Abstract
Chikungunya virus (CHIKV) caused significant outbreaks in Thailand during 2008–2009 and 2018–2020. Despite the COVID-19 pandemic, CHIKV continued to circulate; however, data on its epidemiological, clinical, and genetic characteristics during and after this period remains limited. This study investigated CHIKV infections in Thailand from March 2020 to December 2023. Serum samples (n = 1,264) were collected from patients with suspected CHIKV infection at 14 hospitals across five provinces in central, eastern, and northeastern Thailand. Samples were tested by RT-qPCR and IgM fluorescence immunoassay. CHIKV infection was confirmed in 50.5% (638/1,264) of cases. Infections occurred across all age groups, with the highest prevalence among individuals aged ≥56 years. Clinical symptoms significantly associated with infection included myalgia, arthralgia, rash, and conjunctivitis. Rash was more frequently in individuals aged ≤15 years and was significantly associated with lower viral loads. Arthralgia was more common among older adults and was linked to later illness onset. Myalgia was least frequently reported in younger patients. Thirty-eight complete coding sequences of our Thai CHIKV strains were analyzed in phylogenetic and time-scaled trees alongside 186 global strains and 109 ECSA-IOL strains from GenBank, respectively. Genome analysis revealed that CHIKV strains circulating in Thailand during 2020–2023 belonged to the East/Central/South African–Indian Ocean lineage (ECSA-IOL). These strains did not evolve from earlier ECSA-IOL variants that carried the E1-A226V mutation, which was previously detected in Thailand. Instead, all isolates carried E1-K211E and E2-V264A, along with E1-226A, likely introduced from the Indian subcontinent around 2016–2017. This introduction triggered a major outbreak between late 2018 and 2020, followed by sustained transmission. The 2020–2023 Thai strains exhibited high genetic similarity to those from neighboring countries, with multiple nonsynonymous mutations suggesting ongoing viral adaptation. Understanding CHIKV epidemiology, clinical features, and evolution supports improved surveillance, diagnostics, and public health interventions.