Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron
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Issue Date
2022-05-24Author
Teng, I-Ting
Nazzari, Alexandra F.
Choe, Misook
Liu, Tracy
de Souza, Matheus Oliveira
Petrova, Yuliya
Tsybovsky, Yaroslav
Wang, Shuishu
Zhang, Baoshan
Artamonov, Mykhaylo
Madan, Bharat
Huang, Aric
Lopez Acevedo, Sheila N.
Pan, Xiaoli
Ruckwardt, Tracy J.
DeKosky, Brandon J.
Mascola, John R.
Misasi, John
Sullivan, Nancy J.
Zhou, Tongqing
Kwong, Peter D.
Publisher
Public Library of Science
Type
Article
Article Version
Scholarly/refereed, publisher version
Rights
This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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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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Citation
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
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Except where otherwise noted, this item's license is described as: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.