Background

Oropouche virus (OROV) is a segmented negative-sense RNA virus first identified in Trinidad and Tobago in the 1950s, possessing three genomic segments: L (6.85 kb), M (4.36 kb), and S (0.95 kb). For decades, it was considered an enzootic disease confined to the Amazon basin of South America; however, in 2023, a rapid expansion of its geographic range in Brazil raised concerns within the international public health community.

The primary vectors are biting midges of the Culicoides genus, particularly Culicoides paraensis. In urban environments, Culex quinquefasciatus also acts as a secondary vector. Infection causes fever (≥38 °C), headache, myalgia, and arthralgia, lasting 2–4 days. Rarely, cases of meningitis, encephalitis, Guillain-Barré syndrome, and vertical transmission have been reported. However, the extent to which this virus can spread outside of South America, and the routes of transmission following introduction, remained unclear at the genomic level.

Key Findings

The Pedro Kourí Tropical Medicine Institute in Cuba and researchers at the Fiocruz institute in Brazil sequenced the complete genomes of 39 samples with Ct values ≤28.5 from 147 confirmed OROV cases identified in Cuba between May and July 2024. The Illumina MiSeq platform was used in conjunction with the COVIDSeq kit, incorporating OROV-specific primers.

Phylogenetic analyses, using IQ-TREE v2.1.1 and BEAST 1.10, revealed that all 39 sequences formed a single clade (OROV-CU) within the OROVBR-2015-2025 lineage, which is currently circulating in Brazil. The posterior probability reached a maximum of 1.0, and the geographic origin converged on the state of Acre, Brazil (Bayes factor 21.3). The estimated time of the most recent common ancestor (tMRCA) was February 10, 2024 (95% HPD: January 4–March 17). The first confirmed case was reported on May 27, indicating approximately 3 months of undetected transmission.

Spatial diffusion analysis showed that the virus entered through the central provinces (Ciego de Ávila, Sancti Spíritus, and Camagüey) and then spread simultaneously westward and eastward. The rate of spread was 1.90 km per day (95% HPD 0.77–3.18 km), and 70% of transmission events involved distances greater than 10 km. In contrast, analysis of the Amazon outbreak in Brazil using the same methodology showed that only 30% of transmission events involved long distances, suggesting that movement between cities played a major role in the spread of the virus in Cuba. By August 28, a total of 506 confirmed cases had been reported in 99 of the 168 municipalities, but no severe cases were observed within the study cohort.

Implications and Outlook

This study provides the first genomic evidence of the spread of OROV from South America to a Caribbean island nation. The finding that a single introduction led to a nationwide outbreak highlights the potential for similar scenarios to occur in other tropical and subtropical countries with frequent international travel. Indeed, the clustering of a European traveler's isolate with the Cuban clade suggests the possibility of secondary transmission across the Atlantic.

However, there are also limitations. Only 26.5% of confirmed cases were sequenced, and samples with high Ct values were excluded, which may have resulted in the omission of some of the early transmission pathways. In Cuba, multiple mosquito species have been found to carry the virus, but the primary vector has not yet been identified. It is also possible that some of the early cases were misdiagnosed as dengue fever, highlighting the need for improved diagnostic capabilities.

Why It Matters

Given that there are no vaccines or specific treatments for OROV, surveillance and vector control are the only available defenses. The "single introduction → 3 months of undetected transmission → nationwide spread" pattern identified in this study has direct implications for the design of airport and port quarantine measures. Because fever and headache are common symptoms of dengue and Zika viruses, it is necessary to implement protocols for the early application of OROV RT-PCR to travelers from endemic regions.

Furthermore, the rate of spread of 1.90 km per day and the proportion of long-distance transmission events (70%) demonstrate that traditional strategies of concentrating vector control efforts in the initial outbreak area may not be sufficient to contain the virus. In regions with high densities of Culicoides midges, such as the Caribbean coast and Southeast Asia, it is essential to establish proactive surveillance networks to prepare for potential OROV introduction scenarios. The 39 complete genome sequences deposited in GISAID (EPI_ISL_19611792–19611830) provide readily available resources for the design of diagnostic primers and for ongoing genomic monitoring.