| Summary: | Chikungunya virus (CHIKV) is a mosquito-borne virus belonging to the genus<i> Alphavirus</i>. The virus is transmitted to humans by the bite of infected female<i> Aedes </i>mosquitoes, primarily <i>Aedes aegypti</i>. CHIKV infection is spreading worldwide, and it periodically sparks new outbreaks. There are no specific drugs or effective vaccines against CHIKV. The interruption of pathogen transmission by mosquito control provides the only effective approach to the control of CHIKV infection. Many studies have shown that CHIKV can be transmitted among the <i>Ae. aegypti</i> through vertical transmission. The previous chikungunya fever outbreaks in Thailand during 2008−2009 were caused by CHIKV, the East/Central/South African (ECSA) genotype. Recently, there have been 3794 chikungunya cases in 27 provinces reported by the Bureau of Epidemiology of Health Ministry, Thailand during 1 January−16 June 2019; however, the cause of the re-emergence of CHIKV outbreaks is uncertain. Therefore, the aims of this study were to detect and analyze the genetic diversity of CHIKV infection in field-caught mosquitoes. Both female and male <i>Ae. aegypti</i> were collected from endemic areas of Thailand, and CHIKV detection was done by using <i>E1</i>-nested RT-PCR and sequencing analysis. A total of 1646 <i>Ae. aegypti</i> samples (900 females and 746 males) were tested. CHIKV was detected in 54 (3.28%) and 14 samples (0.85%) in female and male mosquitoes, respectively. Seventeen samples of female <i>Ae. aegypti</i> collected from the Ubon Ratchathani, Chiang Rai, Chiang Mai, Nakhon Sawan, and Songkhla provinces found mutation at <i>E1</i>: A226V. Interestingly, <i>E1</i>: K211E mutation was observed in 50 samples collected from Nong Khai, Bangkok, Prachuap Khiri Khan, and Krabi. In addition, the phylogenetic tree indicated that CHIKV in <i>Ae. aegypti</i> samples were from the Indian Ocean Clade and East/South African Clade. Both clades belong to the ECSA genotype. The information obtained from this study could be used for prediction, epidemiological study, prevention, and effective vector control of CHIKV. For instance, a novel CHIKV strain found in new areas has the potential to lead to a new outbreak. Health authorities could plan and apply control strategies more effectively given the tools provided by this research.
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