Circulation of two chikungunya variants during an outbreak in Bali, Indonesia, 2021–2022

BACKGROUND: The Bali Provincial Health Office reported 921 cases of suspected chikungunya disease (20.6 incidences/100,000 population) from Oct-2021 to Jun-2022. Sixty-eight samples were collected during the outbreak and underwent further molecular and serological investigations to confirm chikungunya virus (CHIKV) as the causal pathogen of the outbreak and to characterize the associated CHIKV variants. METHODS: Samples were tested for CHIKV and dengue virus (DENV) RNA, anti-CHIKV IgM, and anti-DENV IgM. CHIKV RNA positive specimens were subjected to whole genome sequencing for phylogenetic and mutation analyses. RESULTS: Fifty-two samples were positive for CHIKV mono-infection, four were positive for DENV mono-infection, and seven were probable CHIKV/DENV co-infection. Sequence analysis of 21 recovered CHIKV whole genomes demonstrated high nucleotide similarity of 99.75-99.98% between variants. Genome comparison revealed that the variants were monophyletic and belonged to the Asian lineage. Genomic analysis identified several unique amino acid substitutions, with two major circulating viral variants defined by changes in nsp2 and nsp3: nsp2 I486/nsp3 T224 detected in Nov-Dec -2021, and nsp2 I486V/nsp3 T224I detected throughout Nov-2021 to Jan-2022. CONCLUSION: Overall, the suspected chikungunya disease outbreak from Oct-2021 to Jun-2022 was attributed to CHIKV of Asian lineage and characterized by two closely related viral variants. The detection of a few dengue cases highlights the clinical overlap between these arboviral diseases. These findings underscore the value of integrated molecular and genomic surveillance for distinguishing co-circulating arboviruses, continued genomic surveillance to support early detection of circulating variants, and for improving early detection and response to chikungunya outbreaks.