Zombie fixable viability stain

Cells were washed in PBS and resuspended in PBS with Zombie Fixable Viability Stain (Biolegend, #423102, #423103) as per the manufacturer’s protocol. Antibodies for surface staining were then diluted into FACS buffer (PBS + 2% FBS + 2 mM EDTA) and added to the cells. The staining panel consisted of APC/Cy7-conjugated anti-CD3 (Biolegend, #344818), PE/Cy7-conjugated anti-CD4 (Biolegend #357410) and APC-conjugated anti-CD8 (Biolegend, #344722). Stained cells were washed in FACS buffer and fixed in 1% paraformaldehyde prior to analysis. Samples were run on an LSRII cytometer (BD Biosciences). Data were analyzed using the FlowJo V10 Software (Treestar). All flow cytometric datasets were pre-gated from a lymphocyte scatter gate (FSC vs. SSC) to identify singlet cells, and then sequentially gated on live cells (Zombie negative/low) and CD3⁺CD8⁻ T cells. Productively infected cells were identified as GFP+ cells. The gating strategy is illustrated in Supplementary Fig. S2.