RNA sequencing analysis of cells infected with chimeric EV-A71 strains in which the 3C protease region was swapped with other strains of EV-A71
The EV-A71 genome has accumulated mutations since the virus was first detected in 1969. To characterize the polymorphism of the EV-A71 3C protease, we performed RNA sequencing using chimeric EV-A71 strains carrying the 3C protease from a clinical strain. The chimeric EV-A71 was generated using a reverse genetic system and inoculated into RD-S cells.  Gene expression profiling analysis of RD-S cells infected with the chimeric EV-A71 strains was performed. Overall design: The 3C protease coding sequence in the EV-A71 genome (strain SK-EV-006) was swapped to the sequence of the clinical strain of 3C protease. The 3C protease sequence from the clinical strains 1095/Japan 97 or 7F-AUS-6-99 was used. The RD-S cells were infected with the chimeric EV-A71 at an MOI of 1.0, extracted total RNA at 16 h post-infection, and analyzed by RNA sequencing.