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Viruses are responsible for half of the cases of disease emergences on the cultivated plants. This predominance of emergent viruses can be explained by their broad genetic diversity, their high multiplication level and their rapid adaptation. The sorghum cultivation has been recently intensified worldwide in response to climate change and in a view to agro-diversification. While several virus species have been reported on sorghum, up to now, the viral prevalence and the emergence risks on sorghum in Africa have never been investigated. We will present here the methodology used for an exploratory analysis of sorghum-infecting viruses in Togo. A sampling survey was conducted across the country, 154 and 257 symptomatic leaf samples were collected on sorghum and maize, respectively. All the samples were analyzed using the virion-associated nucleic acid (VANA) metagenomics approach and HiSeq Illumina sequencing. Overall, 75% and 7% of the VANA reads and contigs respectively obtained from maize and sorghum samples shared identity with plant viruses. Specifically, we detected sequences of five previously described virus species: Maize streak virus (Geminiviridae), Maize yellow mosaic virus (Solemoviridae), Sugarcane mosaic virus (Potiviridae), Zea mays chrysovirus and Zea mays chrysovirus 1 (Chrysoviridae), Maize-associated totivirus, Maize-associated totivirus 1, Maize-associated totivirus 2 and Maize-associated totivirus 3 (Totiviridae) and original sequences of five undescribed virus species: Badna-like, Gemini-like, Mito-like, Endorna-like and Partiti-like virus on sorghum and maize. Maize streak virus (MSV), maize-associated totivirus species and maize yellow mosaic virus (MaYMV), were the most frequent viruses on maize with respectively prevalence of 58%, 30% and 24%. On sorghum, endorna-like virus, partiti-like virus and MSV were the most prevalent viruses with 14.9%, 6.5% and 1.3%, respectively. These high throughput sequencing and metagenomics technologies will al

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus

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 agricu, SCOPUS: ar.j, info:eu-repo/semantics/published

Rice yellow mottle virus (RYMV) in Madagascar Island provides an opportunity to study the spread of a plant virus disease after a relatively recent introduction in a large and isolated country with a heterogeneous host landscape ecology. Here, we take advantage of field survey data on the occurrence of RYMV disease throughout Madagascar dating back to the 1970s, and of virus genetic data from ninety-four isolates collected since 1989 in most regions of the country to reconstruct the epidemic history. We find that the Malagasy isolates belong to a unique recombinant strain that most likely entered Madagascar through a long-distance introduction from the most eastern part of mainland Africa. We infer the spread of RYMV as a continuous process using a Bayesian statistical framework. In order to calibrate the time scale in calendar time units in this analysis, we pool the information about the RYMV evolutionary rate from several geographical partitions. Whereas the field surveys and the phylogeographic reconstructions both point to a rapid southward invasion across hundreds of kilometers throughout Madagascar within three to four decades, they differ on the inferred origin location and time of the epidemic. The phylogeographic reconstructions suggest a lineage displacement and unveil a re-invasion of the northern regions that may have remained unnoticed otherwise. Despite ecological differences that could affect the transmission potential of RYMV in Madagascar and in mainland Africa, we estimate similar invasion and dispersal rates. We could not identify environmental factors that have a relevant impact on the lineage dispersal velocity of RYMV in Madagascar. This study highlights the value and complementarity of (historical) nongenetic and (more contemporaneous) genetic surveillance data for reconstructing the history of spread of plant viruses., SCOPUS: ar.j, info:eu-repo/semantics/published

The virome is an essential component of the phytobiome as viruses correspond to the most abundant and diverse biological entity in Nature and interact with all living organisms. The recent advances in high-throughput sequencing (HTS) has proven efficient for characterizing within-host diversity of several viruses, which has shed light on the influence of this diversity on the global fitness and virulence of viruses. We here aimed at evaluating the impact of rice management on the within-host diversity of Rice yellow mottle virus (RYMV) in order to optimize the cultural practices and to limit the burden of Rice yellow mottle disease in Africa. We worked on rice plants collected from traditional and intensive rice fields in East Africa, which is the center of origin of Rice yellow mottle virus. Interestingly, several strains with contrasted pathogenic and epidemiological parameters co -exist in this region and recombination between strains were identified recently. We selected twelve RYMV sympto-matic samples from fields managed under different types of practices that were analyzed using two HTS strategies: a metagenomics-based approach and a RYMV specific sequencing approach. Combining both strategies, we tested if the RYMV was associated with other viral species in rice, and if some cases of co-infections between RYMV strains occurred. Both approaches indicate a significant within-host RYMV diversity, which allows us to perceive the diversification processes of RYMV strains at the field scale. The detection of recombinants and the comparison of the within-host genetic diversity depending on the cultivation practices are underway.

Rice yellow mottle virus (RYMV) causes high losses to rice production in Africa. Several sources of varietal high resistance are available but the emergence of virulent pathotypes that are able to overcome one or two resistance alleles can sometimes occur. Both resistance spectra and viral adaptability have to be taken into account to develop sustainable rice breeding strategies against RYMV. In this study, we extended previous resistance spectrum analyses by testing the rymv1-4 and rymv1-5 alleles that are carried by the rice accessions Tog5438 and Tog5674, respectively, against isolates that are representative of RYMV genetic and pathogenic diversity. Our study revealed a hypervirulent pathotype, named thereafter pathotype T′, that is able to overcome all known sources of high resistance. This pathotype, which is spatially localized in West-Central Africa, appears to be more abundant than previously suspected. To better understand the adaptive processes of pathotype T′, molecular determinants of resistance breakdown were identified via Sanger sequencing and validated through directed mutagenesis of an infectious clone. These analyses confirmed the key role of convergent nonsynonymous substitutions in the central part of the viral genome-linked protein to overcome RYMV1-mediated resistance. In addition, deep-sequencing analyses revealed that resistance breakdown does not always coincide with fixed mutations. Actually, virulence mutations that are present in a small proportion of the virus population can be sufficient for resistance breakdown. Considering the spatial distribution of RYMV strains in Africa and their ability to overcome the RYMV resistance genes and alleles, we established a resistance-breaking risk map to optimize strategies for the deployment of sustainable and resistant rice lines in Africa.