{"doi":"10.1371/journal.pone.0268767","title":"Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron","abstract":"Since the outbreak of the COVID-19 pandemic, widespread infections have allowed SARS-CoV-2 to evolve in human, leading to the emergence of multiple circulating variants. Some of these variants show increased resistance to vaccine-elicited immunity, convalescent plasma, or monoclonal antibodies. In particular, mutations in the SARS-CoV-2 spike have drawn attention. To facilitate the isolation of neutralizing antibodies and the monitoring of vaccine effectiveness against these variants, we designed and produced biotin-labeled molecular probes of variant SARS-CoV-2 spikes and their subdomains, using a structure-based construct design that incorporated an N-terminal purification tag, a specific amino acid sequence for protease cleavage, the variant spike-based region of interest, and a C-terminal sequence targeted by biotin ligase. These probes could be produced by a single step using in-process biotinylation and purification. We characterized the physical properties and antigenicity of these probes, comprising the N-terminal domain (NTD), the receptor-binding domain (RBD), the RBD and subdomain 1 (RBD-SD1), and the prefusion-stabilized spike ectodomain (S2P) with sequences from SARS-CoV-2 variants of concern or of interest, including variants Alpha, Beta, Gamma, Epsilon, Iota, Kappa, Delta, Lambda, Mu, and Omicron. We functionally validated probes by using yeast expressing a panel of nine SARS-CoV-2 spike-binding antibodies and confirmed sorting capabilities of variant probes using yeast displaying libraries of plasma antibodies from COVID-19 convalescent donors. We deposited these constructs to Addgene to enable their dissemination. Overall, this study describes a matrix of SARS-CoV-2 variant molecular probes that allow for assessment of immune responses, identification of serum antibody specificity, and isolation and characterization of neutralizing antibodies.","journal":"PLoS ONE","year":2022,"id":249003,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":29,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9493,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":229154,"name":"Alexandra F. Nazzari","orcid":"0000-0003-1891-8541","position":1,"is_corresponding":false},{"id":293305,"name":"Misook Choe","orcid":null,"position":2,"is_corresponding":false},{"id":622891,"name":"Tracy Liu","orcid":"0000-0003-0671-8390","position":3,"is_corresponding":false},{"id":302420,"name":"Matheus Oliveira de Souza","orcid":"0000-0003-0357-1995","position":4,"is_corresponding":false},{"id":303498,"name":"Yuliya Petrova","orcid":null,"position":5,"is_corresponding":false},{"id":229148,"name":"Yaroslav Tsybovsky","orcid":"0000-0002-2159-5248","position":6,"is_corresponding":false},{"id":229157,"name":"Shuishu Wang","orcid":"0000-0002-0865-4522","position":7,"is_corresponding":false},{"id":229158,"name":"Baoshan Zhang","orcid":"0000-0002-0165-1513","position":8,"is_corresponding":false},{"id":889067,"name":"Mykhaylo Artamonov","orcid":"0000-0002-0848-2054","position":9,"is_corresponding":false},{"id":302419,"name":"Bharat Madan","orcid":"0000-0002-7376-9991","position":10,"is_corresponding":false},{"id":506740,"name":"Aric Huang","orcid":"0000-0001-8203-4818","position":11,"is_corresponding":false},{"id":302418,"name":"Sheila N. López Acevedo","orcid":"0000-0003-2778-4696","position":12,"is_corresponding":false},{"id":302421,"name":"Xiaoli Pan","orcid":"0000-0002-5033-7272","position":13,"is_corresponding":false},{"id":105610,"name":"Tracy J. Ruckwardt","orcid":"0000-0002-0007-7169","position":14,"is_corresponding":false},{"id":108827,"name":"Brandon J. DeKosky","orcid":"0000-0001-6406-0836","position":15,"is_corresponding":false},{"id":105614,"name":"John R. Mascola","orcid":"0000-0002-5293-4695","position":16,"is_corresponding":false},{"id":302423,"name":"John Misasi","orcid":"0000-0001-7169-2639","position":17,"is_corresponding":false},{"id":266889,"name":"Nancy J. Sullivan","orcid":"0000-0002-2159-2039","position":18,"is_corresponding":false},{"id":105631,"name":"Tongqing Zhou","orcid":"0000-0002-3935-4637","position":19,"is_corresponding":false},{"id":105633,"name":"Peter D. 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