Sequence analysis of cloned dengue virus type 2 genome (New Guinea-C strain)

Abstract

Sequences totalling 5472 nucleotides (nt) from four complementary DNA (cDNA) clones of the dengue virus type 2 (DEN-2) RNA (New Guinea strain, NGS-C) have been reported previously [Yaegashi et al., Gene 46 (1986) 257–267; Putnak etal., Virology 163 (1988) 93-103]. This report describes the complete nucleotide sequence, with the exception of about 7 nt at the 5' -noncoding region, of this RNA genome derived from several cDNA clones. It is 10723 nt in length and contains a single long open reading frame of 10173 nt, encoding a polyprotein of 3391 amino acids. The genomic organization is similar to that of other flaviviruses that have recently been reported. Among the three DEN-2 strains — the Jamaica genotype (DEN-2JAM), the DEN-2NGS-C, and the S1 candidate vaccine strain derived from Puerto Rico (PR)-159 isolate (DEN-2S1) —which have been sequenced to date, the amino acid sequences of the polyproteins bear 94%–99% similarity. When the amino acid sequences of DEN-2NGS-C are compared with those of the other two strains, the variations are greater in the DEN-2S1 than in the DEN-2JAM. When DEN-2 and DEN-4 are compared, the overall amino acid identities range from 30% to 80% in both the structural and nonstructural proteins; whereas between DEN-2 and DEN-1, they range from 68% to 79% in the region encoding the structural proteins and the nonstructural protein NS1.