Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron
Name
journal.pone.0268767.pdf
Description
Published version
Size
6.03 MB
Format
Adobe PDF
Checksum (MD5)
bcbdc23f7bf4c3d572c62cc7806fd8e5
Author(s)
Teng, I-Ting
Nazzari, Alexandra F
Choe, Misook
Liu, Tracy
Oliveira de Souza, Matheus
Petrova, Yuliya
Tsybovsky, Yaroslav
Wang, Shuishu
Zhang, Baoshan
Artamonov, Mykhaylo
Date Issued
2022
Journal
PLoS ONE
Publisher
Public Library of Science (PLoS)
Citation
Teng, I-Ting, Nazzari, Alexandra F, Choe, Misook, Liu, Tracy, Oliveira de Souza, Matheus et al. 2022. "Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron." PLoS ONE, 17 (5).
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1371/JOURNAL.PONE.0268767
