LOW-LEVEL CIRCULATION OF CHIKUNGUNYA VIRUS DURING COVID-19 MOBILITY RESTRICTIONS IN THE KLANG VALLEY, MALAYSIA

Abstract

Chikungunya virus (CHIKV) and dengue virus (DENV) co-circulate in Malaysia, share Aedes mosquito vectors, and present with overlapping early clinical manifestations, making laboratory confirmation essential for accurate diagnosis. This study aimed to identify CHIKV infections among patients clinically suspected of dengue but testing negative for dengue markers during the COVID-19 pandemic and to characterize any detected viruses genomically. From May 2020 to May 2021, 917 serum specimens from patients at the Universiti Malaya Medical Centre who were negative for dengue NS1 antigen, anti-dengue IgM, and DENV RNA were screened for CHIKV using a validated in-house pan-Alphavirus RT-PCR targeting the conserved nsP4 gene. One specimen (0.11%) tested positive. Complete genome sequencing generated an approximately 11.6 kb genome, and phylogenetic analysis placed the isolate within the East/Central/South African (ECSA) genotype, clustering closely with strains from Myanmar and Thailand. The isolate carried amino acid substitutions of epidemiological relevance (E1-211E, E1-226A, and E2-264A), characteristic of a regionally adapted ECSA lineage capable of efficient transmission by Ae. aegypti. These genomic features support persistence of a regional endemic lineage rather than a new introduction. The exceptionally low detection rate during Malaysia’s Movement Control Order (MCO) period further supports evidence that CHIKV transmission is strongly shaped by human mobility and behavioral exposure patterns. Recovery of a complete genome during this period provides a valuable baseline for monitoring viral evolution or re-emergence as mobility returns to pre-pandemic levels. Integrating CHIKV testing into dengue-negative febrile illness workups and maintaining genomic surveillance will be essential for early detection of resurgence.