Two waves of activation drive systemic innate immune responses to alphavirus infection

Using mutant viruses with altered lymph node (LN) tropism, we show that the extent of VEEV LN infection is positively associated with systemic induction of IFN-I and other proinflammatory cytokines.

Further, robust IFN-I induction requires coordinated activation of multiple IRF-7-dependent pathways, with Toll-like receptor (TLR) and RIG-I-like receptor (RLR) pathways playing distinct, nonredundant roles. Combining targeted cell depletion and Visium HD spatial transcriptomics, we uncover a two-wave innate immune response to infection in vivo, with early cytokine induction driven by VEEV-infected myeloid cells at 8 hours post-infection (hpi), and a second wave dominated by uninfected bystander cells once active infection in the LN subsides by 16hpi.