Abstract
African swine fever virus (ASFV) has a major global economic impact. With a case fatality in domestic pigs approaching 100%, it currently presents the largest threat to animal farming. Although genomic differences between attenuated and highly virulent ASFV strains have been identified, the molecular determinants for virulence at the level of gene expression have remained opaque. Here we characterise the transcriptome of ASFV genotype II Georgia 2007/1 (GRG) during infection of the physiologically relevant host cells, porcine macrophages. In this study we applied Cap Analysis Gene Expression sequencing (CAGE-seq) to map the 5’ ends of viral mRNAs at 5 and 16 hpi. A bioinformatics analysis of the sequence context surrounding the transcription start sites (TSSs) enabled us to characterise the global early and late promoter landscape of GRG. We compared transcriptome maps of the GRG isolate and the lab-attenuated BA71V strain that highlighted GRG virulent-specific transcripts belonging to multigene families including two newly characterised MGF 100 genes I7L and I8L. Structural homology modelling suggest that I7L and I8L encode unorthodox SH2 domain proteins with the potential to interfere with the host’s immune response. In parallel, we monitored transcriptome changes in the infected host cells, which showed a pro-inflammatory immune response with the upregulation of NF-kB activated genes, innate immunity, as well as lysosome components including S100 proteins.
Author Summary African swine fever virus (ASFV) causes a haemorrhagic fever in domestic pigs and wild boar with mortality rates approaching 100%, for which there are no approved vaccines or antivirals. The highly-virulent ASFV Georgia 2007/1 strain was the first isolated when ASFV spread from Africa to the Caucasus region in 2007. From here it has spread through Eastern Europe, and more recently across Asia. We have used an RNA-based next generation sequencing technique called CAGE-seq to map the starts of viral genes across the ASFV Georgia 2007/1 strain DNA genome. This has allowed us to investigate how it controls its viral gene expression during different stages of infection in macrophage cells. We have characterised which genes are expressed at different levels during early or late stages of infection, and compared them to the non-virulent ASFV-BA71V strain to identify key genes that enhance virulence. We have discovered new genes, and predicted the likely roles of uncharacterised genes during ASFV infection. In parallel we have investigated how the host cells respond to ASFV infection, which has revealed how the virus early on suppresses components of the host immune response to ultimately win the arms race against its porcine host.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Corrected in-text figure references and figure order incorrect in pdf conversion.