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

Ogbe, Ane; Kronsteiner, Barbara; Skelly, Donal T.; Pace, Matthew; Brown, Anthony; Adland, Emily; Adair, Kareena; Akhter, Hossain Delowar; Ali, Mohammad; Ali, Serat-E; Angyal, Adrienn; Ansari, M. Azim; Arancibia-Cárcamo, Carolina V.; Brown, Helen; Chinnakannan, Senthil; Conlon, Christopher; de Lara, Catherine; de Silva, Thushan; Dold, Christina; Dong, Tao; Donnison, Timothy; Eyre, David; Flaxman, Amy; Fletcher, Helen; Gardner, Joshua; Grist, James T.; Hackstein, Carl-Philipp; Jaruthamsophon, Kanoot; Jeffery, Katie; Lambe, Teresa; Lee, Lian; Li, Wenqin; Lim, Nicholas; Matthews, Philippa C.; Mentzer, Alexander J.; Moore, Shona C.; Naisbitt, Dean J.; Ogese, Monday; Ogg, Graham; Openshaw, Peter; Pirmohamed, Munir; Pollard, Andrew J.; Ramamurthy, Narayan; Rongkard, Patpong; Rowland-Jones, Sarah; Sampson, Oliver; Screaton, Gavin; Sette, Alessandro; Stafford, Lizzie; Thompson, Craig; Thomson, Paul J.; Thwaites, Ryan; Vieira, Vinicius; Weiskopf, Daniela; Zacharopoulou, Panagiota; Turtle, Lance; Klenerman, Paul; Goulder, Philip; Frater, John; Barnes, Eleanor; Dunachie, Susanna

Identification of protective T cell responses against SARS-CoV-2 requires distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity to other coronaviruses. Here we show a range of T cell assays that differentially capture immune function to characterise SARS-CoV-2 responses. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) are found in 168 PCR-confirmed SARS-CoV-2 infected volunteers, but are rare in 119 uninfected volunteers. Highly exposed seronegative healthcare workers with recent COVID-19-compatible illness show T cell response patterns characteristic of infection. By contrast, >90% of convalescent or unexposed people show 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 assay and antigen selection. Memory responses to specific non-spike proteins provide a method to distinguish recent infection from pre-existing immunity in exposed populations.