West Nile virus (WNV), 1 a mosquito-borne member of Flaviviridae family that consists of more than 70 human pathogens, was first isolated in 1937 from the blood of a female patient in the West Nile district of Uganda (1). Since then, the virus has been isolated in humans, birds, and bird-feeding mosquitoes, Culex univittatus. Serological studies revealed a broad distribution of the virus in Africa, West Asia including India, and the Middle East, but only occasionally isolated in Europe, and is thought to be spread by migratory birds (Ref. 2, for reviews, seeRefs. 3 and 4). WNV belongs to the Japanese encephalitis serocomplex group, which includes St. Louis encephalitis, Murray Valley encephalitis, Kunjin virus, and Japanese encephalitis virus (5, 6). WNV was not previously isolated in the Western hemisphere. The first outbreak of WNV infections occurred in New York in 1999 (7-10) in which 62 people were confirmed to be infected, seven of which were fatal. Since then, transmission of WNV is spreading rapidly throughout the United States; 12 states along the eastern seaboard in 2000 to 25 states and the District of Columbia by 2001 (3).WNV, like other flaviviruses, contain a positive (ϩ)-strand RNA of ϳ11 kb in length that is capped at the 5Ј-end and nonpolyadenylated at the 3Ј-end. WNV RNA contains conserved sequence elements within the 5Ј-and 3Ј-terminal regions (TR), which include two self-complementary cyclization motifs (5Ј-CYC and 3Ј-CYC) of 9 nt in length (11). There is a highly conserved stem-loop structure within the 3Ј-terminal 96 nt of 3Ј-UTR of flaviviral RNAs and a less conserved stem-loop structure within 5Ј-UTR (12-14) (for reviews, see Refs. 4,15,and 16). In addition, there is a potential pseudoknot tertiary structure within the 3Ј-terminal stem-loop structure of WNV RNA (17). Several host proteins have been shown to bind to the 5Ј-and 3Ј-UTR although their functional role in viral RNA replication has not been clearly established (18 -21) (for a review, see Ref. 22). By mutational analysis, the 3Ј stem-loop region within the 3Ј-UTR was shown to be important for viral replication in vivo (23,24) and in vitro (25).The flaviviral RNA genome encodes a single polyprotein precursor that were processed co-translationally and posttranslationally into three structural proteins (capsid, C; precursor membrane, prM; its processed form, membrane protein, M; and the envelope, E) and at least seven nonstructural proteins, NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5 (for reviews, see Refs. 4,15,and 16). NS3 is a multifunctional protein; the N-terminal region of NS3 contains the serine protease domain and it requires NS2B for cleavage at the junctions of 2A-2B, 2B-3, 3-4A, and 4B-5. NS3 contains conserved motifs found in RNA helicases of the DEXH family (for reviews, see Refs. 4,15,and 16). Purified NS3 was shown to possess NTPase and RNA helicase activities (26 -32) as well as 5Ј-RNA triphosphatase activity (33, 34), the first enzyme required in 5Ј-cap synthesis.NS5 is the largest of the flaviviral nonstructural pro...