Segment-dependent phylogenetic resolution reveals geographic and host sampling gaps in Oropouche virus genomes
- 1Ross University School of Medicine
Abstract
Background. Oropouche virus (OROV) has been reported in areas beyond its historical Amazonian range since 2023, accompanied by rapid growth in publicly available genomic data. However, the extent to which these data provide reliable phylogenetic and epidemiological resolution, and whether that resolution differs among genome segments, has not been systematically examined. Methods. Nucleotide sequences annotated under Orthobunyavirus oropoucheense were retrieved from NCBI Virus (accessed 13 May 2025) and filtered to retain records at least 70% of the reference length for each segment, yielding 898 S, 831 M, and 832 L sequences. Segments were aligned independently with MAFFT, and maximum-likelihood phylogenies were inferred with IQ-TREE using ModelFinder and ultrafast bootstrap approximation. Trees were annotated with collection date, country, and host in iTOL. Results. Phylogenetic resolution differed among segments. Contemporary Brazilian sequences formed a largely unresolved region in the S segment tree, whereas the M and L trees resolved recent clusters to differing degrees. Resolution did not track segment length: the M tree resolved contemporary structure more strongly than the longer L tree, and total tree length was approximately 3.5 times greater in the M tree despite near-identical taxon sampling. Sequences collected before 2010 were recovered in supported clusters in all three segment trees, although their configuration differed by segment. These sequences were also predominantly non-Brazilian and non-human, preventing collection date, geographic origin, and host from being separated as explanations for the observed clustering. The species-level query also retained three reassortant viruses, which may influence segment-specific topologies; sequences annotated to the United States were Iquitos virus rather than OROV. Two Italian sequences clustered with Cuban sequences across all three trees, concordant with published travel histories. Conclusions. Publicly available sequences contain phylogenetic structure that differs among the S, M, and L segment trees, but interpretation is constrained by uneven temporal, geographic, and host sampling and by the inclusion of reassortant species in a species-level dataset. The concentration of sequences from Brazil and human hosts, together with limited representation of non-human hosts, restricts inference about OROV diversity and ecology. Broader and more balanced genomic surveillance would improve the ability to resolve OROV evolutionary and transmission patterns.
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BibTeX
@misc{siam2026segmentdependent,
title = {{Segment-dependent phylogenetic resolution reveals geographic and host sampling gaps in Oropouche virus genomes}},
author = {R. Siam and A. H. A. Elbehery},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.05.764562},
url = {https://www.biorxiv.org/content/10.64898/2026.11.05.764562v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Segment-dependent phylogenetic resolution reveals geographic and host sampling gaps in Oropouche virus genomes
AU - R. Siam
AU - A. H. A. Elbehery
PY - 2026
DA - 2026/11/05
PB - bioRxiv
DO - 10.64898/2026.11.05.764562
UR - https://www.biorxiv.org/content/10.64898/2026.11.05.764562v1
AB - Background. Oropouche virus (OROV) has been reported in areas beyond its historical Amazonian range since 2023, accompanied by rapid growth in publicly available genomic data. However, the extent to which these data provide reliable phylogenetic and epidemiological resolution, and whether that resolution differs among genome segments, has not been systematically examined. Methods. Nucleotide sequences annotated under Orthobunyavirus oropoucheense were retrieved from NCBI Virus (accessed 13 May 2025) and filtered to retain records at least 70% of the reference length for each segment, yielding 898 S, 831 M, and 832 L sequences. Segments were aligned independently with MAFFT, and maximum-likelihood phylogenies were inferred with IQ-TREE using ModelFinder and ultrafast bootstrap approximation. Trees were annotated with collection date, country, and host in iTOL. Results. Phylogenetic resolution differed among segments. Contemporary Brazilian sequences formed a largely unresolved region in the S segment tree, whereas the M and L trees resolved recent clusters to differing degrees. Resolution did not track segment length: the M tree resolved contemporary structure more strongly than the longer L tree, and total tree length was approximately 3.5 times greater in the M tree despite near-identical taxon sampling. Sequences collected before 2010 were recovered in supported clusters in all three segment trees, although their configuration differed by segment. These sequences were also predominantly non-Brazilian and non-human, preventing collection date, geographic origin, and host from being separated as explanations for the observed clustering. The species-level query also retained three reassortant viruses, which may influence segment-specific topologies; sequences annotated to the United States were Iquitos virus rather than OROV. Two Italian sequences clustered with Cuban sequences across all three trees, concordant with published travel histories. Conclusions. Publicly available sequences contain phylogenetic structure that differs among the S, M, and L segment trees, but interpretation is constrained by uneven temporal, geographic, and host sampling and by the inclusion of reassortant species in a species-level dataset. The concentration of sequences from Brazil and human hosts, together with limited representation of non-human hosts, restricts inference about OROV diversity and ecology. Broader and more balanced genomic surveillance would improve the ability to resolve OROV evolutionary and transmission patterns.
ER -