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

Souley Issaka,Simon Dellicour,Paul Bastide,Mandev S Gill,Silla Semballa,Philippe Lemey,Agnès Pinel-Galzi,Séverin Aké,Eugénie Hébrard,Oumar Traoré,Régis Dimitri Skopé Longué,Marie-Jo Dugué,Denis Fargette,Stéphane Guindon,Yacouba Séré

doi:10.1093/ve/veab072

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 data sets was revisited in the 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 favours pathogen emergence and spread.

Highlights

Rice yellow mottle virus (RYMV) was first isolated in 1966 in East Africa (Bakker 1974) and in 1975 in West Africa (Fauquet and Thouvenel 1977)
The temporal signal was detected at the deepest nodes of the phylogenetic tree with a low correlation coefficient
A strong temporal and spatial signal is required to reconstruct the spatiotemporal spread of RYMV along the Niger River and to compare it to early field reports and to recent changes in rice cultivation

Summary

Introduction

Rice yellow mottle virus (RYMV) was first isolated in 1966 in East Africa (Bakker 1974) and in 1975 in West Africa (Fauquet and Thouvenel 1977). The introduction of RYMV in the Niger Valley to the west of the country and in the Diffa district to the east of the country, close to Lake Chad, had different geographic and genetic origins (Fig. 4A). They both originated from areas where rice cultivation had been extended after the construction of dams in the early 1980s. RYMV in the Niger Valley was introduced from the Kompienga Lake area (11◦04′N; 0◦42′E) in Burkina Faso southwest of the Republic of Niger (Fig. 4E). We explored an alternative hypothesis, i.e. whether a major and recent change in rice cultivation triggered the introduction of RYMV of the Niger Valley

Methods

Results

Conclusion