For silencing a gene in the context of infection, I usually transfect the cells with the siRNA specific to the desired gene and then infecting 24 hrs later. It has worked well for me. I use lipofectamine for transfection of the siRNA.
siRNA acts upon any RNA target, human or viral (present in human organism), mRNA or other long RNA. Just design eg 3 siRNAs using your seq of choice, and order- you can easily do it with Silencer Select siRNAs (Life Tech web page) or other, eg Dharmacon