Next-generation sequencing sheds light on the interaction between virus and cell during foot-and-mouth disease virus persistent infection

Foot-and-mouth disease virus (FMDV) infection can be either persistent or acute in susceptible animals. The mechanisms involved in FMDV replication and clearance during persistent infection remain unclear. To identify host factors that are critical for FMDV replication during persistent infection, we used RNA-seq to compare the transcriptomes of infected (BHK-Op) cells and bystander (BHK-VEC) cells, which are exposed to FMDV but not infected. In total, 1917 genes were differentially expressed between BHK-Op cells and BHK-VEC cells, which were involved in ribosome biogenesis, cell cycle, and dilated cardiomyopathy. We further identified host genes potentially involved in viral clearance during persistent FMDV infection by comprehensive crossover analysis of differentially expressed genes in ancestral host cells, evolved infected host cells, and evolved bystander cells, which are resistant to infection by wild-type FMDV and FMDV-Op that co-evolved with host cells during persistent infection. Among the identified genes were Cav1 and Ccnd1. Subsequent experiments showed that knockdown of Cav1 and Ccnd1 in host cells significantly promoted and inhibited FMDV replication, respectively, confirming that the overexpression of Cav1 and the downregulation of Ccnd1 contribute to virus clearance during persistent FMDV infection. In addition, we found that BHK-Op cells contained mixtures of multiple genotypes of FMDV viruses, shedding light on the diversity of FMDV genotypes during persistent infection. Our findings provide a detailed overview of the responses of infected cells and bystander cells to persistent FMDV infection.