Genetic diversity and epidemic histories of rice yellow mottle virus in Ghana

•A decade of sampling shed light on the distribution and diversity of RYMV in Ghana.•Phylogeographic analyses identified some of the routes of RYMV dispersion in Ghana.•Phylodynamics highlighted dispersions or extinctions of different RYMV lineages. Rice yellow mottle virus (RYMV) has persisted as a...

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Published in:	Virus research Vol. 329; p. 199106
Main Authors:	Omiat, Emmanuel Gilbert, Asante, Maxwell Darko, Traoré, Valentin Stanislas Edgar, Oppong, Allen, Ifie, Beatrice Elohor, Ofosu, Kirpal Agyemang, Aribi, Jamel, Pinel-Galzi, Agnès, Comte, Aurore, Fargette, Denis, Hébrard, Eugénie, Traoré, Oumar, Offei, Samuel Kwame, Danquah, Eric Yirenkyi, Poulicard, Nils
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 01-05-2023 Elsevier
Subjects:	Biodiversity Epidemiological surveillance Genetic Variation Ghana - epidemiology Life Sciences Oryza Phylogeography Phytopathology and phytopharmacy Plant Breeding Plant Viruses - genetics Solemoviridae Spatio-temporal dynamics Systematics, Phylogenetics and taxonomy Vegetal Biology Ghana Epidemiological surveillance Spatio-temporal dynamics Phylogeography Solemoviridae Solemoviridae Phylogeography Spatio-temporal dynamics Epidemiological surveillance
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Summary:	•A decade of sampling shed light on the distribution and diversity of RYMV in Ghana.•Phylogeographic analyses identified some of the routes of RYMV dispersion in Ghana.•Phylodynamics highlighted dispersions or extinctions of different RYMV lineages. Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections confirmed that RYMV is circulating in most of these regions. Coat protein gene and complete genome sequencings revealed that RYMV in Ghana almost exclusively belongs to the strain S2, one of the strains covering the largest area in West Africa. We also detected the presence of the S1ca strain which is being reported for the first time outside its area of origin. These results suggested a complex epidemiological history of RYMV in Ghana and a recent expansion of S1ca to West Africa. Phylogeographic analyses reconstructed at least five independent RYMV introductions in Ghana for the last 40 years, probably due to rice cultivation intensification in West Africa leading to a better circulation of RYMV. In addition to identifying some routes of RYMV dispersion in Ghana, this study contributes to the epidemiological surveillance of RYMV and helps to design disease management strategies, especially through breeding for rice disease resistance.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0168-1702 1872-7492
DOI:	10.1016/j.virusres.2023.199106