West Nile virus (WNV), dengue virus, and Zika virus are examples of flaviviruses that cause large outbreaks and pose major public health concerns worldwide. Therefore there is an urgent need for effective vaccines and antivirals. However to attain this, a better understanding of the interplay between virus infection and host innate immune response is desirable. To this end we employed an in-vitro screening with a library of recombinant WNV each producing a unique artificial pre-microRNA (amiR) hairpin in the 3’UTR of its genome. Processing pre-amiR via the microRNA biogenesis pathway results in production of amiR that targets a specific known mRNA transcript. By the power of natural selection, viruses that silence critical host genes that controls virus replication will be enriched. We have generated a WNV library encoding 204 pre-amiRs targeting 102 interferon-stimulated genes (ISGs) by circular polymerase extension reaction. Thereafter the library was passaged three times in wild type (WT) and interferon-α/β receptor deficient (IFNAR-/-) mouse embryonic fibroblasts (MEFs). We found that in WTMEFs and IFNAR-/- MEFs, 95% and 33% of virus population by passage 2 contained a virus producing IFITM3 amiR, indicating that IFITM3 is a critical host gene that controls WNV replication.