Segment-dependent phylogenetic resolution reveals geographic and host sampling gaps in Oropouche virus genomes

In Oropouche virus, phylogenetic resolution varies by genome segment, with the M segment tree showing ~3.5× greater total tree length than the longer L segment despite similar taxon sampling.

• Why it matters: Rapid growth in public Oropouche virus genomes may not yield consistent evolutionary or epidemiological resolution, and segment-specific differences could reflect sampling gaps or dataset artifacts.
• What they did: They retrieved Orthobunyavirus oropoucheense sequences from NCBI Virus (accessed 13 May 2025), filtered to ≥70% reference length, aligned S, M, and L separately, and inferred maximum-likelihood trees with IQ-TREE plus ultrafast bootstraps.
• The result: Pre-2010 sequences formed supported clusters in all three segment trees but with different configurations, and interpretation was constrained by uneven Brazil/human sampling plus reassortant species and misannotations (e.g., United States records labeled as Iquitos virus).

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