title: Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site.
abstract: In this study, the complete genomic sequence of chikungunya virus (CHIK; S27 African prototype) was determined and the presence of an internal polyadenylation [I-poly(A)] site was confirmed within the 3' non-translated region (NTR) of this strain. The complete genome was 11805 nucleotides in length, excluding the 5' cap nucleotide, an I-poly(A) tract and the 3' poly(A) tail. It comprised two long open reading frames that encoded the non-structural (2474 amino acids) and structural polyproteins (1244 amino acids). The genetic location of the non-structural and structural proteins was predicted by comparing the deduced amino acid sequences with the known cleavage sites of other alphaviruses, located at the C-terminal region of their virus-encoded proteins. In addition, predicted secondary structures were identified within the 5' NTR and repeated sequence elements (RSEs) within the 3' NTR. Amino acid sequence homologies, phylogenetic analysis of non-structural and structural proteins and characteristic RSEs revealed that although CHIK is closely related to o'nyong-nyong virus, it is in fact a distinct virus. The existence of I-poly(A) fragments with different lengths (e.g. 19, 36, 43, 91, 94 and 106 adenine nucleotides) at identical initiation positions for each clone strongly suggests that the polymerase of the alphaviruses has a capacity to create poly(A) by a template-dependant mechanism such as 'polymerase slippage', as has been reported for vesicular stomatitis virus.
authors.affiliation: Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan1.
authors.forename: Afjal Hossain
authors.initials: AH
authors.lastname: Khan
authors.affiliation: Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan1.
authors.forename: Kouichi
authors.initials: K
authors.lastname: Morita
authors.affiliation: Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan1.
authors.forename: Maria Del Carmen
authors.initials: MDC
authors.lastname: Parquet
authors.affiliation: Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan1.
authors.forename: Futoshi
authors.initials: F
authors.lastname: Hasebe
authors.affiliation: Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan1.
authors.forename: Edward G M
authors.initials: EGM
authors.lastname: Mathenge
authors.affiliation: Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan1.
authors.forename: Akira
authors.initials: A
authors.lastname: Igarashi
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D002646:Chikungunya virus / Q000235:genetics*; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011061:Poly A / Q000378:metabolism; D026723:Polyadenylation / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D014764:Viral Proteins; D011061:Poly A