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Genomic evidence of active circulation of Orthobunyavirus in Ecuador

Abstract:

Background: Between 2023 and 2025, the largest Oropouche fever epidemic recorded in history unfolded across Brazil seeding cases throughout Latin America. In 2024, three cases of Oropouche fever were reported in Ecuador. Methods: An Oropouche fever case detected in Bolívar Province in June 2024 was preliminarily diagnosed as Oropouche virus (OROV) through RT-qPCR and was further processed using next-generation sequencing. Results: Segments L and S of this virus forms a monophyly with another sequence circulating in Ecuador in April 2024 (i.e. PQ863772.1 isolate Ecuador traveler), with an uncertain province origin. Both sequences differ from previous OROV Ecuadorian sequences detected in 2016 and from the OROV strain driving the 2023-2025 epidemic in Brazil. Conclusions: Orthobunyavirus oropoucheense has an endemic circulation in Ecuador. Genomic surveillance of Orthobunyavirus in Ecuador and other regions should be actively pursued—independent of epidemics—to anticipate potential zoonotic outbreaks.