Clinical and Genomic Characterization of Chikungunya Virus Variant reveals a Novel nsP3 H377P Substitution during the 2015 Outbreak in Central Valley of Chiapas, Mexico.
Abstract
Objectives
To characterize the clinical, diagnostic and genomic features of chikungunya virus (CHIKV) infection among patients presenting with an acute dengue-like illness in the inland Central Valley of Chiapas, Mexico, during the 2015 outbreak.
Methods
We retrospectively tested sera from 80 suspected cases using qRT-PCR, virus isolation, ELISA, indirect immunofluorescence, full-genome sequencing and phylogenetic analyses compared Central Valley isolates with contemporary CHIKV sequences from Mexico and the Americas.
Results
Sixty-seven patients (84%) were CHIKV-positive, including four CHIKV-DENV coinfections and serological evidence of prior DENV exposure in (60%) of cases. Fever and polyarthralgia occurred in all confirmed cases; headache, myalgia, conjunctivitis, rash, lymphadenopathy, and lymphopenia were also frequent. Two full genomes (PQ261036, PQ261037) clustered in the Asian/American lineage but formed a distinct subclade from coastal strains, one isolate carried a novel nsP3 H377P substitution in the hypervariable domain.
Conclusions
CHIKV accounted for a substantial proportion of dengue-like illness during this inland outbreak, underscoring the limits of clinical diagnosis where CHIKV and DENV co-circulate. Genomic data revealed distinguishable Asian CHIKV variants and a previously unreported nsP3 substitution, supporting continued genomic surveillance of CHIKV in southern Mexico.