Sequence analysis of the viral core protein and the membrane-associated proteins V1 and NV2 of the flavivirus West Nile virus and of the genome sequence for these proteins.

Cell-associated flaviviruses contain the two membrane proteins V3 and NV2 besides the viral core protein V2 whereas extracellular viruses do contain V2 protein and the two membrane proteins V3 and V1. Since the V1 protein could not be detected in infected cells it has been suggested that V1 is generated from NV2 by proteolytic cleavage during the release of virus from cells (D. Shapiro, W. E. Brandt, and P. K. Russell (1972), Virology 50, 906-911). We have isolated the viral structural proteins V1, V2, and NV2 from the flavivirus West Nile virus and determined their amino-terminal amino acid sequences and amino acid sequences of peptides derived from these proteins. We have also transcribed parts of the viral genome into cDNA and cloned and sequenced this cDNA. The analyses of the protein structure of V1, V2, and NV2 together with the determination of the amino-terminal sequence of V3 (data not shown) have allowed us to identify the nucleotide region coding for the structural proteins V2, NV2, and V1. The primary structure of this nucleotide sequence is presented in this report. The data show that the amino terminus of the viral core protein V2 is followed by the amino termini of the proteins NV2, V1, and V3, respectively. These data for the first time identify the exact order of all structural proteins of a flavivirus identified so far. Our data strongly support the above-mentioned hypothesis that V1 is derived from NV2 by proteolytic cleavage and furthermore indicate that V1 represents the nonglycosylated carboxy-terminal part of NV2 which contains those sequences which anchor NV2 in the viral membrane. A working hypothesis is presented in which two species of cellular enzymes, signalase(s) removing signal sequences and enzymes involved in cleaving polyproteins after a pair of basic amino acids, do generate the proteins V2, NV2, and V1 from the growing peptide chain synthesized during translation of the 42 S genome RNA which functions as mRNA for these proteins.