We report the generation of West Nile virus (WNV) infectious clones for the pathogenic lineage 1 Texas-HC2002 and nonpathogenic lineage 2 Madagascar-AnMg798 strains. The infectious clones exhibited biological properties similar to those of the parental virus isolates. We generated chimeric viruses and found that viral factors within the structural and nonstructural regions of WNV-TX contribute to the control of type I interferon defenses. These infectious clones provide new reagents to study flavivirus immune regulation and pathogenesis. W est Nile virus (WNV) is a neurotropic flavivirus that constitutes the leading cause of mosquito-borne and epidemic encephalitis in humans in the United States (4). WNV is a member of the family Flaviviridae and carries a single-stranded positivesense RNA genome approximately 11 kb in length consisting of a single open reading frame that is translated as a polyprotein to generate 10 viral proteins. Lineage 1 WNV strains represent emerging viruses associated with outbreaks of encephalitis and meningitis in Europe, the Middle East, and now North America, whereas lineage 2 strains are typically nonpathogenic, nonemergent, and geographically confined to Africa and the island country of Madagascar (2, 3, 12). More recently, lineage 1 WNV-associated infections have shifted from causing disease in young children, the elderly, and the immunocompromised to afflicting healthy young adults, indicating that virulence occurs independently of immune senescence or immune deficiencies associated with aging (6, 7). Pathogenic lineage 2 WNV variants have recently emerged in Europe, causing significant WNV-induced disease in humans (17). The increase in virulence of lineage 1 and 2 strains, coupled with a lack of a vaccine or therapeutic agents, continues to present WNV as a significant public health threat.The host innate immune response is the first line of defense during virus infection and is responsible for deterring virus replication and spread within the host. Lineage 1 WNV-TX, but not lineage 2 WNV-MAD, has been shown to inhibit type I interferon (IFN)-induced phosphorylation of STAT1 and STAT2 by blocking the activity of the IFN receptor-associated kinase Tyk2 (9). We found that WNV-TX also blocks an inhibitor of B kinase ε (IKKε)-dependent phosphorylation event on STAT1, resulting in a temporal regulation of STAT1 phosphorylation and subsequent expression of IFN-stimulated genes that are essential for the control of WNV infection (18). However, studies to identify specific viral determinants that regulate WNV inhibition of IFN-mediated signaling have been hindered by the lack of appropriate reagents.To facilitate viral genetic studies of WNV-host interactions that control infection and immunity, we generated a novel infectious clone of WNV-TX (strain TX 2002-HC) and a clone of WNV-MAD (strain Madagascar-AgMg798) (9). The design of each infectious clone is based on the two-plasmid reverse genetics system first described by Kinney et al. (10). In this system, the structural and nonstructu...