Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2

References

• Deeks JJ, Dinnes J, Takwoingi Y, et al. Antibody tests for identification of current and past infection with SARS-CoV-2. Cochrane Database Syst Rev. 2020;6:CD013652.
   PubMedGoogle Scholar
• Kontou PI, Braliou GG, Dimou NL, et al. Antibody tests in detecting SARS-CoV-2 infection: a meta-analysis. Diagnostics (Basel). 2020;10(5):319.
   PubMedGoogle Scholar
• Hotop SK, Abd El Wahed A, Beutling U. et al. Serological analysis of Herpes B virus at individual epitope resolution: from two-dimensional peptide arrays to multiplex bead flow assays. Anal Chem. 2019;91(17):11030–11037.
   PubMed Web of Science ®Google Scholar
• Heiss K, Heidepriem J, Fischer N, et al. Rapid response to pandemic threats: immunogenic epitope detection of pandemic pathogens for diagnostics and vaccine development using peptide microarrays. J Proteome Res. 2020;19(11):4339–4354.
   PubMed Web of Science ®Google Scholar
• Szymczak LC, Kuo HY, Mrksich M. Peptide arrays: development and application. Anal Chem. 2018;90(1):266–282.
   PubMed Web of Science ®Google Scholar
• Jiang HW, Li Y, Zhang HN, et al. SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses. Nat Commun. 2020;11(1):3581.
   PubMed Web of Science ®Google Scholar
• Wang H, Wu X, Zhang X, et al. SARS-CoV-2 proteome microarray for mapping COVID-19 antibody interactions at amino acid resolution. ACS Cent Sci. 2020;6(12):2238–2249.
   PubMed Web of Science ®Google Scholar
• Yoshida S, Ono C, Hayashi H, et al. SARS-CoV-2-induced humoral immunity through B cell epitope analysis in COVID-19 infected individuals. Sci Rep. 2021;11(1):5934.
   PubMed Web of Science ®Google Scholar
• Heidepriem J, Dahlke C, Kobbe R, et al. Longitudinal development of antibody responses in COVID-19 patients of different severity with ELISA, peptide, and glycan arrays: an immunological case series. Pathogens. 2021;10(4):438.
   PubMed Web of Science ®Google Scholar
• Ladner JT, Henson SN, Boyle AS, et al. Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses. Cell Rep Med. 2021;2(1):100189.
   PubMedGoogle Scholar
• Mishra N, Huang X, Joshi S, et al. Immunoreactive peptide maps of SARS-CoV-2. Commun Biol. 2021;4(1):225.
   PubMed Web of Science ®Google Scholar
• Holenya P, Lange PJ, Reimer U, et al. Peptide microarray-based analysis of antibody responses to SARS-CoV-2 identifies unique epitopes with potential for diagnostic test development. Eur J Immunol. 2021;51(7):1839–1849.
   PubMed Web of Science ®Google Scholar
• Poh CM, Carissimo G, Wang B, et al. Two linear epitopes on the SARS-CoV-2 spike protein that elicit neutralising antibodies in COVID-19 patients. Nat Commun. 2020;11(1):2806.
   PubMed Web of Science ®Google Scholar
• Li Y, Lai DY, Zhang HN, et al. Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients. Cell Mol Immunol. 2020;17(10):1095–1097.
   PubMed Web of Science ®Google Scholar
• Heffron AS, McIlwain SJ, Amjadi MF, et al. The landscape of antibody binding in SARS-CoV-2 infection. PLoS Biol. 2021;19(6):e3001265.
   PubMed Web of Science ®Google Scholar
• Schwarz T, Heiss K, Mahendran Y, et al. SARS-CoV-2 proteome-wide analysis revealed significant epitope signatures in COVID-19 patients. Front Immunol. 2021;12:629185.
   PubMed Web of Science ®Google Scholar
• Frank R. Spot-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support. Tetrahedron. 1992;48(42):9217–9232.
   Web of Science ®Google Scholar
• Dikmans AB U, Schmeisser E, Thiele S, et al. SC2: a novel process for manufacturing multipurpose high-density chemical microarrays. QSAR Comb Sci. 2006;25(11):1069–1080.
   Google Scholar
• Wang TT, Lien CZ, Liu S, et al. Effective Heat Inactivation of SARS-CoV-2. medRxiv. 2020:2020.04.29.20085498.
   Google Scholar
• Pettersen EF, Goddard TD, Huang CC, et al. UCSF chimera–a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612.
   PubMed Web of Science ®Google Scholar
• Grifoni A, Weiskopf D, Ramirez SI, et al. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell. 2020;181(7):1489–1501. e15.
   PubMed Web of Science ®Google Scholar
• Lopandic Z, Protic-Rosic I, Todorovic A, et al. IgM and IgG immunoreactivity of SARS-CoV-2 recombinant M protein. Int J Mol Sci. 2021;22(9):4951.
   PubMed Web of Science ®Google Scholar
• Postler TS, Martinez-Navio JM, Yuste E, et al. Evidence against extracellular exposure of a highly immunogenic region in the C-terminal domain of the simian immunodeficiency virus gp41 transmembrane protein. J Virol. 2012;86(2):1145–1157.
   PubMed Web of Science ®Google Scholar
• Jespersen MC, Peters B, Nielsen M, et al. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017;45(W1):W24–W29.
   PubMed Web of Science ®Google Scholar
• Zhao P, Praissman JL, Grant OC, et al. Virus-receptor interactions of glycosylated SARS-CoV-2 spike and human ACE2 receptor. Cell Host Microbe. 2020;28(4):586–601 e6.
   PubMed Web of Science ®Google Scholar
• Roltgen K, Boyd SD. Antibody and B cell responses to SARS-CoV-2 infection and vaccination. Cell Host Microbe. 2021;29(7):1063–1075.
   PubMed Web of Science ®Google Scholar
• Marot S, Malet I, Leducq V, et al. Rapid decline of neutralizing antibodies against SARS-CoV-2 among infected healthcare workers. Nat Commun. 2021;12(1):844.
   PubMed Web of Science ®Google Scholar
• Arbour N, Cote G, Lachance C, et al. Acute and persistent infection of human neural cell lines by human coronavirus OC43. J Virol. 1999;73(4):3338–3350.
   PubMed Web of Science ®Google Scholar
• Vibholm LK, Nielsen SSF, Pahus MH, et al. SARS-CoV-2 persistence is associated with antigen-specific CD8 T-cell responses. EBioMedicine. 2021;64:103230.
   PubMed Web of Science ®Google Scholar
• Becker M, Strengert M, Junker D, et al. Exploring beyond clinical routine SARS-CoV-2 serology using MultiCoV-Ab to evaluate endemic coronavirus cross-reactivity. Nat Commun. 2021;12(1):1152.
   PubMed Web of Science ®Google Scholar
• Cook N, Xu L, Hegazy S, et al. Multiplex assessment of SARS-CoV-2 antibodies improves assay sensitivity and correlation with neutralizing antibodies. Clin Biochem. 2021;97:54–61.
   PubMed Web of Science ®Google Scholar
• Harvey WT, Carabelli AM, Jackson B, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19(7):409–424.
   PubMed Web of Science ®Google Scholar