Oropouche Virus in Loreto, Peru (2023-2024): Case Distribution, Genome Sequencing, and Phylogenetic Insights.

Undiagnosed acute febrile illness (AFI) remains elevated in the Peruvian Amazon. The contribution of Oropouche virus (OROV) to AFI in Loreto was quantified, and its recent circulation was contextualized using targeted molecular testing and phylogenomic analysis. Using a novel research-use-only OROV real-time quantitative polymerase chain reaction test across seven surveillance sites, 1,000 AFI samples were rescreened in a setting where undiagnosed presentations were common (70% lacked a confirmed etiology at enrollment). Oropouche virus was detected in 7.1% of cases, with nearly all consensus genomes recovered from specimens with a cycle threshold value ≤30, underscoring the importance of early-phase sampling for sequencing success. Positive results occurred at all seven locations, including the remote riverine community of San Lorenzo, indicating broad geographic distribution and supporting ongoing endemic transmission rather than a single localized outbreak. Exposure patterns were consistent with peridomestic, vector-mediated acquisition: animal contact was common (63.4%), whereas contact with symptomatic individuals (12.7%) and recent travel (35.7%) were infrequent, supporting local, not person-to-person or travel-related, transmission. Oropouche virus cases peaked in January to February 2024, temporally overlapping with the seasonal rise in AFIs, indicating synchronous circulation with other endemic pathogens. Phylogenetic arrangement of contemporary Peruvian strains within established South American diversity further supports ongoing local transmission consistent with regional patterns. Together, these findings indicate that OROV accounts for a meaningful portion of AFI in Loreto and that the routine inclusion of OROV testing, paired with genomic surveillance, can close diagnostic gaps, improve situational awareness, and guide targeted public health action.