Reemergence of chikungunya in Mauritius driven by a novel lineage with pandemic potential

Chikungunya virus is re-emerging globally, with transmission increasingly shaped by climate change and expanding vector ranges. In March 2025, Mauritius experienced a chikungunya outbreak nearly two decades after the major epidemic in 2005-2006. We conducted an integrated epidemiological, genomic, and entomological investigation as part of the national public health response. A total of 851 confirmed cases were reported across nine districts and Rodrigues Island, of which 51 samples underwent Next Generation Sequencing. Phylogenetic reconstruction and analysis showed that the outbreak was seeded by multiple introductions of a novel East-Central-South African lineage from Réunion Island and traced its origin to a central Africa clade carrying the Aedes albopictus adaptive mutations E1-A226V, E2-L210Q, and E2-I211T. Transmission was closely associated with a rainfall-driven increase in vector abundance. These findings highlight the need for integrated genomic, ecological, and epidemiological surveillance to anticipate and mitigate arbovirus re-emergence under climate change.