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

Megan Schwarz; Denis Torre; Daniel Lozano-Ojalvo; Anthony T. Tan; Tommaso Tabaglio; Slim Mzoughi; Rodrigo Sanchez-Tarjuelo; Nina Le Bert; Joey Ming Er Lim; Sandra Hatem; Kevin Tuballes; Carmen Camara; Eduardo Lopez-Granados; Estela Paz-Artal; Rafael Correa-Rocha; Alberto Ortiz; Marcos Lopez-Hoyos; Jose Portoles; Isabel Cervera; Maria Gonzalez-Perez; Irene Bodega-Mayor; Patricia Conde; Jesús Oteo-Iglesias; Alberto M. Borobia; Antonio J. Carcas; Jesús Frías; Cristóbal Belda-Iniesta; Jessica S.Y. Ho; Kemuel Nunez; Saboor Hekmaty; Kevin Mohammed; William M. Marsiglia; Juan Manuel Carreño; Arvin C. Dar; Cecilia Berin; Giuseppe Nicoletti; Isabella Della Noce; Lorenzo Colombo; Cristina Lapucci; Graziano Santoro; Maurizio Ferrari; Kai Nie; Manishkumar Patel; Vanessa Barcessat; Sacha Gnjatic; Jocelyn Harris; Robert Sebra; Miriam Merad; Florian Krammer; Seunghee Kim-schulze; Ivan Marazzi; Antonio Bertoletti; Jordi Ochando; Ernesto Guccione

doi:10.1038/s41587-022-01347-6

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

Megan Schwarz, Denis Torre, Daniel Lozano-Ojalvo, Anthony T. Tan, Tommaso Tabaglio, Slim Mzoughi, Rodrigo Sanchez-Tarjuelo, Nina Le Bert, Joey Ming Er Lim, Sandra Hatem, Kevin Tuballes, Carmen Camara, Eduardo Lopez-Granados, Estela Paz-Artal, Rafael Correa-Rocha, Alberto Ortiz, Marcos Lopez-Hoyos, Jose Portoles, Isabel Cervera, Maria Gonzalez-PerezIrene Bodega-Mayor, Patricia Conde, Jesús Oteo-Iglesias, Alberto M. Borobia, Antonio J. Carcas, Jesús Frías, Cristóbal Belda-Iniesta, Jessica S.Y. Ho, Kemuel Nunez, Saboor Hekmaty, Kevin Mohammed, William M. Marsiglia, Juan Manuel Carreño, Arvin C. Dar, Cecilia Berin, Giuseppe Nicoletti, Isabella Della Noce, Lorenzo Colombo, Cristina Lapucci, Graziano Santoro, Maurizio Ferrari, Kai Nie, Manishkumar Patel, Vanessa Barcessat, Sacha Gnjatic, Jocelyn Harris, Robert Sebra, Miriam Merad, Florian Krammer, Seunghee Kim-schulze, Ivan Marazzi, Antonio Bertoletti, Jordi Ochando, Ernesto Guccione

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	1680-1689
Number of pages	10
Journal	Nature Biotechnology
Volume	40
Issue number	11
DOIs	https://doi.org/10.1038/s41587-022-01347-6
State	Published - Nov 2022

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10.1038/s41587-022-01347-6

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Schwarz, M., Torre, D., Lozano-Ojalvo, D., Tan, A. T., Tabaglio, T., Mzoughi, S., Sanchez-Tarjuelo, R., Le Bert, N., Lim, J. M. E., Hatem, S., Tuballes, K., Camara, C., Lopez-Granados, E., Paz-Artal, E., Correa-Rocha, R., Ortiz, A., Lopez-Hoyos, M., Portoles, J., Cervera, I., ... Guccione, E. (2022). Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR. Nature Biotechnology, 40(11), 1680-1689. https://doi.org/10.1038/s41587-022-01347-6

@article{85637276ffeb4b3f9e3c7f8ba5e90f36,

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

abstract = "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.",

author = "Megan Schwarz and Denis Torre and Daniel Lozano-Ojalvo and Tan, {Anthony T.} and Tommaso Tabaglio and Slim Mzoughi and Rodrigo Sanchez-Tarjuelo and {Le Bert}, Nina and Lim, {Joey Ming Er} and Sandra Hatem and Kevin Tuballes and Carmen Camara and Eduardo Lopez-Granados and Estela Paz-Artal and Rafael Correa-Rocha and Alberto Ortiz and Marcos Lopez-Hoyos and Jose Portoles and Isabel Cervera and Maria Gonzalez-Perez and Irene Bodega-Mayor and Patricia Conde and Jes{\'u}s Oteo-Iglesias and Borobia, {Alberto M.} and Carcas, {Antonio J.} and Jes{\'u}s Fr{\'i}as and Crist{\'o}bal Belda-Iniesta and Ho, {Jessica S.Y.} and Kemuel Nunez and Saboor Hekmaty and Kevin Mohammed and Marsiglia, {William M.} and Carre{\~n}o, {Juan Manuel} and Dar, {Arvin C.} and Cecilia Berin and Giuseppe Nicoletti and {Della Noce}, Isabella and Lorenzo Colombo and Cristina Lapucci and Graziano Santoro and Maurizio Ferrari and Kai Nie and Manishkumar Patel and Vanessa Barcessat and Sacha Gnjatic and Jocelyn Harris and Robert Sebra and Miriam Merad and Florian Krammer and Seunghee Kim-schulze and Ivan Marazzi and Antonio Bertoletti and Jordi Ochando and Ernesto Guccione",

note = "Funding Information: Research reported in this publication was supported in part by an ISMMS seed fund to E.G. and a Dean{\textquoteright}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. S{\'a}nchez, J. Baranda, S. Baztan-Morales, M. Castillo de la Osa, A. Comins-Boo, C. del {\'A}lamo Mayo, S. Gil-Manso, B. Gonzalez, S. Hatem, J. Irure-Ventura, I. Miguens, S. Mu{\~n}oz Martinez, M. Pereira, C. Rodrigues-Guerreiro, M. Rodriguez-Garcia, M.P. Rojo-Portol{\'e}s 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 {\textquoteleft}A way to achieve Europe{\textquoteright} 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{\textquoteright}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. We acknowledge F. Buongiorno and S. Romano for technical help and B. Corneo, T. Blenkinsop, C. Schaniel, R. Kumar and M. Cerrone for help in coordinating recruitment. Funding Information: A.B., A.T. and N.L.B. declare the filling of a patent application relating to the use of peptide pools in whole blood for detection of SARS-CoV-2 T cells (pending). E.G., J.O., M.S., D.T. and D.L.O. declare the filling of a patent application relating to the qTACT and dqTACT assays (pending). S.G. reports consultancy and/or advisory roles for Merck and OncoMed, and research funding from Bristol-Myers Squibb, Celgene, Genentech, Immune Design, Janssen R&D, Pfizer, Regeneron and Takeda. G.N., I.D.N. and L.C. are employees of Hyris Ltd, manufacturer of the bCUBE machine described in this article. C.L., G.S. and M.F. are employees of Synlab Italy. The other authors declare no competing interests. Funding Information: Research reported in this publication was supported in part by an ISMMS seed fund to E.G. and a Dean{\textquoteright}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. S{\'a}nchez, J. Baranda, S. Baztan-Morales, M. Castillo de la Osa, A. Comins-Boo, C. del {\'A}lamo Mayo, S. Gil-Manso, B. Gonzalez, S. Hatem, J. Irure-Ventura, I. Miguens, S. Mu{\~n}oz Martinez, M. Pereira, C. Rodrigues-Guerreiro, M. Rodriguez-Garcia, M.P. Rojo-Portol{\'e}s 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 {\textquoteleft}A way to achieve Europe{\textquoteright} 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{\textquoteright}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. We acknowledge F. Buongiorno and S. Romano for technical help and B. Corneo, T. Blenkinsop, C. Schaniel, R. Kumar and M. Cerrone for help in coordinating recruitment. Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2022",

month = nov,

doi = "10.1038/s41587-022-01347-6",

language = "English",

volume = "40",

pages = "1680--1689",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "11",

}

Schwarz, M, Torre, D, Lozano-Ojalvo, D, Tan, AT, Tabaglio, T, Mzoughi, S, Sanchez-Tarjuelo, R, Le Bert, N, Lim, JME, Hatem, S, Tuballes, K, Camara, C, Lopez-Granados, E, Paz-Artal, E, Correa-Rocha, R, Ortiz, A, Lopez-Hoyos, M, Portoles, J, Cervera, I, Gonzalez-Perez, M, Bodega-Mayor, I, Conde, P, Oteo-Iglesias, J, Borobia, AM, Carcas, AJ, Frías, J, Belda-Iniesta, C, Ho, JSY, Nunez, K, Hekmaty, S, Mohammed, K, Marsiglia, WM, Carreño, JM, Dar, AC , Berin, C, Nicoletti, G, Della Noce, I, Colombo, L, Lapucci, C, Santoro, G, Ferrari, M, Nie, K , Patel, M, Barcessat, V, Gnjatic, S, Harris, J, Sebra, R, Merad, M, Krammer, F, Kim-schulze, S , Marazzi, I, Bertoletti, A, Ochando, J & Guccione, E 2022, 'Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR', Nature Biotechnology, vol. 40, no. 11, pp. 1680-1689. https://doi.org/10.1038/s41587-022-01347-6

TY - JOUR

T1 - Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR

AU - Schwarz, Megan

AU - Torre, Denis

AU - Lozano-Ojalvo, Daniel

AU - Tan, Anthony T.

AU - Tabaglio, Tommaso

AU - Mzoughi, Slim

AU - Sanchez-Tarjuelo, Rodrigo

AU - Le Bert, Nina

AU - Lim, Joey Ming Er

AU - Hatem, Sandra

AU - Tuballes, Kevin

AU - Camara, Carmen

AU - Lopez-Granados, Eduardo

AU - Paz-Artal, Estela

AU - Correa-Rocha, Rafael

AU - Ortiz, Alberto

AU - Lopez-Hoyos, Marcos

AU - Portoles, Jose

AU - Cervera, Isabel

AU - Gonzalez-Perez, Maria

AU - Bodega-Mayor, Irene

AU - Conde, Patricia

AU - Oteo-Iglesias, Jesús

AU - Borobia, Alberto M.

AU - Carcas, Antonio J.

AU - Frías, Jesús

AU - Belda-Iniesta, Cristóbal

AU - Ho, Jessica S.Y.

AU - Nunez, Kemuel

AU - Hekmaty, Saboor

AU - Mohammed, Kevin

AU - Marsiglia, William M.

AU - Carreño, Juan Manuel

AU - Dar, Arvin C.

AU - Berin, Cecilia

AU - Nicoletti, Giuseppe

AU - Della Noce, Isabella

AU - Colombo, Lorenzo

AU - Lapucci, Cristina

AU - Santoro, Graziano

AU - Ferrari, Maurizio

AU - Nie, Kai

AU - Patel, Manishkumar

AU - Barcessat, Vanessa

AU - Gnjatic, Sacha

AU - Harris, Jocelyn

AU - Sebra, Robert

AU - Merad, Miriam

AU - Krammer, Florian

AU - Kim-schulze, Seunghee

AU - Marazzi, Ivan

AU - Bertoletti, Antonio

AU - Ochando, Jordi

AU - Guccione, Ernesto

N1 - Funding Information: 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. We acknowledge F. Buongiorno and S. Romano for technical help and B. Corneo, T. Blenkinsop, C. Schaniel, R. Kumar and M. Cerrone for help in coordinating recruitment. Funding Information: A.B., A.T. and N.L.B. declare the filling of a patent application relating to the use of peptide pools in whole blood for detection of SARS-CoV-2 T cells (pending). E.G., J.O., M.S., D.T. and D.L.O. declare the filling of a patent application relating to the qTACT and dqTACT assays (pending). S.G. reports consultancy and/or advisory roles for Merck and OncoMed, and research funding from Bristol-Myers Squibb, Celgene, Genentech, Immune Design, Janssen R&D, Pfizer, Regeneron and Takeda. G.N., I.D.N. and L.C. are employees of Hyris Ltd, manufacturer of the bCUBE machine described in this article. C.L., G.S. and M.F. are employees of Synlab Italy. The other authors declare no competing interests. Funding Information: 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. We acknowledge F. Buongiorno and S. Romano for technical help and B. Corneo, T. Blenkinsop, C. Schaniel, R. Kumar and M. Cerrone for help in coordinating recruitment. Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2022/11

Y1 - 2022/11

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85131899160&partnerID=8YFLogxK

U2 - 10.1038/s41587-022-01347-6

DO - 10.1038/s41587-022-01347-6

M3 - Article

AN - SCOPUS:85131899160

SN - 1087-0156

VL - 40

SP - 1680

EP - 1689

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 11

ER -

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

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