Detection of Chikungunya virus in The Gambia through a newly implemented sentinel surveillance program

Abstract

We characterized 01 autochthonous chikungunya virus (CHIKV) case from (The Gambia) through a newly implemented local arboviruses surveillance program highlighting the first notification of the virus in the Country. Identified virus is closely related to CHIKV West African genotype detected in Kedougou (Senegal) in 2023 and responsible of a large outbreak with up to 300 confirmed cases. This work describes the first genomic proof subregional spread of CHIKV West African genotype in West Africa.

CDC Trioplex diagnostic assay underperforms in detection of circulating Chikungunya West African genotype

“…In response to the spread of Chikungunya virus (CHIKV) in Gambia ( 4 ) and in Burkina Faso ( 2 ) and the potential occurrence of an unprecedented number of CF cases in the subregion, we evaluated the performance of the donated CDC Trioplex RT-qPCR detection system for regular use, which allows the simultaneous detection of Zika virus, Dengue virus, and CHIKV using a set of serum samples collected during the initial phase of the ongoing epidemic in Senegal.…”

“…The detection shift of approximately two logs in quantity can potentially increase the false negative rate when using the CDC Trioplex PCR in samples with intermediate to low viral load (Ct values > Ct 28). The CHIKV WA genotype circulating in Senegal can still be detected by the IPD in-house assay ( 4 ). The in silico analysis revealed no mismatches of this oligonucleotide set when aligned to a broad range of previously described and newly determined contemporary CHIKV WA genotype sequences (Fig.…”