War, trade and agriculture spread rice disease across Africa

Since the mid-1800s, human activities have rapidly facilitated the spread of rice yellow mottle virus (RYMV), a pathogen that infects rice, far and wide across Africa, according to a new study led by Eugénie Hébrard, at the Institut de Recherche pour le Développement (IRD, France), published June 17, 2025 in the open-access journal PLOS Pathogens.

RYMV is a pathogen that infects rice and a few related grass species, and that poses a major threat to rice production in Africa. In the new study, researchers investigated how human history has shaped the spread of RYMV, looking at how distinct strains of RYMV evolved in different locations and times.

The research team compared the gene sequences that code for a viral protein or the full-length viral genomes, fromup to 335 virus samples collected across more than 770,000 square miles in East Africa between 1966 and 2020. Based on variations and similarities in the gene sequences, the researchers found evidence that RYMV emerged in the middle of the 1800s in the Eastern Arc Mountains, a biodiversity hotspot, located in what is now Tanzania, where people grew rice slash-and-burn agriculture. Several spillovers of RYMV from wild grasses into cultivated rice were identified, with the virus rapidly spreading to the nearby rice growing areas, including Kilombero valley and the Morogoro region in southern Tanzania.

The study also suggested that humans transported RYMV long distances in infected rice plant matter at multiple points in history. The virus spread along the caravan routes from the Indian Ocean Coast to Lake Victoria in the second half of the 1800s, from East Africa to West Africa at the end of the 1800s, from Lake Victoria to the north of Ethiopia in the second half of the 1900s, and then on to Madagascar at the end of 1970s. Unexpectedly, it moved from the Kilombero Valley to the southern end of Lake Malawi toward the end of the First World War, likely due to rice being a staple food for troops.

Altogether, these findings suggest that transporting contaminated rice seeds was a major factor in spreading RYMV across long distances, not only within East Africa, but also in bringing it from East Africa to West Africa and Madagascar. The researchers conclude that, due to human activities, RYMV can spread as efficiently as some highly mobile zoonotic viruses that humans have contracted from animals. The study also sheds light on the risk of transmitting RYMV and other plant viruses from Africa to other continents.

The authors add, “This paper highlights the role of human history in the transmission of plant pathogens and underscores the risks of intercontinental transmission. The paradoxical role of seeds in the spread of a major pest of rice - which is not seed transmitted, but seed associated – is explained in the light of rice biology and agronomy. This study is a major achievement of a long-term, multilateral and interdisciplinary partnership.”

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In your coverage, please use this URL to provide access to the freely available paper in PLOS Pathogens: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1013168

Citation: Ndikumana I, Onaga G, Pinel-Galzi A, Rocu P, Hubert J, Wéré HK, et al. (2025) Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: An historical and phylogeographical retrospective. PLoS Pathog 21(6): e1013168. https://doi.org/10.1371/journal.ppat.1013168

Movie caption: Spatio-temporal dispersion of rice yellow mottle virus throughout East Africa visualized by Evolaps. https://www.evolaps.org/

Movie credit: François Chevenet, © Mapbox © OpenStreetMap, CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

High-resolution movie link: https://plos.io/3Z30MRn

Author Countries: Belgium, Cote d’Ivoire, France, Kenya, Rwanda, Singapore, Tanzania, United States

Funding: This work was partly supported by the French National Research Agency as an “Investissements d’avenir” program (ANR-10-LABX-001-01 Labex Agro) coordinated by Agropolis Foundation (project no. 1504-004 E-SPACE to IN, EPG, NP, DF, EH) and by a bilateral project between Kenya and France (PHC PAMOJA no 36128PK to HKW, AA, MNW, EH) cofunded by National Commission for Science, Technology and Innovation (NACOSTI) and Ministère de l’Europe et des Affaires Etrangères (MEAE). PR’s internship at the University of Montpellier was founded by the I-SITE MUSE through the Key Initiative “Data and Life Sciences”. SD acknowledges support from the Fonds National de la Recherche Scientifique (F.R.S.-FNRS, Belgium; grant n°F.4515.22), from the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek - Vlaanderen, FWO, Belgium; grant n°G098321N), from the European Union Horizon 2020 projects MOOD (grant agreement n°874850) and LEAPS (grant agreement n°101094685). GO acknowledges support from the Plant Health Initiative (PHI) funded by the CGIAR Trust Fund. The funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication.