Molecular characterization of chikungunya virus in febrile patients from central Kerala by RT-PCR assay

Chikungunya fever, caused by infection with mosquito-borne alphavirus is an acute nonfatal illness characterized by fever, rash, myalgia, arthralgia and sometimes inflammatory arthritis. During 2007, central Kerala experienced a chikungunya fever epidemic of unprecedented magnitude. There were unusual skin manifestations like peeling of scrotal skin, non-healing ulcer and soft tissue necrosis. cDNA copy of a portion of the viral genome was synthesized in a reverse transcription reaction in the presence of specific primers for the E1 region of the S27 African strain of chikungunya virus (CHIKV) followed by polymerase chain reaction (PCR) amplification. Among 23 patients sampled, nine cases were found CHIKV positive. In PCR confirmed cases, the knees and ankles were the joints commonly affected. Our results suggest that the viraemia could be detected in blood during the first seven days of illness only. Three mismatches observed in the DNA sequence indicate that the virus may be a deviant of the African prototype.