Porcine reproductive and respiratory syndrome virus (PRRSV) mainly infects porcine alveolar macrophages (PAMs), resulting in
porcine reproductive and respiratory syndrome (
PRRS) in pigs. Most of the transcriptomic studies on PAMs infected with PRRSV conducted thus far have made use of microarray technology. Here, we investigated the transcriptome of PAMs in vitro at 12 h post-
infection with two European PRRSV strains characterized by low (Lelystad, LV) and high (Lena) virulence through
RNA-Seq. The expression levels of genes,
isoforms, alternative transcription start sites (TSS) and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation upon
infection with the two strains. Gene ontology analysis confirmed that
infection of PAMs with both the Lena and LV strains affected signaling pathways directly linked to the innate immune response, including
interferon regulatory factors (IRF), RIG1-like receptors, TLRs and PKR pathways. The results confirmed that
interferon signaling is crucial for transcriptional regulation during PAM
infection. IFN-β1 and IFN-αω, but not IFN-α, were up-regulated following
infection with either the LV or Lena strain. The down-regulation of canonical pathways, such as the interplay between the innate and adaptive immune responses, cell death and TLR3/TLR7 signaling, was observed for both strains, but Lena triggered a stronger down-regulation than LV. This analysis contributes to a better understanding of the interactions between PRRSV and PAMs and outlines the differences in the responses of PAMs to strains with different levels of virulence, which may lead to the development of new PRRSV control strategies.