Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley

Abstract

To investigate the spread of Rice yellow mottle virus (RYMV) along the Niger River, regular sampling of virus isolates was conducted along 500 km of the Niger Valley in the Republic of Niger and was complemented by additional sampling in neighbouring countries in West Africa and Central Africa. The spread of RYMV into and within the Republic of Niger was inferred as a continuous process using a Bayesian statistical framework applied previously to reconstruct its dispersal history in West Africa, East Africa and Madagascar. The spatial resolution along this section of the Niger River was the highest implemented for RYMV and possibly for any plant virus. We benefited from the results of early field surveys of the disease for the validation of the phylogeographic reconstruction, and from the well-documented history of rice cultivation changes along the Niger River for their interpretation. As a prerequisite, the temporal signal of the RYMV datasets was revisited in light of recent methodological advances. The role of the hydrographic network of the Niger Basin in RYMV spread was examined, and the link between virus population dynamics and the extent of irrigated rice was assessed. RYMV was introduced along the Niger River in the Republic of Niger in the early 1980s from areas to the southwest of the country where rice was increasingly grown. Viral spread was triggered by a major irrigation scheme made of a set of rice perimeters along the river valley. The subsequent spatial and temporal host continuity and the inoculum build-up allowed for a rapid spread of RYMV along the Niger River, upstream and downstream, over hundreds of kilometres, and led to the development of severe epidemics. There was no evidence of long-distance dissemination of the virus through natural water. Floating rice in the main meanders of the Middle Niger did not contribute to virus dispersal from West Africa to Central Africa. RYMV along the Niger River is an insightful example of how agricultural intensification favors pathogen emergence and spread.

Rapid evolution of an RNA virus to escape recognition by a rice nucleotide‐binding and leucine‐rich repeat domain immune receptor

“…To further extend this analysis and monitor the variability of the CP in natural populations, we analyzed the CP sequence diversity in a panel of 595 RYMV isolates that is representative of the diversity of the virus and described in Issaka et al . (2021). This showed that the CP residues that are mutated in the RB variants are highly conserved in natural populations (Table 1).…”

“… 2 The sequences of the coat protein of the set of 595 isolates described in Issaka et al . (2021) and available in public databases were used. Residues in gray correspond to the reference sequence from the CIa isolate. …”

“…The CP sequences of the set of 595 RYMV isolates described in Issaka et al . (2021) were used to analyze the variability of the CP in natural populations. This set of RYMV isolates comprised 261 isolates from West and Central Africa, 240 isolates from East Africa, and 94 isolates from Madagascar.…”

“…1Positions refer to the sequence of the CIa isolate.2The sequences of the coat protein of the set of 595 isolates described inIssaka et al (2021) and available in public databases were used. Residues in gray correspond to the reference sequence from the CIa isolate.Ó 2022 The Authors New Phytologist Ó 2022 New Phytologist Foundation.New Phytologist (2023) 237: 900-913 www.newphytologist.com…”

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

“…RYMV is also one of the major model for plant virus molecular epidemiology (Trovão et al, 2015;Pagán, Fraile & García-Arenal, 2016). Continental-scale molecular epidemiology studies were undertaken (Pinel-Galzi et al, 2009, 2015, and compared to RYMV field epidemiology (Rakotomalala et al, 2019;Issaka et al, 2021), revealing a strong geographic structuration of genetic diversity (Pinel-Galzi et al, 2015). Various viral strains may however overlap in some regions, as exemplified by the coexistence of several RYMV strains in Côte d'Ivoire (N'Guessan et al, 2000), or at the local scale in Tanzania (Kanyeka et al, 2007).…”