Respective shRNA target sequences in CHIKV Capsid, E1 and nsP1 genes.

shRNAs were designed against CHIKV structural genes (Capsid and E1) and non-structural gene (nsP1) and were named accordingly to its gene targeta. According to the guidelines for designing an effective shRNA construct, the antisense target sequence was incorporated with an additional AA dinucleotide at its 5′ end and has an optimal length of 21-mer. In the scrambled shRNA controls, underlined nucleotides refer to mismatch to its original target sequenceb. Sequence location refers to the location of the shRNA target sequence in the Indonesia 0706aTw CHIKV genomec.