV-2. Using a public dataset of over 38,000 viral genomes from the early phase of the pandemic, capturing both inter- and within-host genetic viral diversity, we determined the evolutionary profile of epitopes and the differences across proteins, waves and SARS-CoV-2 variants, which have important implications for genomic surveillance and vaccine design. Lastly, we show that mutations in Spike and Nucleocapsid epitopes are under stronger selection between than within patients, suggesting that most of the selective pressure for immune evasion occurs upon transmission between hosts.
Article activity feed
-
SciScore for 10.1101/2022.06.01.494373: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources High-density peptide array (HDPA): To analyze the antibody responses to SARS-CoV-2 at the epitope level we used a recently developed high-density peptide array (HDPA), the PEPperCHIP® Microarray (PEPperPRINT GmbH, Germany), covering the proteome of the SARS-CoV-2 isolate Wuhan-Hu-1 as well as the four seasonal hCoVs OC43, HKU1, NL63 and 229E (see Table S12 for accession numbers used). HKU1suggested: NoneMicroarrays were then washed (three times with PBS-T for 1 minute) and peptide binding was detected with isotype-specific secondary goat anti-human IgG (Fc) DyLight680 (ThermoFisher Scientific) and goat … SciScore for 10.1101/2022.06.01.494373: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources High-density peptide array (HDPA): To analyze the antibody responses to SARS-CoV-2 at the epitope level we used a recently developed high-density peptide array (HDPA), the PEPperCHIP® Microarray (PEPperPRINT GmbH, Germany), covering the proteome of the SARS-CoV-2 isolate Wuhan-Hu-1 as well as the four seasonal hCoVs OC43, HKU1, NL63 and 229E (see Table S12 for accession numbers used). HKU1suggested: NoneMicroarrays were then washed (three times with PBS-T for 1 minute) and peptide binding was detected with isotype-specific secondary goat anti-human IgG (Fc) DyLight680 (ThermoFisher Scientific) and goat anti-human IgA (alpha chain) DyLight800 (Rockland Immunochemicals) antibodies at a final concentration of 0.1 μg/ml and 1 μg/ml, respectively (in 10% RL/PBS-T for 45 minutes at room temperature). anti-human IgGsuggested: (Rockland Cat# 609-145-130, RRID:AB_2614820)anti-human IgAsuggested: (Rockland Cat# 609-145-130, RRID:AB_2614820)To identify the top IgG and IgA antibody responses of the human serum samples, the averaged intensity values were sorted by decreasing spot intensities. IgAsuggested: NoneSoftware and Algorithms Sentences Resources Using ImageJ software the resulting 32-bit gray-scale TIFF files were converted into 16-bit gray-scale TIFF files and then further analyzed using the PepSlide® Analyzer (SICASYS ImageJsuggested: (ImageJ, RRID:SCR_003070)Pymol was used for visualization. Pymolsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Sensitivity limitations of PhIP-seq to broadly detected polio epitopes have been previously reported (20, 22) and might contribute to the observed differences, similarly affecting detectability of CoV antigens. Such limitations are not observed in our HDPA approach (44) which typically yielded strong polio responsiveness in over 90% of sampled individuals (45). Importantly, the cross-reactivity in identified B cell epitope sites positively relates to previous infections with seasonal common cold hCoVs. This suggests that immune memory conferred by previous seasonal hCoV infections positively influences SARS-CoV-2-specific antibody responses and may explain the large portion of SARS-CoV-2-infected individuals with mild and asymptomatic disease symptoms (4). Notably, there was little to no correlation between cross-reactivity and immune response in COVID-19 negative patients, suggesting that resistance to infection is not easily explained by cross reactivity. However, this molecular cross-reactivity can pose important complications in serological tests, particularly when studying asymptomatic patients. Cross-reactivity in immunodominant epitopes can be molecular determinants of strong immunity in individuals and therefore may serve as the basis for future pan-coronavirus vaccine design strategies. In turn, mutations in these cross-reactive epitopes can potentially breach pre-existing immune protection conferred by previous viral exposures, contributing to viral evolution, immun...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
