Characterization of the African Swine Fever Virus transcriptome and the associated innate immune response reveals key features of virulence

African Swine Fever Virus (ASFV) represents a looming threat to animal health, food safety and to the livestock industry. Virulent strains of ASFV cause a severe and often fatal illness, while attenuated strains are usually associated with mild symptoms. Naturally-occurring attenuated strains are typically deleted of more than 20 genes located at the viral genome’s extremities. Whether other key differences between virulent and attenuated ASFV strains may contribute to the virulence phenotype remains however largely unexplored. In this work, we sought to determine how the dynamics of viral gene expression may shape the host’s innate immune response to ASFV infection and contribute to ASFV virulence. We conducted a medium-throughput transcriptomic study to characterize the viral transcriptome of a panel of virulent and attenuated strains (171 viral genes), as well as the host response of ASFV-infected macrophages (92 host genes). Our results indicate that the two viral pathotypes exhibit global differences in the dynamics of genome replication and viral transcription. Virulent ASFV strains displayed a burst of viral transcription early on, while attenuated strains tended to replicate to higher levels at late time points. The host response was much more pronounced in cells infected with attenuated strains compared to virulent ones, with higher expression levels of some interferon-stimulated gene and innate immunity sensors; and of the inducible chaperone HSP70.2, among others. Unexpectedly, genotype I and genotype II virulent strains exhibited some notable differences in viral genome replication kinetics and in the host response they provoked, with higher levels of pro-inflammatory cytokines being induced by genotype II strains. Confocal imaging analysis of ASFV-infected primary macrophages revealed that attenuated strains induced a much stronger NF-kB response than virulent ones, as evidenced by the levels of p65 translocation to the nucleus. We identified a group of 26 viral genes that were either expressed at higher levels or at an earlier stage of infection by virulent strains. Two viral factors from this group, R298L and H233R, inhibit the type I Interferon response in a reporter cell line system, and may thus represent novel virulence factors. This work sheds new light on the mechanistical drivers of ASFV virulence and may in the long run help to better understand the protection offered by ASFV Live-Attenuated Vaccine candidates.