The Chikungunya virus, a global arbovirus, is currently causing a major outbreak in the Western African region, with the highest cases reported in Senegal and Burkina Faso. Recent molecular evolution analyses reveal that the strain responsible for the epidemic belongs to the West African genotype, with new mutations potentially impacting viral replication, antigenicity, and host adaptation. Real-time genomic monitoring is needed to track the virus's spread in new regions. A scalable West African genotype amplicon-based Whole Genome Sequencing for multiple Next Generation Sequencing platforms has been developed to support genomic investigations and identify epidemiological links during the virus's ongoing spread. This technology will help identify potential threats and support real-time genomic investigations in the ongoing spread of the virus.

The authors have declared no competing interest.

This work was funded by the NIH West African Center for Emerging Infectious Diseases (grant number U01AI151801-01) and the Africa CDC Pathogen Genomics Initiative funds (CARES grant 4306-22-EIPHLSS-GENOMICS).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Clinical samples in this study were collected on CHIKV positive human samples according to the guidelines of the Declaration of Helsinki, and approved by the Senegalese national ethics committee for health research (protocol code SEN20/08 approved on 6 April 2020).

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All data produced in the present study are available upon reasonable request to the authors