Cassava (Manihot esculenta Crantz) is a vital crop in Rwanda where it ranks as the third most consumed staple. However, cassava productivity remains below its yield potential due to several constraints, including important viral diseases, such as cassava brown streak disease (CBSD). Because various factors can be addressed to mitigate the impact of viral diseases, it is essential to identify routes of virus contamination in the cassava agrosystems from the seed system to farmer's practices and knowledge. The present study aimed at (1) assessing the current cassava seed system and farmers' practices and their knowledge of the biotic constraints to cassava production, (2) determining the status of CBSD as well as critical factors associated with its spread through the seed system channels, and (3) determining factors that influence cassava productivity in Rwanda. A cross-sectional study was carried out from May to September 2019 in 13 districts of Rwanda. A total of 130 farmers and cassava fields were visited, and the incidence and severity of CBSD were evaluated. CBSD was detected in all cassava-producing districts. The highest field incidence of CBSD was recorded in the Nyanza district (62%; 95% CI = 56–67%) followed by the Bugesera district (60%; 95% CI = 54–65%), which recorded the highest severity score of 3.0 ± 0.6. RT-PCR revealed the presence of CBSD at the rate of 35.3%. Ugandan cassava brown streak virus was predominant (21.5%) although cassava brown streak virus was 4% and mixed infection was 10%. An informal cassava seed system was dominant among individual farmers, whereas most cooperatives used quality seeds. Cassava production was found to be significantly influenced by the use of fertilizer, size of the land, farming system, cassava viral disease, and type of cassava varieties grown (p < 0.001). Disease management measures were practiced by a half of participants only. Factors found to be significantly associated with CBSD infection (p < 0.05) were the source of cuttings, proximity to borders, age of cassava, and knowledge of CBSD transmission and management.

Cassava is one of the most important staple crops in Africa and its production is seriously damaged by viral diseases. In this study, we identify for the first time and characterize the genome organization of novel ampeloviruses infecting cassava plants in diverse geographical locations using three high-throughput sequencing protocols [Virion-Associated Nucleotide Acid (VANA), dsRNA and total RNA], and we provide a first analysis of the diversity of these agents and of the evolutionary forces acting on them. Thirteen new Closteroviridae isolates were characterized in field-grown cassava plants from the Democratic Republic of Congo (DR Congo), Madagascar, Mayotte, and Reunion islands. The analysis of the sequences of the corresponding contigs (ranging between 10,417 and 13,752 nucleotides in length) revealed seven open reading frames. The replication-associated polyproteins have three expected functional domains: methyltransferase , helicase, and RNA-dependent RNA polymerase (RdRp). Additional open reading frames code for a small transmembrane protein, a heat-shock protein 70 homolog (HSP70h), a heat shock protein 90 homolog (HSP90h), and a major and a minor coat protein (CP and CPd respectively). Defective genomic variants were also identified in some cassava accessions originating from Madagascar and Reunion. The isolates were found to belong to two species tentatively named Manihot esculenta-associated virus 1 and 2 (MEaV-1 and MEaV-2). Phylogenetic analyses showed that MEaV-1 and MEaV-2 belong to the genus Ampelovirus, in particular to its subgroup II. MEaV-1 was found in all of the countries of study, while MEaV-2 was only detected in Madagascar and Mayotte. Recombination analysis provided evidence of intraspecies recombination occurring between the isolates from Madagascar and Mayotte. No clear association with visual symptoms in the cassava host could be identified.