Nucleotide Sequence of Yellow Fever Virus: Implications for Flavivirus Gene Expression and Evolution

Abstract

The sequence of the entire RNA genome of the type flavivirus, yellow fever virus, has been obtained. Inspection of this sequence reveals a single long open reading frame of 10,233 nucleotides, which could encode a polypeptide of 3411 amino acids. The structural proteins are found within the amino-terminal 780 residues of this polyprotein; the remainder of the open reading frame consists of nonstructural viral polypeptides. This genome organization implies that mature viral proteins are produced by posttranslational cleavage of a polyprotein precursor and has implications for flavivirus RNA replication and for the evolutionary relation of this virus family to other RNA viruses.

Development and Characterization of New Peptidomimetic Inhibitors of the West Nile Virus NS2B–NS3 Protease

“…27 The viral RNA-dependent RNA The polyprotein precursor is arranged in the following order from N-to C-terminus: CprM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5 (Figure 1.5). 23,24,26,39,40 Host proteases cleave the polyprotein at the following junctions, C/prM, prM/E, E/NS1, whereas the viral protease (NS2B-NS3) is considered to cleave at the NS2A/NS2B, NS2B/NS3, NS3/NS4A, and NS4B/NS5 protein junctions. 41 However, the viral replication can not begin until all single proteins are cleaved and released from the polyprotein precursor.…”

Geographic distribution and evolution of yellow fever viruses based on direct sequencing of genomic cDNA fragments

“…This encodes a single polyprotein of about 3400 amino acid residues in the gene order 5' C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5 3' (Rice et al, 1985). The YF virions contain a nucleocapsid C and two surface proteins, a membrane-associated M and an envelope glycoprotein E which may or may not be glycosylated (Deubel et al, 1987;Ballinger-Crabtree & Miller, 1990).…”

“…Two amino acid changes, threonine to arginine at position 380 related to RGD sequence, and proline to histidine at position 390, may alter flavivirus attachment or entry (Hahn et al, 1987). (iv) The gene fragment contained an Nglycosylation site of the form asparagine prolinethreonine at amino acid position 309 which could serve as a carbohydrate attachment site (Schlesinger et al, 1983;Rice et al, 1985;Deubel et al, 1987).…”

“…Two primer sequences were selected among several DNA probes complementary to 17D strain YF viral RNA (Rice et al, 1985) for cross-reactive hybridization (Kerschner et al, 1986) against the different YF RNAs (data not shown). The oligonucleotide used for cDNA priming on RNA from West African YF strains was complementary to 5' AUGGGGGAUGCTGCUUGG-GA 3', which corresponds to nucleotides 1237 to 1256 in the 17D strain YF virus E gene.…”

The phylogeny of yellow fever virus 17D vaccines

“…The strain 17D-204-Pasteur is the vaccine strain from the Institute Pasteur [9] whereas the strain 17D-204-USA derived from the American Type Culture Collection in passage number 234 and was not used for vaccine production [14].…”