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Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron
Teng, I-Ting Nazzari, Alexandra F. Choe, Misook Liu, Tracy de Souza, Matheus Oliveira Petrova, Yuliya Tsybovsky, Yaroslav Wang, Shuishu Zhang, Baoshan Artamonov, Mykhaylo
Teng, I-Ting
Nazzari, Alexandra F.
Choe, Misook
Liu, Tracy
de Souza, Matheus Oliveira
Petrova, Yuliya
Tsybovsky, Yaroslav
Wang, Shuishu
Zhang, Baoshan
Artamonov, Mykhaylo
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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.
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2022-05-24
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Public Library of Science
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Teng_2022.pdf
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Teng I-T, Nazzari AF, Choe M, Liu T, Oliveira de Souza M, Petrova Y, et al. (2022) Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron. PLoS ONE 17(5): e0268767. https://doi.org/10.1371/journal.pone.0268767