Chikungunya virus in dengue-suspected patients: Molecular evidence from the 2019 outbreak in Yangon, Myanmar

Chikungunya virus (CHIKV) and dengue virus (DENV) frequently co-occur in Myanmar and present with overlapping symptoms, complicating diagnosis. During the 2019 dengue outbreak in Yangon, Myanmar, molecular data on CHIKV were limited among dengue-suspected patients and there were no publicly available CHIKV genome sequences from Yangon in international databases. To address this gap and potential diagnostic overlap, we investigated the prevalence of CHIKV infection and described the genomic characteristics of detected strains.

Serum samples from 267 dengue-suspected patients collected in 2019 were screened for anti-CHIKV IgM and IgG by in-house ELISA and 211 samples with sufficient remaining volume were further analyzed by RT-qPCR, isolation of the virus, and whole-genome sequencing for mutation analysis.

CHIKV antibodies were found in 24.7% (66/267) of samples (IgM 3.4%, IgG 21.3%), and viral RNA was detected in 10.9% (23/211) of samples. Fifteen viral isolates were successfully obtained (7.1% of those tested), including two co-detections with DENV-2 by RT-PCR. All isolates belonged to the East/Central/South African genotype, Indian Ocean Lineage (ECSA-IOL), and clustered with strains from Thailand, China, and Mandalay, Myanmar. Whole-genome analysis identified 33 non-synonymous mutations across nonstructural and structural proteins, including mutations previously reported in regional ECSA-IOL strains such as E1:K211E and E2:V264A, with 11 amino acid changes not previously reported in available Myanmar reference sequences.

Serological and molecular findings indicate CHIKV circulation during the 2019 dengue outbreak in Yangon and highlight the limitations of single-target testing. Serological evidence indicate the presence of anti-CHIKV IgM and IgG antibodies, reflecting CHIKV exposure within the study population. Notably, all RNA-positive cases were seronegative for both IgM and IgG, a pattern consistent with the temporal dynamics of infection and the inherent constraints of serological detection in co-endemic settings. Molecular co-detection with DENV-2 and genomic findings highlight the potential value of multiplex diagnostic approaches in co-endemic settings.

This study documents CHIKV detection and genomic characterization in dengue-suspected patients in Yangon and highlights the potential value of multiplex diagnostic approaches and continued genomic surveillance as broader public health considerations for arboviral detection in Myanmar.