ABSTRACT

Sugarcane (Saccharum spp.) is an important interspecific hybrid crop grown for sugar and ethanol production in tropical and subtropical regions around the world. However, its vegetative propagation makes it vulnerable to viral diseases which pose a serious threat to crop yield and quality. Several viruses belonging to species in the genus Mastrevirus, family Geminiviridae are known to infect sugarcane including maize streak virus, saccharum streak virus, sugarcane chlorotic streak virus, sugarcane streak Egypt virus, sugarcane streak Reunion virus, sugarcane streak virus, sugarcane striate virus and sugarcane white streak virus (SWSV), (Boukari et al., 2020).

In Côte d’Ivoire, sugarcane streak mosaic virus (SCSMV; genus Poacevirus, family Potyviridae) is reported as an emerging virus affecting a wide range of sugarcane varieties in the country (Daugrois et al., 2020; Sorho et al., 2020). With the aim of developing a holistic method for controlling its spread on areas cultivated by SUCAF-CI (a sugar company in Côte d’Ivoire), we undertook an inventory of the viruses present on its sites. Twenty-four samples were collected from SUCAF-CI germplasm collections and nurseries, and leaves were analysed by rolling circle amplification with random hexamers followed by nanopore sequencing using a MinION device as described by Ben Chehida et al. (2021). One sugarcane leaf sample (SC_BC38) with peculiar symptoms (Figure 1) collected in a sugarcane field of the Centre National de Recherche Agronomique of Côte d’Ivoire, located c. 50 kilometers from SUCAF-CI, was also screened.