Genomic characterization, origin, and local transmission of Oropouche Virus in Bolivia in 2024
Authors: Valdez Joel Alejandro Chuquimia , Arantes Ighor , Martínez Sebastián Sasías , Mendoza Cleidy Orellana , Loayza Nelly Mendoza , Marquina Jhonatan D. , Laura Helen Castillo , Kacic Roxana Salamanca , Morales Maya Xochitl Espinoza , Gresh Lionel , Gómez Mariela Martínez , Méndez-Rico Jairo , Bello Gonzalo , Naveca Felipe Gomes , Mafayle Leidy Roxana Loayza 
Published: December 2024

SummaryBackgroundThe Oropouche virus (OROV) is an arthropod-borne virus that causes an acute febrile illness similar to other arboviral diseases. In 2024, Oropouche cases sharply increased in several countries of the Americas, including Bolivia. Here, we performed a genomic study to investigate the origin and spread of OROV in the Bolivian Amazon region.MethodsFull-length OROV genomes from 34 positive samples collected in the three affected Bolivian departments during 2024 were sequenced using an amplicon-based approach. Maximum Likelihood (ML) phylogenetic analyses of separate viral segments were conducted to identify the responsible viral lineage. Bayesian phylogeographic analysis of concatenated viral segments was used to reconstruct the viral spatiotemporal dispersion pattern within the country.FindingsEpidemiological data shows that the first OROV-positive cases in 2024 in Bolivia were reported in samples collected from the Pando department during mid-January, and the peak of OROV-positive cases occurred in mid-April. The phylogenetic analysis of OROV genomes revealed that all cases detected in Bolivia belong to the novel reassortant OROV clade that drove the recent epidemic in Brazil. Our phylogeographic analysis detected at least two exportation events of OROV from the Brazilian state of Acre to the Bolivian municipalities of Guayaramerín and Riberalta, both located in the Beni department, with subsequent dissemination to municipalities of Pando and La Paz departments. Viral introductions probably occurred between early October and early November 2023, thus indicating a lag of about three months between OROV introduction and detection in Bolivia.InterpretationOur findings confirm that OROV spread at least twice from the western Brazilian Amazon to the neighboring Bolivian department of Beni in late 2023, successfully establishing regional transmission chains. The introduction and spread of OROV in Bolivia coincides with the Amazonian rainy season, from November to April, a period likely marked by an increase in vector abundance. These findings underscore the critical need for active OROV surveillance across the cross-border Amazonian region between Brazil and Bolivia. They also confirm the potential for sustained OROV transmission within the Bolivian Amazon, highlighting the importance of preparedness for future outbreaks.FundingThis publication was in part supported by the Cooperative Agreement Number NU50CK000639 awarded to the Pan American Health Organization and funded by the Centers for Disease Control and Prevention. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention or the Department of Health and Human Services.Research in contextEvidence before this studyBefore 2024, large outbreaks of Oropouche virus (OROV) were predominantly reported in the Amazon regions of Brazil and Peru. However, in 2024, significant outbreaks first emerged in the Brazilian Amazon region. They were soon followed by a surge of cases in the neighboring South American countries of Bolivia, Colombia, and Peru. We searched PubMed and preprint servers (medRxiv and bioRxiv) available as of October 25, 2024, for studies examining the circulation of OROV in Bolivia, using the terms [“Oropouche” AND “Bolivia”]. We identified only one study that reported a few anecdotal cases of past OROV infections in Bolivia, relying on serological tests and a couple of reviews.Added value of this studyThis is the first study to analyze the genomic characteristics of OROV circulating in Bolivia. In this study, we sequenced 34 full-length OROV genomes, representing 10% of all RT-qPCR-confirmed OROV cases across Pando, Beni, and La Paz departments between January and May 2024. The OROV detected in Bolivia belongs to the novel reassortant lineage recently identified in Brazil. We identified at least two introductions of OROV from the western Brazilian Amazon region into the neighboring Bolivian department of Beni around late 2023, followed by its spread to other regions within Bolivia during the rainy season. Our estimates indicate that the virus circulated in Bolivia for approximately three months before the first case was detected.Implications of all the available evidenceOur study confirms that the novel OROV reassortant lineage recently identified in Brazil rapidly disseminated across the Amazonian border into Bolivia. The successful establishment of OROV in Bolivia indicates that the country possesses suitable ecological conditions to support sustained transmissions of this arbovirus. Our findings also emphasize the crucial need for active and sustained molecular surveillance of OROV in the Bolivian Amazon region to enable the timely detection of new outbreaks in the country.