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Journal of General Virology (2002), 83, 3075-3084.
© 2002 Society for General Microbiology

Animal: RNA Viruses

Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site

Afjal Hossain Khan1, Kouichi Morita1, Maria del Carmen Parquet1, Futoshi Hasebe1, Edward G. M. Mathenge1 and Akira Igarashib,1

Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan1

Author for correspondence: Kouichi Morita. Fax +81 95 849 7830. email moritak{at}net.nagasaki-u.ac.jp

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.




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