Entire genome characterization of Chikungunya virus from the 2008-2009 outbreaks in Thailand

The resurgence of Chikungunya virus (CHIKV) in the southern, northeastern and northern parts of Thailand, inflicting approximately 46,000 reported cases since October 2008 until December 2009, has raised public health concerns. In the present study, we characterized nearly complete genome sequences of four CHIKV isolates obtained from 2008 to 2009 outbreaks in Thailand. Phylogenetic analysis was performed to determine the relationships of the study viruses with previously reported isolates. Results showed that 2008-2009 Thailand isolates belonged to the East, Central and South African genotype and were most closely related to isolates detected in Malaysia and Singapore in 2008. This was in contrast to isolates from all previous outbreaks in Thailand which were caused by an Asian genotype. We describe several novel mutations in Thailand isolates that warrants further investigation on characterization of CHIKV from different parts of the country to better understand the molecular epidemiology of Chikungunya fever outbreaks in Thailand.