T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses

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Ane Ogbe

University of Oxford

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Barbara Kronsteiner

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Donal T. Skelly

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Matthew Pace

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Anthony Brown

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Emily Adland

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Kareena Adair

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Hossain Delowar Akhter

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Mohammad Ali

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Serat-E Ali

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Adrienn Angyal

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M. Azim Ansari

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Carolina V Arancibia-Carcamo

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Helen Brown

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Senthil Chinnakannan

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Christopher P Conlon

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Catherine de Lara

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Thushan de Silva

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Christina Dold

Oxford Vaccine Group, University of Oxford

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Tao Dong Dong

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Timothy Donnison

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David W Eyre

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Amy Flaxman

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Helen A Fletcher

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Joshua Gardner

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James T Grist

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Carl-Philipp Hackstein

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Kanoot Jaruthamsophon

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Katie Jeffrey

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Teresa Lambe

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Lian Lee

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Wenqin Li

Lawrence Livermore National Laboratory

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Nicholas Lim

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Philippa C Matthews

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Alexander J Mentzer

Group Leader, Wellcome Centre for Human Genetics, University of Oxford

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Shona C. Moore

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Dean J Naisbitt

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Monday Ogese

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Graham Ogg

Oxford University Hospitals

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Peter Openshaw

Professor of Experimental Medicine

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Munir Pirmohamed

University of Liverpool

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Andrew J. Pollard

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Narayan Ramamurthy

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Patpong Rongkard

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Sarah Rowland-Jones

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Oliver L Sampson

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Gavin Screaton

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Alessandro Sette

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Lizzie Stafford

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Craig Thompson

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Paul J Thomson

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Ryan Thwaites

Imperial College London

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Vinicius Vieira

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Daniela Weiskopf

La Jolla Institute for Immunology

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Panagiota Zacharopoulou

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Lance Turtle

University of Liverpool

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Paul Klenerman

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Philip Goulder

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John Frater

University of Oxford

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Eleanor Barnes

Oxford University

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Susanna Dunachie

NIHR Global Research Professor, University of Oxford

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A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.

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