Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR

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Fast, high-throughput methods for measuring the level and duration of protective immune responses to SARS-CoV-2 are needed to anticipate the risk of breakthrough infections. Here we report the development of two quantitative PCR assays for SARS-CoV-2-specific T cell activation. The assays are rapid, internally normalized and probe-based: qTACT requires RNA extraction and dqTACT avoids sample preparation steps. Both assays rely on the quantification of CXCL10 messenger RNA, a chemokine whose expression is strongly correlated with activation of antigen-specific T cells. On restimulation of whole-blood cells with SARS-CoV-2 viral antigens, viral-specific T cells secrete IFN-γ, which stimulates monocytes to produce CXCL10. CXCL10 mRNA can thus serve as a proxy to quantify cellular immunity. Our assays may allow large-scale monitoring of the magnitude and duration of functional T cell immunity to SARS-CoV-2, thus helping to prioritize revaccination strategies in vulnerable populations.
Research reported in this publication was supported in part by an ISMMS seed fund to E.G. and a Dean’s office grant to E.G. and I.M. We gratefully acknowledge use of the services and facilities of the Tisch Cancer Institute supported by the National Cancer Institute (NCI) Cancer Center Support grant (no. P30 CA196521), in particular the Hess sequencing core and the BiNGS shared facility. M.S. was supported by an NCI training grant (no. T32CA078207). J.S.Y.H. is supported by the Charles H. Revson Foundation. We acknowledge the technical contribution of D.A. Sánchez, J. Baranda, S. Baztan-Morales, M. Castillo de la Osa, A. Comins-Boo, C. del Álamo Mayo, S. Gil-Manso, B. Gonzalez, S. Hatem, J. Irure-Ventura, I. Miguens, S. Muñoz Martinez, M. Pereira, C. Rodrigues-Guerreiro, M. Rodriguez-Garcia, M.P. Rojo-Portolés and D. San Segundo. We also acknowledge Beckman Coulter for donating the equipment required for the determination of spike-specific IgG antibodies. W.M. was supported by grant no. NCI K00CA212474. This work was supported by ISMMS seed fund to J.O.; Instituto de Salud Carlos III, grant no. COV20-00668 to R.C.R.; Instituto de Salud Carlos III, Spanish Ministry of Science and Innovation (COVID-19 Research Call grant no. COV20/00181) cofinanced by European Development Regional Fund ‘A way to achieve Europe’ to E.P.-A.; Instituto de Salud Carlos III, Spain (grant no. COV20/00170); Government of Cantabria, Spain (grant no. 2020UIC22-PUB-0019) to M.L.H.; Instituto de Salud Carlos III (grant no. PI16CIII/00012) to P.P.; Fondo Social Europeo e Iniciativa de Empleo Juvenil YEI (grant no. PEJ2018-004557-A) to M.P.E. and grant no. REDInREN 016/009/009 ISCIII. This project has received funding from the European Union’s Horizon 2020 research and innovation program VACCELERATE under grant agreement no. 101037867 to J.O. S.G. is supported by grant nos. U24CA224319, U01DK124165 and P30 CA196521.