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

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; Poulicard, Nils

doi:10.1016/j.virusres.2023.199106

Cited by 2 publications

(1 citation statement)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Rice accounts for 21% of global caloric consumption (Zhao et al, 2020). It is a staple food crop across Asia and Latin America and becoming increasingly so in mainland Africa (Muthayya et al, 2014; Omiat et al, 2023). The global rice consumption and production for 2022 was projected at nearly 520 and 504 million tons, respectively (Tang et al, 2022; USDA, 2022), indicating a deficit of production relative to consumption.…”

Section: Introductionmentioning

confidence: 99%

Coat protein genealogy and complete genome characterization of field isolates of rice yellow mottle virus from Zambia

Mulenga,

Komatsubara,

Sichilima

et al. 2023

Journal of Phytopathology

View full text Add to dashboard Cite

Rice yellow mottle virus (RYMV) is widespread in mainland Africa and adjoining islands but to date its occurrence in Zambia is unknown. In March 2022, field surveys were conducted in Luapula, Northern, Western and Eastern provinces of Zambia to determine the occurrence of RYMV and its genetic relationship with global isolates of the virus. Thirty‐three paddy rice fields were visited and 108 leaf tissue samples were collected for analysis. The incidence of yellow mottle symptoms ranged from 25% to 43% in 10 (30.3%) of 33 fields and RYMV was detected in 35 (32.4%) of 108 samples by RT‐PCR with virus‐specific primers. A subset of 27 RYMV‐positive samples was constituted from which full‐length (720 bp) coat protein (CP) regions were amplified followed by bidirectional Sanger sequencing. Phylogenetic analysis of the CP cistron revealed distinct clustering of the isolates from Zambia in a monophyletic clade as subtype of the RYMV strain S4. Three isolates were randomly selected and used to obtain complete RYMV genomes of 4448–4449 nucleotides (nt). Comparative analysis of both the CP and the complete RYMV genomes from Zambia with their corresponding sequences in GenBank revealed that they shared 92%–93.2% nt identities with strain S4 isolates. These results confirm for the first time occurrence of RYMV strain S4 in Zambia and further reinforce the need for phytosanitary vigilance to safeguard rice production in Zambia.

show abstract

Section: Introductionmentioning

confidence: 99%

Coat protein genealogy and complete genome characterization of field isolates of rice yellow mottle virus from Zambia

Mulenga,

Komatsubara,

Sichilima

et al. 2023

Journal of Phytopathology

View full text Add to dashboard Cite

show abstract

Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot

Billard,

Barro,

Sérémé

et al. 2023

Virus Evolution

View full text Add to dashboard Cite

The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at local scale remain scarce, in spite of potential implications for crop protection. Here we describe a five-years (2015-2019) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon and Karfiguela). It confirmed one irrigated site as a disease hotspot, and also found one rainfed lowland site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a five-meter distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site-scale (ca. 520 ha), and also within various specific fields (25 meters side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20% or less in 2015-2016, to more than 65% in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation in controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.

show abstract

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

Cited by 2 publications

References 44 publications

Coat protein genealogy and complete genome characterization of field isolates of rice yellow mottle virus from Zambia

Coat protein genealogy and complete genome characterization of field isolates of rice yellow mottle virus from Zambia

Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot

Contact Info

Product

Resources

About