Résumé
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 allow the development of inexpensive, fast, standardized and effective molecular diagnostic methods for all currently known or unknown viral diseases on sorghum.