Single-cell spatial immune landscape of ASFV-infected porcine lung microenvironment

African swine fever virus (ASFV) infection leads to severe lung lesions in the host, yet detailed insights into the in vivo immune response of the lung microenvironment to ASFV infection at the single-cell level remain limited. Here, we mapped the spatial immune landscape of the porcine lung microenvironment upon ASFV infection at single-cell resolution using an in situ multi-gene mRNA co-detection method. We delineated the transcriptional dynamics of candidate genes in different immune cell types within the pig lungs upon ASFV infection. Additionally, we observed the dynamic changes in the number and spatial distribution of specific immune cell types in the lung microenvironment during ASFV infection. Moreover, the expression correlation between viral multi-gene family genes and host genes related to antiviral responses and apoptosis was identified. Our findings highlight the impact of viral genes on the host lung microenvironment and the complex viral-host interactions, providing insights into ASFV immune responses in porcine lungs at an in vivo level.