Co-Circulation of 2 Oropouche Virus Lineages, Amazon Basin, Colombia, 2024

Abstract

In early 2024, explosive outbreaks of Oropouche virus (OROV) linked to a novel lineage were documented in the Amazon Region of Brazil. We report the introduction of this lineage into Colombia and its co-circulation with another OROV lineage. Continued surveillance is needed to prevent further spread of OROV in the Americas.

Keywords: Amazon Basin; Colombia; Leticia; Oropouche virus; fever; lineages; outbreak; reassortant; reassortment; sequencing; vector-borne infections; viruses; zoonoses.

Figure 1

Time-scaled Bayesian phylogeographic analysis of large and small segments of co-circulating Oropouche virus lineages, Amazon Basin, Colombia, 2024. Bayesian phylogenetic trees of large (A) and small (B) gene segments were estimated by using the Bayesian Markov chain Monte Carlo method (>100 million generations) in Beast (https://beast.community) and ModelFinder in IQ-TREE (http://www.iqtree.org) (ultrafast bootstrapping and 1,000 replicates). Red solid circles indicate viruses from this study that begin with LET for Leticia, Colombia. Phylogeny branches are colored according to their descendant place of origin. Best-fit model was selected according to Bayesian information criteria, and a strict molecular clock model was used. Bayesian posterior values (>0.8) are annotated at specific nodes of the trees. Sequences from this study were compared with reference sequences from other studies. Main clusters are indicated by using the following reference labels: BR-2015-2024 cluster represents the recent outbreak of the new OROV lineage in Brazil during 2015–2024; PE/CO/EC-2008-2021 cluster represents sequences from Colombia, Peru, and Ecuador during 2008–2021; and BR-2009-2018 cluster represents sequences from Brazil during 2009–2018. Scale bar indicates nucleotide substitutions per site.

Figure 2

Time-scaled Bayesian phylogeographic analysis of medium segments of co-circulating Oropouche virus lineages, Amazon Basin, Colombia, 2024. Bayesian phylogenetic tree of medium gene segments were estimated by using the Bayesian Markov chain Monte Carlo method (>100 million generations) in Beast (https://beast.community) and ModelFinder in IQ-TREE (http://www.iqtree.org) (ultrafast bootstrapping and 1,000 replicates). Red solid circles indicate viruses from this study that begin with LET for Leticia, Colombia. Phylogeny branches are colored according to their descendant place of origin. Best-fit model was selected according to Bayesian information criteria, and uncorrelated relaxed molecular clock model was used. Bayesian posterior values (>0.8) are annotated at specific nodes of the trees. Sequences from this study were compared with reference sequences from other studies. Main clusters are indicated by using the following reference labels: BR-2015-2024 cluster represents the recent outbreak of the new OROV lineage in Brazil during 2015–2024; PE/CO/EC-2008-2021 cluster represents sequences from Colombia, Peru, and Ecuador during 2008–2021; and BR-2009-2018 cluster represents sequences from Brazil during 2009–2018. Scale bar indicates nucleotide substitutions per site.

Figure 3

Leticia municipality and Three Borders (Colombia, Peru, and Brazil) region in study of co-circulation of 2 Oropouche virus lineages, Amazon Basin, Colombia, 2024. Symbols indicate residential locations of 8 patients infected with OROV in Leticia municipality. Colored circles and diamonds indicate patients infected with each OROV lineage. Macedonia, Vereda Santa Sofia, Santa Rosa de Yavari, and Tabatinga correspond to indigenous communities or cities. Map was created by using QGIS 3.36.0 RC (https://www.qgis.org). OROV, Oropouche virus.