A large-scale epidemic of chikungunya (CHIK) fever occurred in several Indian Ocean islands in 2004 and spread to India and Sri Lanka. In December 2006, a returnee to Japan from Sri Lanka developed an acute febrile illness. The patient was confirmed to have CHIK fever after reverse transcription-polymerase chain reaction, and specific IgM and IgG detection. CHIK virus was isolated from the serum specimen collected at the acute stage. The isolated virus developed two different sizes of plaques. Two sub-strains with different genetic and biological characteristics were obtained by plaque purification from one isolate. The entire genome was sequenced and phylogenetic analysis of the E1 genome showed that the sub-strains were of the Central/East African genotype, and were closely related to recent isolates in India. This is the first report of CHIK virus genome sequences isolated from a patient infected in Sri Lanka.
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