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Volume 40 Issue 5
October 2025
    Citation: Yibo Ding, Jiajing Li, Xin Wang, Simone Malagò, Amaro Nunes Duarte-Neto, Xiaohui Ding, Fang Qin, Michela Deiana, Concetta Castilletti, Hongbo Guo, Qiuwei Pan, Wenshi Wang. Phylogenomics and structural modelling feature accelerated evolution of Oropouche virus: 1955 to 2024 .VIROLOGICA SINICA, 2025, 40(5) : 735-747.  http://dx.doi.org/10.1016/j.virs.2025.09.009
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    Phylogenomics and structural modelling feature accelerated evolution of Oropouche virus: 1955 to 2024

    • a. Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China;

    • b. Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, 3015 GD, the Netherlands;

    • c. PhD National Programme in One Health Approaches to Infectious Diseases and Life Science Research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, 27100, Italy;

    • d. Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, 37024, Italy;

    • e. Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, 05508-000, Brazil

    • A large multi-country outbreak of Oropouche virus (OROV), a segmented negative-sense RNA virus, is emerging in Latin America. By analyzing publicly available whole-genome sequences spanning 1955 to 2024, this study reveals accelerated spatiotemporal evolution of OROV, cooperatively driven by genome mutagenesis and segment reassortment. The strains responsible for the 2023-2024 outbreak are universally reassortants, but form two divergent lineages, namely the Brazil and western Amazon basin lineages. This epidemic spreading is primarily fueled by localized transmission within countries and cross-border spread. Phylogenomic analysis further suggests that the S segment of the viral genome originated in Brazil around the 1740s, underwent diversification into five distinct clusters by the 1970s, and experienced rapid proliferation during 2020-2024. In contrast, the L segment originated in Peru around the 1630s and evolved into two independent clusters by the 1850s. Divergent evolutionary pressures have driven distinct patterns of amino acid changes in viral proteins between the Brazil and the western Amazon basin lineages. These mutations are predicted to alter the protein structures and bear functional consequences for viral fitness and transmission. These findings provide critical insights into the evolutionary dynamics of OROV and underscore the necessity of genome surveillance to track the transmission pathways and spatiotemporal evolution.
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      Phylogenomics and structural modelling feature accelerated evolution of Oropouche virus: 1955 to 2024

        Corresponding author: Hongbo Guo, hongbo.guo@xzhmu.edu.cn
        Corresponding author: Qiuwei Pan, q.pan@erasmusmc.nl
        Corresponding author: Wenshi Wang, wenshi.wang@xzhmu.edu.cn
      • a. Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China;
      • b. Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, 3015 GD, the Netherlands;
      • c. PhD National Programme in One Health Approaches to Infectious Diseases and Life Science Research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, 27100, Italy;
      • d. Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, 37024, Italy;
      • e. Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, 05508-000, Brazil
      • Received Date: 12 May 2025
      • Accepted Date: 28 September 2025

      Abstract: A large multi-country outbreak of Oropouche virus (OROV), a segmented negative-sense RNA virus, is emerging in Latin America. By analyzing publicly available whole-genome sequences spanning 1955 to 2024, this study reveals accelerated spatiotemporal evolution of OROV, cooperatively driven by genome mutagenesis and segment reassortment. The strains responsible for the 2023-2024 outbreak are universally reassortants, but form two divergent lineages, namely the Brazil and western Amazon basin lineages. This epidemic spreading is primarily fueled by localized transmission within countries and cross-border spread. Phylogenomic analysis further suggests that the S segment of the viral genome originated in Brazil around the 1740s, underwent diversification into five distinct clusters by the 1970s, and experienced rapid proliferation during 2020-2024. In contrast, the L segment originated in Peru around the 1630s and evolved into two independent clusters by the 1850s. Divergent evolutionary pressures have driven distinct patterns of amino acid changes in viral proteins between the Brazil and the western Amazon basin lineages. These mutations are predicted to alter the protein structures and bear functional consequences for viral fitness and transmission. These findings provide critical insights into the evolutionary dynamics of OROV and underscore the necessity of genome surveillance to track the transmission pathways and spatiotemporal evolution.

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