Journal Article

Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: An historical and phylogeographical retrospective

Pinel-Galzi, Agnès, Fargette, Denis, Chevenet, François, Hébrard, Eugénie, Wéré, Hassan Karakacha, Wéré, Mariam Nyongesa, Gilbert, Erik, Rocu, Pauline, Dugué, Marie-José, Onaga, Geoffrey, Lemey, Philippe, Bastide, Paul, Ndikumana, Innocent, Adego, Antony, Hebrard, Maxime, Poulicard, Nils, Dellicour, Simon, Hubert, Judith, Guindon, Stéphane

2025

Overview

Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and rice history since the second half of the 19 th century. The phylogeography of RYMV in East Africa was reconstructed from coat protein gene sequences (ORF4) of 335 isolates sampled over two million square kilometers between 1966 and 2020. Dispersal patterns obtained from ORF2a and ORF2b, and full-length sequences converged to the same scenario. The following imprints of rice cultivation on RYMV epidemiology were unveiled. RYMV emerged in the middle of the 19 th century in the Eastern Arc Mountains where slash-and-burn rice cultivation was practiced. Several spillovers from wild hosts to cultivated rice occurred. RYMV was then rapidly introduced into the nearby large rice growing Kilombero valley and Morogoro region. Harvested seeds are contaminated by debris of virus infected plants that subsist after threshing and winnowing. Long-distance dispersal of RYMV is consistent (i) with rice introduction along the caravan routes from the Indian Ocean Coast to Lake Victoria in the second half of the 19 th century, (ii) seed movement from East Africa to West Africa at the end of the 19 th century, from Lake Victoria to the north of Ethiopia in the second half of the 20 th century and to Madagascar at the end of the 20 th century, (iii) and, unexpectedly, with rice transport at the end of the First World War as a troop staple food from the Kilombero valley towards the South of Lake Malawi. Overall, RYMV dispersal was associated to a broad range of human activities, some unsuspected. Consequently, RYMV has a wide dispersal capacity. Its dispersal metrics estimated from phylogeographic reconstructions are similar to those of highly mobile zoonotic viruses.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: 19th century / Africa, Eastern - epidemiology / Biodiversity / Biology and Life Sciences / Causes of / Coat protein / Computer and Information Sciences / Cultivation / Disease transmission / Diseases and pests / Dispersal / Distribution / Earth Sciences / Ecology and Environmental Sciences / Epidemiology / Flowers & plants / Gene sequencing / Genetic aspects / Grain cultivation / Host range / Hypotheses / Identification and classification / Lakes / Life Sciences / Microbiology and Parasitology / Mountains / Oryza - virology / People and Places / Phylogeny / Phylogeography / Phytopathology and phytopharmacy / Plant debris / Plant Diseases - history / Plant Diseases - virology / Plant viruses / Plant Viruses - genetics / Research and Analysis Methods / Retrospective Studies / Rice / RNA viruses / Seeds / Slash and burn / Soil contamination / Systematics, Phylogenetics and taxonomy / Valleys / Vegetal Biology / Virology / Virus diseases of plants / Viruses / War / Zoonoses