The majority of the nucleotides in the top loop of the genomic 3′ terminal stem loop structure are cis-acting in a West Nile virus infectious clone

The flavivirus genome RNA terminates with a conserved 3' stem loop (SL) structure that was shown to be essential for virus replication. A stretch of conserved nts is located in the top loop TL) of this structure. Mutation of the TL nts (5' ACAGUGC 3') in a WNV infectious clone indicated that 3 of the 7 TL nts (5' A (C) under barA (G) under bar UG (C) under bar 3') are critical for virus replication. Mutation of 3 of the other nts reduced the efficiency of virus replication. The four 5' TL nts are conserved in both mosquito- and tick-borne flavivirus genomes, while the TL 3' C is conserved in mosquito-bome viruses. The conservation of two or three G-C base pairs in the TL flanking sequences suggests that a stable stem is necessary for precise presentation of the TL sequence. The TL may participate in RNA as well as protein interactions. (C) 2004 Elsevier Inc. All rights reserved.