SARS-CoV-2 host-shutoff impacts innate NK cell functions, but antibody-dependent NK activity is strongly activated through non-spike antibodies

Fielding, C. A. et al. (2022) SARS-CoV-2 host-shutoff impacts innate NK cell functions, but antibody-dependent NK activity is strongly activated through non-spike antibodies. eLife, 11, e74489. (doi: 10.7554/elife.74489) (PMID:35587364) (PMCID:PMC9239683)

Abstract

The outcome of infection is dependent on the ability of viruses to manipulate the infected cell to evade immunity, and the ability of the immune response to overcome this evasion. Understanding this process is key to understanding pathogenesis, genetic risk factors, and both natural and vaccine-induced immunity. SARS-CoV-2 antagonises the innate interferon response, but whether it manipulates innate cellular immunity is unclear. An unbiased proteomic analysis determined how cell surface protein expression is altered on SARS-CoV-2-infected lung epithelial cells, showing downregulation of activating NK ligands B7-H6, MICA, ULBP2, and Nectin1, with minimal effects on MHC-I. This occurred at the level of protein synthesis, could be mediated by Nsp1 and Nsp14, and correlated with a reduction in NK cell activation. This identifies a novel mechanism by which SARS-CoV-2 host-shutoff antagonises innate immunity. Later in the disease process, strong antibody-dependent NK cell activation (ADNKA) developed. These responses were sustained for at least 6 months in most patients, and led to high levels of pro-inflammatory cytokine production. Depletion of spike-specific antibodies confirmed their dominant role in neutralisation, but these antibodies played only a minor role in ADNKA compared to antibodies to other proteins, including ORF3a, Membrane, and Nucleocapsid. In contrast, ADNKA induced following vaccination was focussed solely on spike, was weaker than ADNKA following natural infection, and was not boosted by the second dose. These insights have important implications for understanding disease progression, vaccine efficacy, and vaccine design.

• Item Type: Articles
• Additional Information: This work was partly funded by the MRC/NIHR through the UK Coronavirus Immunology Consortium (CiC; MR/V028448/1). RS was supported by the MRC (MR/S00971X/1), Wellcome Trust (204870/Z/16/Z), and Ser Cymru. ECYW was funded by the MRC (MR/P001602/1, MR/V000489/1). PJL was funded by the Wellcome Trust through a Principal Research Fellowship (210688/Z/18/Z), the MRC (MR/V011561/1), the Addenbrooke’s Charitable Trust and the NIHR Cambridge Biomedical Research Centre. KLD was supported by King’s Together Rapid COVID-19 Call, Huo Family Foundation Award, and a Wellcome Trust Multi-User Equipment Grant 208354/Z/17/Z. CG was supported by the MRC-KCL Doctoral Training Partnership in Biomedical Sciences (MR/N013700/1). BM was supported by an NIHR Academic Clinical Fellowship in Combined Infection Training.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Wilson, Professor Sam
• Authors: Fielding, C. A., Sabberwal, P., Williamson, J. C., Greenwood, E. J. D., Crozier, T. W. M., Zelek, W., Seow, J., Graham, C., Huettner, I., Edgeworth, J. D., Price, D. A., Morgan, B. P., Ladell, K., Eberl, M., Humphreys, I. R., Merrick, B., Doores, K., Wilson, S. J., Lehner, P. J., Wang, E. C. Y., and Stanton, R. J.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: eLife
• Publisher: eLife Sciences Publications
• ISSN: 2050-084X
• ISSN (Online): 2050-084X
• Published Online: 19 May 2022
• Copyright Holders: Copyright © 2022 Fielding et al.
• First Published: First published in eLife 11: e74489
• Publisher Policy: Reproduced under a Creative Commons License