Emergence of a novel reassortant Oropouche virus drives persistent human outbreaks in the Brazilian Amazon region from 2022 to 2024

Abstract

ABSTRACTThe Brazilian western Amazon region is currently experiencing its largest laboratory confirmed Oropouche virus (OROV) outbreak, with nearly 6,000 reported cases in the states of Amazonas (AM), Acre (AC), Rondônia (RO), and Roraima (RR), between August 2022 and March 2024. Here, we sequenced and analyzed 382 full-length OROV genomes from human samples collected between 2022 and 2024 from all four states, aiming to trace the origin and genetic evolution of OROV leading to the current outbreak. Genomic analyses revealed that the recent upsurge of OROV cases in the Brazilian Amazon region coincides with the emergence of a novel reassortant viral lineage containing the M segment of viruses detected in the eastern Amazon region from 2009 to 2018 and the L and S segments of viruses detected in Peru, Colombia, and Ecuador from 2008 to 2021. The novel reassortant OROV lineage likely emerged in the Central region of the AM state between 2010 and 2014 and displayed a long-range silent dispersion during the second half of the 2010s. The 2022-2024 OROV epidemic was spatially segregated into three major subpopulations located in RR, AMACRO (a bordering region between AC, RO, and AM-Southern region), and AM-Central (which includes the Amazonas’ capital, Manaus) regions. The peak of OROV transmissions in all regions occurred during the rainy season in the Amazon basin. Furthermore, our phylodynamics reconstructions showed that OROV spread was driven mainly by short-range (< 2 km) movements, with an average dispersal rate ≤ 1.2 km/day, consistent with the pattern of an active flight of infected vectors. Nevertheless, a substantial proportion (22%) of long-range (> 10 km) OROV migrations were also detected, consistent with viral dispersion via human activities. Our data provides an unprecedented view of the real-time spread and evolution of a neglected emergent human pathogen. Moreover, our results emphasize the need for widespread, long-term genomic surveillance to better understand the real burden of OROV within and beyond the Amazon region.