Representative images of the Comb-CODEX-RNAscope where all pretreatments of CODEX and RNAscope were combined together at the beginning of the experiment. (A) Overview image of lymph node tissues from a rhesus macaque infected with SIVmac251 (Rh4979, 10 dpi), showing CD3 (red), CD20 (green), and DAPI (blue). Scale bar equals 500 microns. (B) The boxed area in A was zoomed to show SIV viral RNA detected by RNAscope and other seven protein markers by CODEX. Scale bar equals 50 microns. (C–L) Individual channel image showing vRNA and protein biomarkers. Scale bar equals 50 microns. Abbreviations: CODEX, CO-detection by indexing; DAPI, 4′,6-diamidino-2-phenylindole; SIV, simian immunodeficiency virus.