Nucleotide sequence of the Barmah Forest virus genome

Barmah Forest virus (BFV) is an atypical alphavirus [Dalgarno, L., Short, N. J., Hardy, C. M., Bell, J. R., Strauss, J. H., and Marshall, I. D. (1984). Virology 133, 416-426] and has been classified as the sole known member of a seventh alphavirus serocomplex. The complete nucleotide sequence of BFV genomic RNA is 11,488 nucleotides in length excluding the poly(A) tail. Two long open reading frames in the RNA encode a nonstructural polyprotein of 2411 amino acids and a structural polyprotein of 1239 amino acids, respectively. The BFV envelope protein E2 is unique among sequenced alphaviruses in having no N-linked glycosylation sites; E1 carries two glycosylation sites. From amino acid sequence comparisons with sequenced alphaviruses BFV is most closely related to Ross River and Semliki Forest viruses. Sequence homology between BFV and other alphaviruses is relatively uniform along the length of the nonstructural and structural polyproteins, providing no evidence that BFV has arisen from recombination between ancestral alphaviruses in the coding region of the genome. The BFV 3' noncoding region of 445 nucleotides has unusual features. There are two unrelated sequence blocks of 48 nucleotides (sequence I) and 47 nucleotides (sequence II) both of which are repeated once. Sequence I is closely related to a repeat in the 3' noncoding region of Ross River and Getah viruses; sequence II is unrelated to repeat blocks in other sequenced alphaviruses. Thus, recombination between ancestral viruses may have played a role in the evolution of the BFV 3' noncoding region.