Epidemiology of chikungunya virus across neglected regions of Indonesia

Acutely febrile patients presenting between September 2017 – 2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. Four hundred and eighty two dengue virus negative patients were enrolled. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4 – 3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands.