Outbreak investigation of reemerging chikungunya virus in Malaysia in 2019–2020

Background Chikungunya virus (CHIKV) is a mosquito-borne pathogen that imposes a substantial public health burden in tropical regions. After a decade of sporadic transmission, Malaysia experienced an alarming resurgence of CHIKV cases in 2019. This study investigated the reemergence of CHIKV in Malaysia following this prolonged period of sporadic transmission. Methods An outbreak investigation was conducted in two phases across three hotspots in Perak, Malaysia (Kampung Baru Air Kuning, Bidor, and Sungkai) between October 2019 and February 2020. Blood samples were collected from 78 subjects and were tested by real-time reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assays (ELISA). CHIKV was isolated and subjected to whole-genome sequencing. The resulting sequences were then analysed using phylogenetic, comparative sequence and selection pressure analyses. Results A high CHIKV positivity rate of 69.2% (54/78) was observed in this study, with a 9.3% (5/54) rate of dengue virus (DENV) coinfection. Phylogenetic analysis revealed that the CHIKV isolates from this study belonged to the East/Central/South African-Indian Ocean Lineage (ECSA-IOL) genotype and clustered with recent outbreak isolates from Thailand, China, Myanmar, Bangladesh, Italy, Pakistan, and India during 2015–2019, rather than the Malaysia isolate from the previous 2009 outbreak. Malaysia 2019 and Thailand 2018 isolates shared relatively higher nucleotide similarity (99.78–99.89%). The reemerging CHIKV in Malaysia harboured E1-226 A, E1-K211E, and E2-V264A which enhance CHIKV fitness in Aedes aegypti , as well as nsP3-R524Opal that is associated with increased virulence. These mutations were consistent with globally circulating epidemic strains during 2015–2019, highlighting vector adaptation and disease severity. Conclusions The reemerging ECSA-IOL strain in Malaysia was genetically distinct from the Malaysia 2009 outbreak strain but closely related to the globally circulating epidemic strains during 2015–2019. Collectively, it was likely introduced from neighbouring Thailand through cross-border transmission.